1
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Dunn-Davies H, Dudnakova T, Nogara A, Rodor J, Thomas AC, Parish E, Gautier P, Meynert A, Ulitsky I, Madeddu P, Caporali A, Baker A, Tollervey D, Mitić T. Control of endothelial cell function and arteriogenesis by MEG3:EZH2 epigenetic regulation of integrin expression. Mol Ther Nucleic Acids 2024; 35:102173. [PMID: 38617973 PMCID: PMC11015509 DOI: 10.1016/j.omtn.2024.102173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/14/2024] [Indexed: 04/16/2024]
Abstract
Epigenetic processes involving long non-coding RNAs regulate endothelial gene expression. However, the underlying regulatory mechanisms causing endothelial dysfunction remain to be elucidated. Enhancer of zeste homolog 2 (EZH2) is an important rheostat of histone H3K27 trimethylation (H3K27me3) that represses endothelial targets, but EZH2 RNA binding capacity and EZH2:RNA functional interactions have not been explored in post-ischemic angiogenesis. We used formaldehyde/UV-assisted crosslinking ligation and sequencing of hybrids and identified a new role for maternally expressed gene 3 (MEG3). MEG3 formed the predominant RNA:RNA hybrid structures in endothelial cells. Moreover, MEG3:EZH2 assists recruitment onto chromatin. By EZH2-chromatin immunoprecipitation, following MEG3 depletion, we demonstrated that MEG3 controls recruitment of EZH2/H3K27me3 onto integrin subunit alpha4 (ITGA4) promoter. Both MEG3 knockdown or EZH2 inhibition (A-395) promoted ITGA4 expression and improved endothelial cell migration and adhesion to fibronectin in vitro. The A-395 inhibitor re-directed MEG3-assisted chromatin remodeling, offering a direct therapeutic benefit by increasing endothelial function and resilience. This approach subsequently increased the expression of ITGA4 in arterioles following ischemic injury in mice, thus promoting arteriogenesis. Our findings show a context-specific role for MEG3 in guiding EZH2 to repress ITGA4. Novel therapeutic strategies could antagonize MEG3:EZH2 interaction for pre-clinical studies.
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Affiliation(s)
- Hywel Dunn-Davies
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building Max Born Crescent, King’s Buildings, Edinburgh EH9 3BF, UK
| | - Tatiana Dudnakova
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Antonella Nogara
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Julie Rodor
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Anita C. Thomas
- Bristol Medical School, Translational Health Sciences, University of Bristol, Research and Teaching Floor Level 7, Queens Building, Bristol Royal Infirmary, Bristol BS2 8HW, UK
| | - Elisa Parish
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Philippe Gautier
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Alison Meynert
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann-UK Building rm. 007, Weizmann Institute of Science Rehovot 76100, Israel
| | - Paolo Madeddu
- Bristol Medical School, Translational Health Sciences, University of Bristol, Research and Teaching Floor Level 7, Queens Building, Bristol Royal Infirmary, Bristol BS2 8HW, UK
| | - Andrea Caporali
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Andrew Baker
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building Max Born Crescent, King’s Buildings, Edinburgh EH9 3BF, UK
| | - Tijana Mitić
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
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2
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Ganesh VS, Riquin K, Chatron N, Lamar KM, Aziz MC, Monin P, O’Leary M, Goodrich JK, Garimella KV, England E, Yoon E, Weisburd B, Aguet F, Bacino CA, Murdock DR, Dai H, Rosenfeld JA, Emrick LT, Ketkar S, Sarusi Y, Sanlaville D, Kayani S, Broadbent B, Isidor B, Pengam A, Cogné B, MacArthur DG, Ulitsky I, Carvill GL, O’Donnell-Luria A. Novel syndromic neurodevelopmental disorder caused by de novo deletion of CHASERR, a long noncoding RNA. medRxiv 2024:2024.01.31.24301497. [PMID: 38496558 PMCID: PMC10942497 DOI: 10.1101/2024.01.31.24301497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Genes encoding long non-coding RNAs (lncRNAs) comprise a large fraction of the human genome, yet haploinsufficiency of a lncRNA has not been shown to cause a Mendelian disease. CHASERR is a highly conserved human lncRNA adjacent to CHD2-a coding gene in which de novo loss-of-function variants cause developmental and epileptic encephalopathy. Here we report three unrelated individuals each harboring an ultra-rare heterozygous de novo deletion in the CHASERR locus. We report similarities in severe developmental delay, facial dysmorphisms, and cerebral dysmyelination in these individuals, distinguishing them from the phenotypic spectrum of CHD2 haploinsufficiency. We demonstrate reduced CHASERR mRNA expression and corresponding increased CHD2 mRNA and protein in whole blood and patient-derived cell lines-specifically increased expression of the CHD2 allele in cis with the CHASERR deletion, as predicted from a prior mouse model of Chaserr haploinsufficiency. We show for the first time that de novo structural variants facilitated by Alu-mediated non-allelic homologous recombination led to deletion of a non-coding element (the lncRNA CHASERR) to cause a rare syndromic neurodevelopmental disorder. We also demonstrate that CHD2 has bidirectional dosage sensitivity in human disease. This work highlights the need to carefully evaluate other lncRNAs, particularly those upstream of genes associated with Mendelian disorders.
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Affiliation(s)
- Vijay S. Ganesh
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kevin Riquin
- Nantes Université, CHU de Nantes, CNRS, INSERM, L’institut du Thorax, Nantes, France
| | - Nicolas Chatron
- Institut Neuromyogène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Equipe Métabolisme énergétique et développement neuronal, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
- Service de génétique, Hospices Civils de Lyon, Lyon, France
| | - Kay-Marie Lamar
- Departments of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Miriam C. Aziz
- Departments of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Pauline Monin
- Service de génétique, Hospices Civils de Lyon, Lyon, France
| | - Melanie O’Leary
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia K. Goodrich
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kiran V. Garimella
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eleina England
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Esther Yoon
- Departments of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Ben Weisburd
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Francois Aguet
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David R. Murdock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lisa T. Emrick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shamika Ketkar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Yael Sarusi
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Damien Sanlaville
- Institut Neuromyogène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Equipe Métabolisme énergétique et développement neuronal, CNRS UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
- Service de génétique, Hospices Civils de Lyon, Lyon, France
| | - Saima Kayani
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Bertrand Isidor
- Nantes Université, CHU de Nantes, CNRS, INSERM, L’institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique médicale, F-44000 Nantes, France
| | - Alisée Pengam
- Nantes Université, CHU de Nantes, Service de Génétique médicale, F-44000 Nantes, France
| | - Benjamin Cogné
- Nantes Université, CHU de Nantes, CNRS, INSERM, L’institut du Thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique médicale, F-44000 Nantes, France
| | - Daniel G. MacArthur
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, Australia
- Centre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Igor Ulitsky
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Gemma L. Carvill
- Departments of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Anne O’Donnell-Luria
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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3
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Monziani A, Ulitsky I. Noncoding snoRNA host genes are a distinct subclass of long noncoding RNAs. Trends Genet 2023; 39:908-923. [PMID: 37783604 DOI: 10.1016/j.tig.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 10/04/2023]
Abstract
Mammalian genomes are pervasively transcribed into different noncoding (nc)RNA classes, each one with its own hallmarks and exceptions. Some of them are nested into each other, such as host genes for small nucleolar RNAs (snoRNAs), which were long believed to simply act as molecular containers strictly facilitating snoRNA biogenesis. However, recent findings show that noncoding snoRNA host genes (ncSNHGs) display features different from those of 'regular' long ncRNAs (lncRNAs) and, more importantly, they can exert independent and unrelated functions to those of the encoded snoRNAs. Here, we review and summarize past and recent evidence that ncSNHGs form a defined subclass among the plethora of lncRNAs, and discuss future research that can further elucidate their biological relevance.
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Affiliation(s)
- Alan Monziani
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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4
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Rapakoulia T, Lopez Ruiz De Vargas S, Omgba PA, Laupert V, Ulitsky I, Vingron M. CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction. Bioinformatics 2023; 39:btad687. [PMID: 37982748 PMCID: PMC10666202 DOI: 10.1093/bioinformatics/btad687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/11/2023] [Accepted: 11/17/2023] [Indexed: 11/21/2023] Open
Abstract
MOTIVATION Identifying target promoters of active enhancers is a crucial step for realizing gene regulation and deciphering phenotypes and diseases. Up to now, several computational methods were developed to predict enhancer gene interactions, but they require either many epigenomic and transcriptomic experimental assays to generate cell-type (CT)-specific predictions or a single experiment applied to a large cohort of CTs to extract correlations between activities of regulatory elements. Thus, inferring CT-specific enhancer gene interactions in unstudied or poorly annotated CTs becomes a laborious and costly task. RESULTS Here, we aim to infer CT-specific enhancer target interactions, using minimal experimental input. We introduce Cell-specific ENhancer Target pREdiction (CENTRE), a machine learning framework that predicts enhancer target interactions in a CT-specific manner, using only gene expression and ChIP-seq data for three histone modifications for the CT of interest. CENTRE exploits the wealth of available datasets and extracts cell-type agnostic statistics to complement the CT-specific information. CENTRE is thoroughly tested across many datasets and CTs and achieves equivalent or superior performance than existing algorithms that require massive experimental data. AVAILABILITY AND IMPLEMENTATION CENTRE's open-source code is available at GitHub via https://github.com/slrvv/CENTRE.
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Affiliation(s)
| | | | | | - Verena Laupert
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Igor Ulitsky
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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5
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Ben-Tov Perry R, Tsoory M, Tolmasov M, Ulitsky I. Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation. Cell Rep 2023; 42:113168. [PMID: 37742186 PMCID: PMC10636608 DOI: 10.1016/j.celrep.2023.113168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/30/2023] [Accepted: 09/08/2023] [Indexed: 09/26/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are expressed in many brain circuits and types of neurons; nevertheless, their functional significance for normal brain functions remains elusive. Here, we study the functions in the central nervous system of Silc1, an lncRNA we have shown previously to be important for neuronal regeneration in the peripheral nervous system. We found that Silc1 is rapidly and strongly induced in the hippocampus upon exposure to novelty and is required for efficient spatial learning. Silc1 production is important for induction of Sox11 (its cis-regulated target gene) throughout the CA1-CA3 regions and proper expression of key Sox11 target genes. Consistent with its role in neuronal plasticity, Silc1 levels decline during aging and in models of Alzheimer's disease. Overall, we describe a plasticity pathway in which Silc1 acts as an immediate-early gene to activate Sox11 and induce a neuronal growth-associated transcriptional program important for learning.
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Affiliation(s)
- Rotem Ben-Tov Perry
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Michael Tsoory
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michael Tolmasov
- Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel.
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6
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Amaral P, Carbonell-Sala S, De La Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, Ulitsky I, Varabyou A, Wells CA, Yandell M, Carninci P, Salzberg SL. The status of the human gene catalogue. Nature 2023; 622:41-47. [PMID: 37794265 PMCID: PMC10575709 DOI: 10.1038/s41586-023-06490-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/27/2023] [Indexed: 10/06/2023]
Abstract
Scientists have been trying to identify every gene in the human genome since the initial draft was published in 2001. In the years since, much progress has been made in identifying protein-coding genes, currently estimated to number fewer than 20,000, with an ever-expanding number of distinct protein-coding isoforms. Here we review the status of the human gene catalogue and the efforts to complete it in recent years. Beside the ongoing annotation of protein-coding genes, their isoforms and pseudogenes, the invention of high-throughput RNA sequencing and other technological breakthroughs have led to a rapid growth in the number of reported non-coding RNA genes. For most of these non-coding RNAs, the functional relevance is currently unclear; we look at recent advances that offer paths forward to identifying their functions and towards eventually completing the human gene catalogue. Finally, we examine the need for a universal annotation standard that includes all medically significant genes and maintains their relationships with different reference genomes for the use of the human gene catalogue in clinical settings.
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Affiliation(s)
- Paulo Amaral
- INSPER Institute of Education and Research, Sao Paulo, Brazil
| | | | - Francisco M De La Vega
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Tempus Labs, Chicago, IL, USA
| | | | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Thomas Gingeras
- Department of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jennifer L Harrow
- Centre for Genomics Research, Discovery Sciences, AstraZeneca, Royston, UK
| | - Artemis G Hatzigeorgiou
- Department of Computer Science and Biomedical Informatics, Universithy of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens, Greece
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Shashikant Pujar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Ales Varabyou
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Christine A Wells
- Stem Cell Systems, Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark Yandell
- Departent of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Human Technopole, Milan, Italy.
| | - Steven L Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA.
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7
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Rosenberg MI, Greenstein E, Buchkovich M, Peres A, Santoni-Rugiu E, Yang L, Mikl M, Vaksman Z, Gibbs DL, Reshef D, Salovin A, Irwin MS, Naranjo A, Ulitsky I, de Alarcon PA, Matthay KK, Weigman V, Yaari G, Panzer JA, Friedman N, Maris JM. Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma. Cell Rep 2023; 42:112879. [PMID: 37537844 PMCID: PMC10551040 DOI: 10.1016/j.celrep.2023.112879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 04/25/2023] [Accepted: 07/13/2023] [Indexed: 08/05/2023] Open
Abstract
Neuroblastoma is a lethal childhood solid tumor of developing peripheral nerves. Two percent of children with neuroblastoma develop opsoclonus myoclonus ataxia syndrome (OMAS), a paraneoplastic disease characterized by cerebellar and brainstem-directed autoimmunity but typically with outstanding cancer-related outcomes. We compared tumor transcriptomes and tumor-infiltrating T and B cell repertoires from 38 OMAS subjects with neuroblastoma to 26 non-OMAS-associated neuroblastomas. We found greater B and T cell infiltration in OMAS-associated tumors compared to controls and showed that both were polyclonal expansions. Tertiary lymphoid structures (TLSs) were enriched in OMAS-associated tumors. We identified significant enrichment of the major histocompatibility complex (MHC) class II allele HLA-DOB∗01:01 in OMAS patients. OMAS severity scores were associated with the expression of several candidate autoimmune genes. We propose a model in which polyclonal auto-reactive B lymphocytes act as antigen-presenting cells and drive TLS formation, thereby supporting both sustained polyclonal T cell-mediated anti-tumor immunity and paraneoplastic OMAS neuropathology.
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Affiliation(s)
- Miriam I Rosenberg
- Hebrew University of Jerusalem, Edmond Safra Campus, Givat Ram, Jerusalem 91904, Israel.
| | - Erez Greenstein
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Ayelet Peres
- Bio-engineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel; Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Eric Santoni-Rugiu
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital and Department of Clinical Medicine, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Lei Yang
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Martin Mikl
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | | | - David L Gibbs
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, WA 98109, USA
| | - Dan Reshef
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Amy Salovin
- Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Meredith S Irwin
- Department of Pediatrics and Division of Hematology-Oncology, Hospital for Sick Children, University of Toronto, 555 University Avenue, Toronto, ON M5G1X8, Canada
| | - Arlene Naranjo
- Department of Biostatistics, University of Florida, Children's Oncology Group Statistics & Data Center, Gainesville, FL, USA
| | - Igor Ulitsky
- Department of Immunology & Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Pedro A de Alarcon
- Department of Pediatrics, Hematology/Oncology, University of Illinois College of Medicine Peoria, Peoria, IL 61605, USA
| | - Katherine K Matthay
- Department of Pediatrics, UCSF School of Medicine, San Francisco, CA 94143, USA
| | | | - Gur Yaari
- Bio-engineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel; Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Jessica A Panzer
- Division of Neurology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - John M Maris
- Department of Pediatrics and Division of Oncology, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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8
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Braun T, Sosnovski KE, Amir A, BenShoshan M, VanDussen KL, Karns R, Levhar N, Abbas-Egbariya H, Hadar R, Efroni G, Castel D, Avivi C, Rosen MJ, Grifiths AM, Walters TD, Mack DR, Boyle BM, Ali SA, Moore SR, Schirmer M, Xavier RJ, Kugathasan S, Jegga AG, Weiss B, Mayer C, Barshack I, Ben-Horin S, Ulitsky I, Beucher A, Ferrer J, Hyams JS, Denson LA, Haberman Y. Mucosal transcriptomics highlight lncRNAs implicated in ulcerative colitis, Crohn's disease, and celiac disease. JCI Insight 2023; 8:e170181. [PMID: 37261910 PMCID: PMC10443795 DOI: 10.1172/jci.insight.170181] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/31/2023] [Indexed: 06/03/2023] Open
Abstract
Ulcerative colitis (UC), Crohn's disease (CD), and celiac disease are prevalent intestinal inflammatory disorders with nonsatisfactory therapeutic interventions. Analyzing patient data-driven cohorts can highlight disease pathways and new targets for interventions. Long noncoding RNAs (lncRNAs) are attractive candidates, since they are readily targetable by RNA therapeutics, show relative cell-specific expression, and play key cellular functions. Uniformly analyzing gut mucosal transcriptomics from 696 subjects, we have highlighted lncRNA expression along the gastrointestinal (GI) tract, demonstrating that, in control samples, lncRNAs have a more location-specific expression in comparison with protein-coding genes. We defined dysregulation of lncRNAs in treatment-naive UC, CD, and celiac diseases using independent test and validation cohorts. Using the Predicting Response to Standardized Pediatric Colitis Therapy (PROTECT) inception UC cohort, we defined and prioritized lncRNA linked with UC severity and prospective outcomes, and we highlighted lncRNAs linked with gut microbes previously implicated in mucosal homeostasis. HNF1A-AS1 lncRNA was reduced in all 3 conditions and was further reduced in more severe UC form. Similarly, the reduction of HNF1A-AS1 ortholog in mice gut epithelia showed higher sensitivity to dextran sodium sulfate-induced colitis, which was coupled with alteration in the gut microbial community. These analyses highlight prioritized dysregulated lncRNAs that can guide future preclinical studies for testing them as potential targets.
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Affiliation(s)
- Tzipi Braun
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Katya E. Sosnovski
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amnon Amir
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Marina BenShoshan
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Kelli L. VanDussen
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Rebekah Karns
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Nina Levhar
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Haya Abbas-Egbariya
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rotem Hadar
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Gilat Efroni
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - David Castel
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Camila Avivi
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Michael J. Rosen
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Center for Pediatric IBD and Celiac Disease, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | | | | | - David R. Mack
- Children’s Hospital of East Ontario, Ottawa, Ontario, Canada
| | | | - Syed Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sean R. Moore
- Department of Pediatrics, University of Virginia, Charlottesville, Virginia, USA
| | | | - Ramnik J. Xavier
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Anil G. Jegga
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Department of Computer Science, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Engineering, Cincinnati, Ohio, USA
| | - Batya Weiss
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chen Mayer
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Iris Barshack
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shomron Ben-Horin
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Igor Ulitsky
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Anthony Beucher
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Jorge Ferrer
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- Regulatory Genomics and Diabetes, Centre for Genomic Regulation, the Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en red Diabetes y enfermedades metabólicas asociadas (CIBERDEM), Spain
| | - Jeffrey S. Hyams
- Connecticut Children’s Medical Center, Hartford, Connecticut, USA
| | - Lee A. Denson
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Yael Haberman
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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9
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Gil N, Perry RBT, Mukamel Z, Tuck A, Bühler M, Ulitsky I. Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus. Cell Rep 2023; 42:112569. [PMID: 37256750 PMCID: PMC10320833 DOI: 10.1016/j.celrep.2023.112569] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/07/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are implicated in a plethora of cellular processes, but an in-depth understanding of their functional features or their mechanisms of action is currently lacking. Here we study Meteor, a lncRNA transcribed near the gene encoding EOMES, a pleiotropic transcription factor implicated in various processes throughout development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in mouse embryonic stem cells, with Meteor repression linked to a change in the subpopulation primed to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus-namely, the underlying DNA element-is required for suppressing Eomes expression following neuronal differentiation. Our results demonstrate the complex regulation that can be conferred by a single locus and emphasize the importance of careful selection of perturbation techniques when studying lncRNA loci.
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Affiliation(s)
- Noa Gil
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Ben-Tov Perry
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Zohar Mukamel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alex Tuck
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel.
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10
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Kshirsagar A, Doroshev SM, Gorelik A, Olender T, Sapir T, Tsuboi D, Rosenhek-Goldian I, Malitsky S, Itkin M, Argoetti A, Mandel-Gutfreund Y, Cohen SR, Hanna JH, Ulitsky I, Kaibuchi K, Reiner O. LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways. Nat Commun 2023; 14:3293. [PMID: 37280197 DOI: 10.1038/s41467-023-38797-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/15/2023] [Indexed: 06/08/2023] Open
Abstract
Lissencephaly-1 (LIS1) is associated with neurodevelopmental diseases and is known to regulate the molecular motor cytoplasmic dynein activity. Here we show that LIS1 is essential for the viability of mouse embryonic stem cells (mESCs), and it governs the physical properties of these cells. LIS1 dosage substantially affects gene expression, and we uncovered an unexpected interaction of LIS1 with RNA and RNA-binding proteins, most prominently the Argonaute complex. We demonstrate that LIS1 overexpression partially rescued the extracellular matrix (ECM) expression and mechanosensitive genes conferring stiffness to Argonaute null mESCs. Collectively, our data transforms the current perspective on the roles of LIS1 in post-transcriptional regulation underlying development and mechanosensitive processes.
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Affiliation(s)
- Aditya Kshirsagar
- Departments of Molecular Genetics and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Svetlana Maslov Doroshev
- Departments of Molecular Genetics and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Gorelik
- Departments of Molecular Genetics and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Tsviya Olender
- Departments of Molecular Genetics and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Sapir
- Departments of Molecular Genetics and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Daisuke Tsuboi
- International Center for Brain Science, Fujita Health University, Toyoake, Japan
| | - Irit Rosenhek-Goldian
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Malitsky
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Maxim Itkin
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Amir Argoetti
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Sidney R Cohen
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Jacob H Hanna
- Departments of Molecular Genetics and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Kozo Kaibuchi
- International Center for Brain Science, Fujita Health University, Toyoake, Japan
| | - Orly Reiner
- Departments of Molecular Genetics and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel.
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11
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 269] [Impact Index Per Article: 269.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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12
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Amaral P, Carbonell-Sala S, De La Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, Ulitsky I, Varabyou A, Wells CA, Yandell M, Carninci P, Salzberg SL. The status of the human gene catalogue. ArXiv 2023:arXiv:2303.13996v1. [PMID: 36994150 PMCID: PMC10055485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Scientists have been trying to identify all of the genes in the human genome since the initial draft of the genome was published in 2001. Over the intervening years, much progress has been made in identifying protein-coding genes, and the estimated number has shrunk to fewer than 20,000, although the number of distinct protein-coding isoforms has expanded dramatically. The invention of high-throughput RNA sequencing and other technological breakthroughs have led to an explosion in the number of reported non-coding RNA genes, although most of them do not yet have any known function. A combination of recent advances offers a path forward to identifying these functions and towards eventually completing the human gene catalogue. However, much work remains to be done before we have a universal annotation standard that includes all medically significant genes, maintains their relationships with different reference genomes, and describes clinically relevant genetic variants.
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Affiliation(s)
- Paulo Amaral
- INSPER Institute of Education and Research, São Paulo, SP, Brasil
| | - Silvia Carbonell-Sala
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Francisco M. De La Vega
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA; Tempus Labs, Inc., Chicago, IL
| | | | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Gingeras
- Department of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Jennifer L Harrow
- Centre for Genomics Research, Discovery Sciences, AstraZeneca, Da Vinci Building. Melbourn Science Park, Royston UK SG8 6HB
| | - Artemis G. Hatzigeorgiou
- Universithy of Thessaly, Department of Computer Science and Biomedical Informatics, Lamia, Greece; Hellenic Pasteur Institute, Athens, Greece
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, D04 V1W8 Dublin, Ireland; Conway Institute of Biomedical and Biomolecular Research, University College Dublin, D04 V1W8 Dublin, Ireland; Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Terence D. Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kim D. Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Shashikant Pujar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama Kanagawa 230-0045 Japan
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ales Varabyou
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Christine A. Wells
- Stem Cell Systems, Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville 3010 Vic Australia
| | - Mark Yandell
- Departent of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Piero Carninci
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Human Technopole, via Rita Levi Montalcini 1, Milan 20157 Italy
| | - Steven L. Salzberg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Immunology and Regenerative Biology; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
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13
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Stark M, Levin M, Ulitsky I, Assaraf YG. Folylpolyglutamate synthetase mRNA G-quadruplexes regulate its cell protrusion localization and enhance a cancer cell invasive phenotype upon folate repletion. BMC Biol 2023; 21:13. [PMID: 36721160 PMCID: PMC9889130 DOI: 10.1186/s12915-023-01525-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 01/23/2023] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Folates are crucial for the biosynthesis of nucleotides and amino acids, essential for cell proliferation and development. Folate deficiency induces DNA damage, developmental defects, and tumorigenicity. The obligatory enzyme folylpolyglutamate synthetase (FPGS) mediates intracellular folate retention via cytosolic and mitochondrial folate polyglutamylation. Our previous paper demonstrated the association of the cytosolic FPGS (cFPGS) with the cytoskeleton and various cell protrusion proteins. Based on these recent findings, the aim of the current study was to investigate the potential role of cFPGS at cell protrusions. RESULTS Here we uncovered a central role for two G-quadruplex (GQ) motifs in the 3'UTR of FPGS mediating the localization of cFPGS mRNA and protein at cell protrusions. Using the MBSV6-loop reporter system and fluorescence microscopy, we demonstrate that following folate deprivation, cFPGS mRNA is retained in the endoplasmic reticulum, whereas upon 15 min of folate repletion, this mRNA is rapidly translocated to cell protrusions in a 3'UTR- and actin-dependent manner. The actin dependency of this folate-induced mRNA translocation is shown by treatment with Latrunculin B and inhibitors of the Ras homolog family member A (RhoA) pathway. Upon folate repletion, the FPGS 3'UTR GQs induce an amoeboid/mesenchymal hybrid cell phenotype during migration and invasion through a collagen gel matrix. Targeted disruption of the 3'UTR GQ motifs by introducing point mutations or masking them by antisense oligonucleotides abrogated cell protrusion targeting of cFPGS mRNA. CONCLUSIONS Collectively, the GQ motifs within the 3'UTR of FPGS regulate its transcript and protein localization at cell protrusions in response to a folate cue, inducing cancer cell invasive phenotype. These novel findings suggest that the 3'UTR GQ motifs of FPGS constitute an attractive druggable target aimed at inhibition of cancer invasion and metastasis.
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Affiliation(s)
- Michal Stark
- grid.6451.60000000121102151The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, 3200003 Haifa, Israel
| | - May Levin
- grid.6451.60000000121102151The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, 3200003 Haifa, Israel ,grid.507132.2Present address: May Levin, MeMed Diagnostics Ltd, Tirat Carmel, Israel
| | - Igor Ulitsky
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Yehuda G. Assaraf
- grid.6451.60000000121102151The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, 3200003 Haifa, Israel
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14
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Sosnovski KE, Braun T, Amir A, Moshel D, BenShoshan M, VanDussen KL, Levhar N, Abbas-Egbariya H, Beider K, Ben-Yishay R, Asad Ali S, Moore SR, Kugathasan S, Abramovich I, Saar EG, Weiss B, Barshack I, Gottlieb E, Geiger T, Ben-Horin S, Ulitsky I, Hyams JS, Denson LA, Haberman Y. GATA6-AS1 regulates intestinal epithelial mitochondrial functions, and its reduced expression is linked to intestinal inflammation and less favorable disease course in ulcerative colitis (UC). J Crohns Colitis 2023:6992499. [PMID: 36655602 DOI: 10.1093/ecco-jcc/jjad006] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Indexed: 01/20/2023]
Abstract
BACKGROUND AND AIMS Widespread dysregulation of long non-coding RNAs (lncRNAs) including a reduction in GATA6-AS1 was noted in inflammatory bowel disease (IBD). We previously reported a prominent inhibition of epithelial mitochondrial functions in UC. However, the connection between reduction of GATA6-AS1 expression and attenuated epithelial mitochondrial functions was not yet defined. METHODS Mucosal transcriptomics was used to conform GATA6-AS1 reduction in several treatment naïve independent human cohorts (n=673). RNA pull-down followed by mass-spectrometry was used to determine GATA6-AS1 interactome. Metabolomics and mitochondrial respiration following GATA6-AS1 silencing in Caco-2, were used to elaborate on GATA6-AS1 functions. RESULTS GATA6-AS1 showed predominant expression in gut epithelia using single cell datasets. GATA6-AS1 levels were reduced in Crohn disease (CD) ileum and in ulcerative colitis (UC) rectum in independent cohorts. Reduced GATA6-AS1 lncRNA was further linked to more severe UC form, and to less favorable UC course. GATA6-AS1 interactome showed robust enrichment for mitochondrial proteins, and included TGM2, an autoantigen in celiac disease that is induced in UC, CD, and celiac, in contrast GATA6-AS1 reduction in these cohorts. GATA6-AS1 silencing resulted in induction of TGM2, and this was coupled with reduction in mitochondrial membrane potential and mitochondrial respiration, as well as in reduction of metabolites linked with aerobic respiration relevant to mucosal inflammation. TGM2 knockdown in GATA6-AS1 deficient cells rescued mitochondrial respiration. CONCLUSIONS GATA6-AS1 levels are reduced in UC, CD, and celiac, and in more severe UC forms. We highlight GATA6-AS1 as a target regulating epithelial mitochondrial functions, potentially through controlling TGM2 levels.
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Affiliation(s)
- Katya E Sosnovski
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tzipi Braun
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Amnon Amir
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Danielle Moshel
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Marina BenShoshan
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Kelli L VanDussen
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Nina Levhar
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Haya Abbas-Egbariya
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Katia Beider
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Rakefet Ben-Yishay
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Syed Asad Ali
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sean R Moore
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | | | - Ifat Abramovich
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Bat Galim, Haifa, Israel
| | - Efrat Glick Saar
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Batya Weiss
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Iris Barshack
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eyal Gottlieb
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Bat Galim, Haifa, Israel
| | - Tamar Geiger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shomron Ben-Horin
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Igor Ulitsky
- Department of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | | | - Lee A Denson
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yael Haberman
- Sheba Medical Center, Tel-Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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15
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Michael D, Feldmesser E, Gonen C, Furth N, Maman A, Heyman O, Argoetti A, Tofield A, Baichman-Kass A, Ben-Dov A, Benbenisti D, Hen N, Rotkopf R, Ganci F, Blandino G, Ulitsky I, Oren M. miR-4734 conditionally suppresses ER stress-associated proinflammatory responses. FEBS Lett 2022; 597:1233-1245. [PMID: 36445168 DOI: 10.1002/1873-3468.14548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 11/07/2022] [Accepted: 11/20/2022] [Indexed: 12/02/2022]
Abstract
Prolonged metabolic stress can lead to severe pathologies. In metabolically challenged primary fibroblasts, we assigned a novel role for the poorly characterized miR-4734 in restricting ATF4 and IRE1-mediated upregulation of a set of proinflammatory cytokines and endoplasmic reticulum stress-associated genes. Conversely, inhibition of this miRNA augmented the expression of those genes. Mechanistically, miR-4734 was found to restrict the expression of the transcriptional activator NF-kappa-B inhibitor zeta (NFKBIZ), which is required for optimal expression of the proinflammatory genes and whose mRNA is targeted directly by miR-4734. Concordantly, overexpression of NFKBIZ compromised the effects of miR-4734, underscoring the importance of this direct targeting. As the effects of miR-4734 were evident under stress but not under basal conditions, it may possess therapeutic utility towards alleviating stress-induced pathologies.
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Affiliation(s)
- Dan Michael
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Feinberg Graduate School, Weizmann Institute of Science, Rehovot, Israel
| | - Ester Feldmesser
- Life Science Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Chagay Gonen
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Furth
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Maman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Heyman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Amir Argoetti
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Adin Tofield
- School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Amichai Baichman-Kass
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Aviyah Ben-Dov
- Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Dan Benbenisti
- Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Nadav Hen
- Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Ron Rotkopf
- Life Science Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Federica Ganci
- IRCSS Regina Elena National Cancer Institute, Rome, Italy
| | | | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Moshe Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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16
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Royer M, Pai B, Menon R, Bludau A, Gryksa K, Perry RBT, Ulitsky I, Meister G, Neumann ID. Nuclear localization of Meg3-ex10 in mice lateral septum after social fear extinction. Mol Psychiatry 2022; 27:3925. [PMID: 36460754 DOI: 10.1038/s41380-022-01873-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Melanie Royer
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, 93053, Germany.,Regensburg Center for Biochemistry, Laboratory for RNA Biology, University of Regensburg, Regensburg, 93053, Germany
| | - Balagopal Pai
- Regensburg Center for Biochemistry, Laboratory for RNA Biology, University of Regensburg, Regensburg, 93053, Germany
| | - Rohit Menon
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, 93053, Germany
| | - Anna Bludau
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, 93053, Germany
| | - Katharina Gryksa
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, 93053, Germany
| | - Rotem Ben-Tov Perry
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Igor Ulitsky
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Gunter Meister
- Regensburg Center for Biochemistry, Laboratory for RNA Biology, University of Regensburg, Regensburg, 93053, Germany
| | - Inga D Neumann
- Department of Behavioural and Molecular Neurobiology, Regensburg Center of Neuroscience, University of Regensburg, Regensburg, 93053, Germany.
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17
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Slobodin B, Sehrawat U, Lev A, Hayat D, Zuckerman B, Fraticelli D, Ogran A, Ben-Shmuel A, Bar-David E, Levy H, Ulitsky I, Dikstein R. Cap-independent translation and a precisely located RNA sequence enable SARS-CoV-2 to control host translation and escape anti-viral response. Nucleic Acids Res 2022; 50:8080-8092. [PMID: 35849342 PMCID: PMC9371909 DOI: 10.1093/nar/gkac615] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 06/09/2022] [Accepted: 07/04/2022] [Indexed: 12/29/2022] Open
Abstract
Translation of SARS-CoV-2-encoded mRNAs by the host ribosomes is essential for its propagation. Following infection, the early expressed viral protein NSP1 binds the ribosome, represses translation, and induces mRNA degradation, while the host elicits an anti-viral response. The mechanisms enabling viral mRNAs to escape this multifaceted repression remain obscure. Here we show that expression of NSP1 leads to destabilization of multi-exon cellular mRNAs, while intron-less transcripts, such as viral mRNAs and anti-viral interferon genes, remain relatively stable. We identified a conserved and precisely located cap-proximal RNA element devoid of guanosines that confers resistance to NSP1-mediated translation inhibition. Importantly, the primary sequence rather than the secondary structure is critical for protection. We further show that the genomic 5'UTR of SARS-CoV-2 drives cap-independent translation and promotes expression of NSP1 in an eIF4E-independent and Torin1-resistant manner. Upon expression, NSP1 further enhances cap-independent translation. However, the sub-genomic 5'UTRs are highly sensitive to eIF4E availability, rendering viral propagation partially sensitive to Torin1. We conclude that the combined NSP1-mediated degradation of spliced mRNAs and translation inhibition of single-exon genes, along with the unique features present in the viral 5'UTRs, ensure robust expression of viral mRNAs. These features can be exploited as potential therapeutic targets.
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Affiliation(s)
- Boris Slobodin
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Urmila Sehrawat
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.,Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anastasia Lev
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Daniel Hayat
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Binyamin Zuckerman
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel.,Gladstone/UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Davide Fraticelli
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ariel Ogran
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Amir Ben-Shmuel
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 7410001 Israel
| | - Elad Bar-David
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 7410001 Israel
| | - Haim Levy
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona 7410001 Israel
| | - Igor Ulitsky
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rivka Dikstein
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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18
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Nissani N, Ulitsky I. Unique features of transcription termination and initiation at closely spaced tandem human genes. Mol Syst Biol 2022; 18:e11210. [PMID: 35848129 DOI: 10.15252/msb.202211210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/07/2022] [Indexed: 11/09/2022] Open
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19
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Ross CJ, Ulitsky I. Discovering functional motifs in long noncoding RNAs. Wiley Interdiscip Rev RNA 2022; 13:e1708. [PMID: 34981665 DOI: 10.1002/wrna.1708] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/19/2021] [Accepted: 12/04/2021] [Indexed: 12/27/2022]
Abstract
Long noncoding RNAs (lncRNAs) are products of pervasive transcription that closely resemble messenger RNAs on the molecular level, yet function through largely unknown modes of action. The current model is that the function of lncRNAs often relies on specific, typically short, conserved elements, connected by linkers in which specific sequences and/or structures are less important. This notion has fueled the development of both computational and experimental methods focused on the discovery of functional elements within lncRNA genes, based on diverse signals such as evolutionary conservation, predicted structural elements, or the ability to rescue loss-of-function phenotypes. In this review, we outline the main challenges that the different methods need to overcome, describe the recently developed approaches, and discuss their respective limitations. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Caroline Jane Ross
- Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
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20
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Bernard LD, Dubois A, Heurtier V, Fischer V, Gonzalez I, Chervova A, Tachtsidi A, Gil N, Owens N, Bates L, Vandormael-Pournin S, Silva JCR, Ulitsky I, Cohen-Tannoudji M, Navarro P. OCT4 activates a Suv39h1-repressive antisense lncRNA to couple histone H3 Lysine 9 methylation to pluripotency. Nucleic Acids Res 2022; 50:7367-7379. [PMID: 35762231 PMCID: PMC9303268 DOI: 10.1093/nar/gkac550] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 06/08/2022] [Accepted: 06/24/2022] [Indexed: 12/17/2022] Open
Abstract
Histone H3 Lysine 9 (H3K9) methylation, a characteristic mark of heterochromatin, is progressively implemented during development to contribute to cell fate restriction as differentiation proceeds. Accordingly, in undifferentiated and pluripotent mouse Embryonic Stem (ES) cells the global levels of H3K9 methylation are rather low and increase only upon differentiation. How global H3K9 methylation levels are coupled with the loss of pluripotency remains largely unknown. Here, we identify SUV39H1, a major H3K9 di- and tri-methylase, as an indirect target of the pluripotency network of Transcription Factors (TFs). We find that pluripotency TFs, principally OCT4, activate the expression of Suv39h1as, an antisense long non-coding RNA to Suv39h1. In turn, Suv39h1as downregulates Suv39h1 transcription in cis via a mechanism involving the modulation of the chromatin status of the locus. The targeted deletion of the Suv39h1as promoter region triggers increased SUV39H1 expression and H3K9me2 and H3K9me3 levels, affecting all heterochromatic regions, particularly peri-centromeric major satellites and retrotransposons. This increase in heterochromatinization efficiency leads to accelerated and more efficient commitment into differentiation. We report, therefore, a simple genetic circuitry coupling the genetic control of pluripotency with the global efficiency of H3K9 methylation associated with a major cell fate restriction, the irreversible loss of pluripotency.
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Affiliation(s)
- Laure D Bernard
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
- Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Agnès Dubois
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
| | - Victor Heurtier
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
- Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Véronique Fischer
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
| | - Inma Gonzalez
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
| | - Almira Chervova
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
| | - Alexandra Tachtsidi
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
- Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Noa Gil
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Nick Owens
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
| | - Lawrence E Bates
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sandrine Vandormael-Pournin
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
| | - José C R Silva
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou510005, Guangdong Province, China
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Michel Cohen-Tannoudji
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells Unit, Department of Developmental and Stem Cell Biology, F-75015 Paris, France
| | - Pablo Navarro
- To whom correspondence should be addressed. Tel: +33 145688285;
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21
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Ron M, Ulitsky I. Context-specific effects of sequence elements on subcellular localization of linear and circular RNAs. Nat Commun 2022; 13:2481. [PMID: 35513423 PMCID: PMC9072321 DOI: 10.1038/s41467-022-30183-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 04/05/2022] [Indexed: 12/24/2022] Open
Abstract
Long RNAs vary extensively in their post-transcriptional fates, and this variation is attributed in part to short sequence elements. We used massively parallel RNA assays to study how sequences derived from noncoding RNAs influence the subcellular localization and stability of circular and linear RNAs, including spliced and unspliced forms. We find that the effects of sequence elements strongly depend on the host RNA context, with limited overlap between sequences that drive nuclear enrichment of linear and circular RNAs. Binding of specific RNA binding proteins underpins some of these differences-SRSF1 binding leads to nuclear enrichment of circular RNAs; SAFB binding is associated with nuclear enrichment of predominantly unspliced linear RNAs; and IGF2BP1 promotes export of linear spliced RNA molecules. The post-transcriptional fate of long RNAs is thus dictated by combinatorial contributions of specific sequence elements, of splicing, and of the presence of the terminal features unique to linear RNAs.
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Affiliation(s)
- Maya Ron
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Igor Ulitsky
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, 76100, Israel.
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22
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Nissani N, Ulitsky I. Unique features of transcription termination and initiation at closely spaced tandem human genes. Mol Syst Biol 2022; 18:e10682. [PMID: 35362230 PMCID: PMC8972054 DOI: 10.15252/msb.202110682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 11/09/2022] Open
Abstract
The synthesis of RNA polymerase II (Pol2) products, which include messenger RNAs or long noncoding RNAs, culminates in transcription termination. How the transcriptional termination of a gene impacts the activity of promoters found immediately downstream of it, and which can be subject to potential transcriptional interference, remains largely unknown. We examined in an unbiased manner the features of the intergenic regions between pairs of 'tandem genes'-closely spaced (< 2 kb) human genes found on the same strand. Intergenic regions separating tandem genes are enriched with guanines and are characterized by binding of several proteins, including AGO1 and AGO2 of the RNA interference pathway. Additionally, we found that Pol2 is particularly enriched in this region, and it is lost upon perturbations affecting splicing or transcriptional elongation. Perturbations of genes involved in Pol2 pausing and R loop biology preferentially affect expression of downstream genes in tandem gene pairs. Overall, we find that features associated with Pol2 pausing and accumulation rather than those associated with avoidance of transcriptional interference are the predominant driving force shaping short tandem intergenic regions.
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Affiliation(s)
- Noa Nissani
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
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23
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Nataraj NB, Noronha A, Lee JS, Ghosh S, Mohan Raju HR, Sekar A, Zuckerman B, Lindzen M, Tarcitano E, Srivastava S, Selitrennik M, Livneh I, Drago-Garcia D, Rueda O, Caldas C, Lev S, Geiger T, Ciechanover A, Ulitsky I, Seger R, Ruppin E, Yarden Y. Nucleoporin-93 reveals a common feature of aggressive breast cancers: robust nucleocytoplasmic transport of transcription factors. Cell Rep 2022; 38:110418. [PMID: 35196484 PMCID: PMC8957480 DOI: 10.1016/j.celrep.2022.110418] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 10/14/2021] [Accepted: 02/01/2022] [Indexed: 12/14/2022] Open
Abstract
By establishing multi-omics pipelines, we uncover overexpression and gene copy-number alterations of nucleoporin-93 (NUP93), a nuclear pore component, in aggressive human mammary tumors. NUP93 overexpression enhances transendothelial migration and matrix invasion in vitro, along with tumor growth and metastasis in animal models. These findings are supported by analyses of two sets of naturally occurring mutations: rare oncogenic mutations and inactivating familial nephrotic syndrome mutations. Mechanistically, NUP93 binds with importins, boosts nuclear transport of importins' cargoes, such as β-catenin, and activates MYC. Likewise, NUP93 overexpression enhances the ultimate nuclear transport step shared by additional signaling pathways, including TGF-β/SMAD and EGF/ERK. The emerging addiction to nuclear transport exposes vulnerabilities of NUP93-overexpressing tumors. Congruently, myristoylated peptides corresponding to the nuclear translocation signals of SMAD and ERK can inhibit tumor growth and metastasis. Our study sheds light on an emerging hallmark of advanced tumors, which derive benefit from robust nucleocytoplasmic transport.
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Affiliation(s)
| | - Ashish Noronha
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Joo Sang Lee
- Cancer Data Science Lab, National Cancer Institute, NIH, Rockville, MD, USA
| | - Soma Ghosh
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Harsha Raj Mohan Raju
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Arunachalam Sekar
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Binyamin Zuckerman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Moshit Lindzen
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Emilio Tarcitano
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Swati Srivastava
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Selitrennik
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ido Livneh
- Technion Integrated Cancer Center (TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | - Diana Drago-Garcia
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Oscar Rueda
- Cancer Research UK Cambridge Institute, University of Cambridge and the Cambridge Cancer Centre, Department of Oncology, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge and the Cambridge Cancer Centre, Department of Oncology, Cambridge, UK
| | - Sima Lev
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Geiger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Aaron Ciechanover
- Technion Integrated Cancer Center (TICC) and the Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Rony Seger
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Eytan Ruppin
- Cancer Data Science Lab, National Cancer Institute, NIH, Rockville, MD, USA
| | - Yosef Yarden
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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24
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Affiliation(s)
- Rotem Ben-Tov Perry
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.,Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel. .,Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
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25
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Degani N, Lubelsky Y, Perry RBT, Ainbinder E, Ulitsky I. Highly conserved and cis-acting lncRNAs produced from paralogous regions in the center of HOXA and HOXB clusters in the endoderm lineage. PLoS Genet 2021; 17:e1009681. [PMID: 34280202 PMCID: PMC8330917 DOI: 10.1371/journal.pgen.1009681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 08/03/2021] [Accepted: 06/24/2021] [Indexed: 12/19/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been shown to play important roles in gene regulatory networks acting in early development. There has been rapid turnover of lncRNA loci during vertebrate evolution, with few human lncRNAs conserved beyond mammals. The sequences of these rare deeply conserved lncRNAs are typically not similar to each other. Here, we characterize HOXA-AS3 and HOXB-AS3, lncRNAs produced from the central regions of the HOXA and HOXB clusters. Sequence-similar orthologs of both lncRNAs are found in multiple vertebrate species and there is evident sequence similarity between their promoters, suggesting that the production of these lncRNAs predates the duplication of the HOX clusters at the root of the vertebrate lineage. This conservation extends to similar expression patterns of the two lncRNAs, in particular in cells transiently arising during early development or in the adult colon. Functionally, the RNA products of HOXA-AS3 and HOXB-AS3 regulate the expression of their overlapping HOX5-7 genes both in HT-29 cells and during differentiation of human embryonic stem cells. Beyond production of paralogous protein-coding and microRNA genes, the regulatory program in the HOX clusters therefore also relies on paralogous lncRNAs acting in restricted spatial and temporal windows of embryonic development and cell differentiation.
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Affiliation(s)
- Neta Degani
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Lubelsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Ben-Tov Perry
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Elena Ainbinder
- Department of Life Sciences Core Facilites, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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26
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Lubelsky Y, Zuckerman B, Ulitsky I. High-resolution mapping of function and protein binding in an RNA nuclear enrichment sequence. EMBO J 2021; 40:e106357. [PMID: 33938020 PMCID: PMC8204871 DOI: 10.15252/embj.2020106357] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 03/14/2021] [Accepted: 03/24/2021] [Indexed: 01/04/2023] Open
Abstract
The functions of long RNAs, including mRNAs and long noncoding RNAs (lncRNAs), critically depend on their subcellular localization. The identity of the sequences that dictate subcellular localization and their high-resolution anatomy remain largely unknown. We used a suite of massively parallel RNA assays and libraries containing thousands of sequence variants to pinpoint the functional features within the SIRLOIN element, which dictates nuclear enrichment through hnRNPK recruitment. In addition, we profiled the endogenous SIRLOIN RNA-nucleoprotein complex and identified the nuclear RNA-binding proteins SLTM and SNRNP70 as novel SIRLOIN binders. Taken together, using massively parallel assays, we identified the features that dictate binding of hnRNPK, SLTM, and SNRNP70 to SIRLOIN and found that these factors are jointly required for SIRLOIN activity. Our study thus provides a roadmap for high-throughput dissection of functional sequence elements in long RNAs.
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Affiliation(s)
- Yoav Lubelsky
- Department of Biological RegulationWeizmann Institute of ScienceRehovotIsrael
| | - Binyamin Zuckerman
- Department of Biological RegulationWeizmann Institute of ScienceRehovotIsrael
| | - Igor Ulitsky
- Department of Biological RegulationWeizmann Institute of ScienceRehovotIsrael
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27
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Finkel Y, Gluck A, Nachshon A, Winkler R, Fisher T, Rozman B, Mizrahi O, Lubelsky Y, Zuckerman B, Slobodin B, Yahalom-Ronen Y, Tamir H, Ulitsky I, Israely T, Paran N, Schwartz M, Stern-Ginossar N. SARS-CoV-2 uses a multipronged strategy to impede host protein synthesis. Nature 2021; 594:240-245. [PMID: 33979833 DOI: 10.1038/s41586-021-03610-3] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/04/2021] [Indexed: 02/07/2023]
Abstract
The coronavirus SARS-CoV-2 is the cause of the ongoing pandemic of COVID-191. Coronaviruses have developed a variety of mechanisms to repress host mRNA translation to allow the translation of viral mRNA, and concomitantly block the cellular innate immune response2,3. Although several different proteins of SARS-CoV-2 have previously been implicated in shutting off host expression4-7, a comprehensive picture of the effects of SARS-CoV-2 infection on cellular gene expression is lacking. Here we combine RNA sequencing, ribosome profiling and metabolic labelling of newly synthesized RNA to comprehensively define the mechanisms that are used by SARS-CoV-2 to shut off cellular protein synthesis. We show that infection leads to a global reduction in translation, but that viral transcripts are not preferentially translated. Instead, we find that infection leads to the accelerated degradation of cytosolic cellular mRNAs, which facilitates viral takeover of the mRNA pool in infected cells. We reveal that the translation of transcripts that are induced in response to infection (including innate immune genes) is impaired. We demonstrate this impairment is probably mediated by inhibition of nuclear mRNA export, which prevents newly transcribed cellular mRNA from accessing ribosomes. Overall, our results uncover a multipronged strategy that is used by SARS-CoV-2 to take over the translation machinery and to suppress host defences.
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Affiliation(s)
- Yaara Finkel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Avi Gluck
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Aharon Nachshon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Roni Winkler
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Fisher
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Batsheva Rozman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Orel Mizrahi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Lubelsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Binyamin Zuckerman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Boris Slobodin
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological, Chemical and Environmental Sciences, Ness Ziona, Israel
| | - Hadas Tamir
- Department of Infectious Diseases, Israel Institute for Biological, Chemical and Environmental Sciences, Ness Ziona, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Tomer Israely
- Department of Infectious Diseases, Israel Institute for Biological, Chemical and Environmental Sciences, Ness Ziona, Israel
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological, Chemical and Environmental Sciences, Ness Ziona, Israel
| | - Michal Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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28
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Mather RL, Parolia A, Carson SE, Venalainen E, Roig-Carles D, Jaber M, Chu SC, Alborelli I, Wu R, Lin D, Nabavi N, Jachetti E, Colombo MP, Xue H, Pucci P, Ci X, Hawkes C, Li Y, Pandha H, Ulitsky I, Marconett C, Quagliata L, Jiang W, Romero I, Wang Y, Crea F. The evolutionarily conserved long non-coding RNA LINC00261 drives neuroendocrine prostate cancer proliferation and metastasis via distinct nuclear and cytoplasmic mechanisms. Mol Oncol 2021; 15:1921-1941. [PMID: 33793068 PMCID: PMC8253100 DOI: 10.1002/1878-0261.12954] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 01/21/2021] [Accepted: 03/30/2021] [Indexed: 12/19/2022] Open
Abstract
Metastatic neuroendocrine prostate cancer (NEPC) is a highly aggressive disease, whose incidence is rising. Long noncoding RNAs (lncRNAs) represent a large family of disease- and tissue-specific transcripts, most of which are still functionally uncharacterized. Thus, we set out to identify the highly conserved lncRNAs that play a central role in NEPC pathogenesis. To this end, we performed transcriptomic analyses of donor-matched patient-derived xenograft models (PDXs) with immunohistologic features of prostate adenocarcinoma (AR+ /PSA+ ) or NEPC (AR- /SYN+ /CHGA+ ) and through differential expression analyses identified lncRNAs that were upregulated upon neuroendocrine transdifferentiation. These genes were prioritized for functional assessment based on the level of conservation in vertebrates. Here, LINC00261 emerged as the top gene with over 3229-fold upregulation in NEPC. Consistently, LINC00261 expression was significantly upregulated in NEPC specimens in multiple patient cohorts. Knockdown of LINC00261 in PC-3 cells dramatically attenuated its proliferative and metastatic abilities, which are explained by parallel downregulation of CBX2 and FOXA2 through distinct molecular mechanisms. In the cell cytoplasm, LINC00261 binds to and sequesters miR-8485 from targeting the CBX2 mRNA, while inside the nucleus, LINC00261 functions as a transcriptional scaffold to induce SMAD-driven expression of the FOXA2 gene. For the first time, these results demonstrate hyperactivation of the LINC00261-CBX2-FOXA2 axes in NEPC to drive proliferation and metastasis, and that LINC00261 may be utilized as a therapeutic target and a biomarker for this incurable disease.
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Affiliation(s)
- Rebecca L Mather
- Cancer Research Group-School of Life Health and Chemical Sciences, The Open University, Milton Keynes, UK
| | - Abhijit Parolia
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sandra E Carson
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Erik Venalainen
- Experimental Therapeutics, BC Cancer Research Centre, Vancouver, Canada
| | - David Roig-Carles
- Cancer Research Group-School of Life Health and Chemical Sciences, The Open University, Milton Keynes, UK
| | - Mustapha Jaber
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Shih-Chun Chu
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Rebecca Wu
- Experimental Therapeutics, BC Cancer Research Centre, Vancouver, Canada
| | - Dong Lin
- Experimental Therapeutics, BC Cancer Research Centre, Vancouver, Canada.,The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Noushin Nabavi
- Experimental Therapeutics, BC Cancer Research Centre, Vancouver, Canada
| | - Elena Jachetti
- Molecular Immunology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Tumori, Milano, Italy
| | - Mario P Colombo
- Molecular Immunology Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Tumori, Milano, Italy
| | - Hui Xue
- Experimental Therapeutics, BC Cancer Research Centre, Vancouver, Canada
| | - Perla Pucci
- Cancer Research Group-School of Life Health and Chemical Sciences, The Open University, Milton Keynes, UK
| | - Xinpei Ci
- The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Cheryl Hawkes
- Cancer Research Group-School of Life Health and Chemical Sciences, The Open University, Milton Keynes, UK
| | - Yinglei Li
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China
| | - Hardev Pandha
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Science, University of Surrey, Guildford, UK
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Crystal Marconett
- Departments of Surgery, Biochemistry and Molecular Medicine, Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Luca Quagliata
- Institute of Pathology, University Hospital Basel, Switzerland
| | - Wei Jiang
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, China
| | - Ignacio Romero
- Cancer Research Group-School of Life Health and Chemical Sciences, The Open University, Milton Keynes, UK
| | - Yuzhuo Wang
- Experimental Therapeutics, BC Cancer Research Centre, Vancouver, Canada.,The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, Canada.,Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - Francesco Crea
- Cancer Research Group-School of Life Health and Chemical Sciences, The Open University, Milton Keynes, UK
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29
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Monteiro JP, Rodor J, Caudrillier A, Scanlon JP, Spiroski AM, Dudnakova T, Pflüger-Müller B, Shmakova A, von Kriegsheim A, Deng L, Taylor RS, Wilson-Kanamori JR, Chen SH, Stewart K, Thomson A, Mitić T, McClure JD, Iynikkel J, Hadoke PW, Denby L, Bradshaw AC, Caruso P, Morrell NW, Kovacic JC, Ulitsky I, Henderson NC, Caporali A, Leisegang MS, Brandes RP, Baker AH. MIR503HG Loss Promotes Endothelial-to-Mesenchymal Transition in Vascular Disease. Circ Res 2021; 128:1173-1190. [PMID: 33703914 PMCID: PMC7610629 DOI: 10.1161/circresaha.120.318124] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/09/2021] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- João P. Monteiro
- The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh
| | - Julie Rodor
- The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh
| | - Axelle Caudrillier
- The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh
| | - Jessica P. Scanlon
- The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh
| | - Ana-Mishel Spiroski
- The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh
| | - Tatiana Dudnakova
- The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh
| | - Beatrice Pflüger-Müller
- Institute for Cardiovascular Physiology, Goethe University
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Alena Shmakova
- The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh
| | - Alex von Kriegsheim
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh
| | - Lin Deng
- The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh
| | - Richard S. Taylor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh
| | - John R. Wilson-Kanamori
- The Queen’s Medical Research Institute, Centre for Inflammation Research, University of Edinburgh
| | - Shiau-Haln Chen
- The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh
| | - Kevin Stewart
- The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh
| | - Adrian Thomson
- The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh
| | - Tijana Mitić
- The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh
| | - John D. McClure
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Centre, University of Glasgow
| | - Jean Iynikkel
- The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh
| | - Patrick W.F. Hadoke
- The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh
| | - Laura Denby
- The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh
| | - Angela C. Bradshaw
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Centre, University of Glasgow
| | | | | | - Jason C. Kovacic
- The Zena and Michael A. Wiener Cardiovascular Institute, School of Medicine at Mount Sinai, New York
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | | | - Neil C. Henderson
- The Queen’s Medical Research Institute, Centre for Inflammation Research, University of Edinburgh
| | - Andrea Caporali
- The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh
| | - Matthias S. Leisegang
- Institute for Cardiovascular Physiology, Goethe University
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Ralf P. Brandes
- Institute for Cardiovascular Physiology, Goethe University
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Andrew H. Baker
- The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh
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30
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Herold I, Zolti A, Garduño-Rosales M, Wang Z, López-Giráldez F, Mouriño-Pérez RR, Townsend JP, Ulitsky I, Yarden O. The GUL-1 Protein Binds Multiple RNAs Involved in Cell Wall Remodeling and Affects the MAK-1 Pathway in Neurospora crassa. Front Fungal Biol 2021; 2:672696. [PMID: 37744127 PMCID: PMC10512220 DOI: 10.3389/ffunb.2021.672696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/19/2021] [Indexed: 09/26/2023]
Abstract
The Neurospora crassa GUL-1 is part of the COT-1 pathway, which plays key roles in regulating polar hyphal growth and cell wall remodeling. We show that GUL-1 is a bona fide RNA-binding protein (RBP) that can associate with 828 "core" mRNA species. When cell wall integrity (CWI) is challenged, expression of over 25% of genomic RNA species are modulated (2,628 mRNAs, including the GUL-1 mRNA). GUL-1 binds mRNAs of genes related to translation, cell wall remodeling, circadian clock, endoplasmic reticulum (ER), as well as CWI and MAPK pathway components. GUL-1 interacts with over 100 different proteins, including stress-granule and P-body proteins, ER components and components of the MAPK, COT-1, and STRIPAK complexes. Several additional RBPs were also shown to physically interact with GUL-1. Under stress conditions, GUL-1 can localize to the ER and affect the CWI pathway-evident via altered phosphorylation levels of MAK-1, interaction with mak-1 transcript, and involvement in the expression level of the transcription factor adv-1. We conclude that GUL-1 functions in multiple cellular processes, including the regulation of cell wall remodeling, via a mechanism associated with the MAK-1 pathway and stress-response.
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Affiliation(s)
- Inbal Herold
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Avihai Zolti
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Marisela Garduño-Rosales
- Departamento de Microbiología, CICESE (Centro de Investigación Científica y Educación Superior de Ensenada), Ensenada, Mexico
| | - Zheng Wang
- Department of Biostatistics, Yale University, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Francesc López-Giráldez
- Yale Center for Genome Analysis, Department of Genetics, Yale University, New Haven, CT, United States
| | - Rosa R. Mouriño-Pérez
- Departamento de Microbiología, CICESE (Centro de Investigación Científica y Educación Superior de Ensenada), Ensenada, Mexico
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale University, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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31
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Gil N, Ulitsky I. Inefficient splicing curbs noncoding RNA transcription. Nat Struct Mol Biol 2021; 28:327-328. [PMID: 33767453 DOI: 10.1038/s41594-021-00582-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Noa Gil
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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32
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Bennett M, Ulitsky I, Alloza I, Vandenbroeck K, Miscianinov V, Mahmoud AD, Ballantyne M, Rodor J, Baker AH. Novel Transcript Discovery Expands the Repertoire of Pathologically-Associated, Long Non-Coding RNAs in Vascular Smooth Muscle Cells. Int J Mol Sci 2021; 22:1484. [PMID: 33540814 PMCID: PMC7867340 DOI: 10.3390/ijms22031484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 01/23/2023] Open
Abstract
Vascular smooth muscle cells (VSMCs) provide vital contractile force within blood vessel walls, yet can also propagate cardiovascular pathologies through proliferative and pro-inflammatory activities. Such phenotypes are driven, in part, by the diverse effects of long non-coding RNAs (lncRNAs) on gene expression. However, lncRNA characterisation in VSMCs in pathological states is hampered by incomplete lncRNA representation in reference annotation. We aimed to improve lncRNA representation in such contexts by assembling non-reference transcripts in RNA sequencing datasets describing VSMCs stimulated in vitro with cytokines, growth factors, or mechanical stress, as well as those isolated from atherosclerotic plaques. All transcripts were then subjected to a rigorous lncRNA prediction pipeline. We substantially improved coverage of lncRNAs responding to pro-mitogenic stimuli, with non-reference lncRNAs contributing 21-32% for each dataset. We also demonstrate non-reference lncRNAs were biased towards enriched expression within VSMCs, and transcription from enhancer sites, suggesting particular relevance to VSMC processes, and the regulation of neighbouring protein-coding genes. Both VSMC-enriched and enhancer-transcribed lncRNAs were large components of lncRNAs responding to pathological stimuli, yet without novel transcript discovery 33-46% of these lncRNAs would remain hidden. Our comprehensive VSMC lncRNA repertoire allows proper prioritisation of candidates for characterisation and exemplifies a strategy to broaden our knowledge of lncRNA across a range of disease states.
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MESH Headings
- Aorta/cytology
- Coronary Vessels/cytology
- Cytokines/pharmacology
- Datasets as Topic
- Enhancer Elements, Genetic
- Gene Expression Profiling
- Humans
- Intercellular Signaling Peptides and Proteins/pharmacology
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/metabolism
- Myocytes, Smooth Muscle/drug effects
- Myocytes, Smooth Muscle/metabolism
- Plaque, Atherosclerotic/metabolism
- RNA, Long Noncoding/analysis
- RNA, Long Noncoding/isolation & purification
- RNA-Seq
- Stress, Mechanical
- Transcription, Genetic/drug effects
- Transcriptome
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Affiliation(s)
- Matthew Bennett
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK; (M.B.); (V.M.); (A.D.M.); (M.B.); (J.R.)
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Iraide Alloza
- Inflammation & Biomarkers Group, Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903 Barakaldo, Spain; (I.A.); (K.V.)
| | - Koen Vandenbroeck
- Inflammation & Biomarkers Group, Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903 Barakaldo, Spain; (I.A.); (K.V.)
- Ikerbasque, Basque Foundation for Science, 3 María Díaz Haroko Kalea, 48013 Bilbao, Spain
| | - Vladislav Miscianinov
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK; (M.B.); (V.M.); (A.D.M.); (M.B.); (J.R.)
| | - Amira Dia Mahmoud
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK; (M.B.); (V.M.); (A.D.M.); (M.B.); (J.R.)
| | - Margaret Ballantyne
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK; (M.B.); (V.M.); (A.D.M.); (M.B.); (J.R.)
| | - Julie Rodor
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK; (M.B.); (V.M.); (A.D.M.); (M.B.); (J.R.)
| | - Andrew H. Baker
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK; (M.B.); (V.M.); (A.D.M.); (M.B.); (J.R.)
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33
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Ross CJ, Rom A, Spinrad A, Gelbard-Solodkin D, Degani N, Ulitsky I. Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences. Genome Biol 2021; 22:29. [PMID: 33430943 PMCID: PMC7798263 DOI: 10.1186/s13059-020-02247-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Animal genomes contain thousands of long noncoding RNA (lncRNA) genes, a growing subset of which are thought to be functionally important. This functionality is often mediated by short sequence elements scattered throughout the RNA sequence that correspond to binding sites for small RNAs and RNA binding proteins. Throughout vertebrate evolution, the sequences of lncRNA genes changed extensively, so that it is often impossible to obtain significant alignments between sequences of lncRNAs from evolutionary distant species, even when synteny is evident. This often prohibits identifying conserved lncRNAs that are likely to be functional or prioritizing constrained regions for experimental interrogation. RESULTS We introduce here LncLOOM, a novel algorithmic framework for the discovery and evaluation of syntenic combinations of short motifs. LncLOOM is based on a graph representation of the input sequences and uses integer linear programming to efficiently compare dozens of sequences that have thousands of bases each and to evaluate the significance of the recovered motifs. We show that LncLOOM is capable of identifying specific, biologically relevant motifs which are conserved throughout vertebrates and beyond in lncRNAs and 3'UTRs, including novel functional RNA elements in the CHASERR lncRNA that are required for regulation of CHD2 expression. CONCLUSIONS We expect that LncLOOM will become a broadly used approach for the discovery of functionally relevant elements in the noncoding genome.
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Affiliation(s)
- Caroline Jane Ross
- Department of Biological Regulation, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Aviv Rom
- Department of Biological Regulation, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Amit Spinrad
- Department of Biological Regulation, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Dikla Gelbard-Solodkin
- Department of Biological Regulation, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Neta Degani
- Department of Biological Regulation, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, 76100, Rehovot, Israel.
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34
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Zagorac S, de Giorgio A, Dabrowska A, Kalisz M, Casas-Vila N, Cathcart P, Yiu A, Ottaviani S, Degani N, Lombardo Y, Tweedie A, Nissan T, Vance KW, Ulitsky I, Stebbing J, Castellano L. SCIRT lncRNA Restrains Tumorigenesis by Opposing Transcriptional Programs of Tumor-Initiating Cells. Cancer Res 2020; 81:580-593. [PMID: 33172932 DOI: 10.1158/0008-5472.can-20-2612] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/05/2020] [Accepted: 11/05/2020] [Indexed: 11/16/2022]
Abstract
In many tumors, cells transition reversibly between slow-proliferating tumor-initiating cells (TIC) and their differentiated, faster-growing progeny. Yet, how transcriptional regulation of cell-cycle and self-renewal genes is orchestrated during these conversions remains unclear. In this study, we show that as breast TIC form, a decrease in cell-cycle gene expression and increase in self-renewal gene expression are coregulated by SOX2 and EZH2, which colocalize at CpG islands. This pattern was negatively controlled by a novel long noncoding RNA (lncRNA) that we named Stem Cell Inhibitory RNA Transcript (SCIRT), which was markedly upregulated in tumorspheres but colocalized with and counteracted EZH2 and SOX2 during cell-cycle and self-renewal regulation to restrain tumorigenesis. SCIRT specifically interacted with EZH2 to increase EZH2 affinity to FOXM1 without binding the latter. In this manner, SCIRT induced transcription at cell-cycle gene promoters by recruiting FOXM1 through EZH2 to antagonize EZH2-mediated effects at target genes. Conversely, on stemness genes, FOXM1 was absent and SCIRT antagonized EZH2 and SOX2 activity, balancing toward repression. These data suggest that the interaction of an lncRNA with EZH2 can alter the affinity of EZH2 for its protein-binding partners to regulate cancer cell state transitions. SIGNIFICANCE: These findings show that a novel lncRNA SCIRT counteracts breast tumorigenesis by opposing transcriptional networks associated with cell cycle and self-renewal.See related commentary by Pardini and Dragomir, p. 535.
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Affiliation(s)
- Sladjana Zagorac
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), London, United Kingdom
| | - Alex de Giorgio
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), London, United Kingdom
| | - Aleksandra Dabrowska
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), London, United Kingdom
| | - Mark Kalisz
- Epithelial Carcinogenesis Group, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
| | | | - Paul Cathcart
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), London, United Kingdom
| | - Angela Yiu
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), London, United Kingdom
| | - Silvia Ottaviani
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), London, United Kingdom
| | - Neta Degani
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot, Israel
| | - Ylenia Lombardo
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), London, United Kingdom.,Nature Communications, The Macmillan Campus, London, United Kingdom
| | - Alistair Tweedie
- University of Sussex, School of life Sciences, John Maynard Smith Building, Falmer, Brighton, United Kingdom
| | - Tracy Nissan
- University of Sussex, School of life Sciences, John Maynard Smith Building, Falmer, Brighton, United Kingdom
| | - Keith W Vance
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Igor Ulitsky
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot, Israel
| | - Justin Stebbing
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), London, United Kingdom
| | - Leandro Castellano
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Imperial Centre for Translational and Experimental Medicine (ICTEM), London, United Kingdom. .,University of Sussex, School of life Sciences, John Maynard Smith Building, Falmer, Brighton, United Kingdom
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35
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Koffler-Brill T, Taiber S, Anaya A, Bordeynik-Cohen M, Rosen E, Kolla L, Messika-Gold N, Elkon R, Kelley MW, Ulitsky I, Avraham KB. Identification and characterization of key long non-coding RNAs in the mouse cochlea. RNA Biol 2020; 18:1160-1169. [PMID: 33131415 DOI: 10.1080/15476286.2020.1836456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The auditory system is a complex sensory network with an orchestrated multilayer regulatory programme governing its development and maintenance. Accumulating evidence has implicated long non-coding RNAs (lncRNAs) as important regulators in numerous systems, as well as in pathological pathways. However, their function in the auditory system has yet to be explored. Using a set of specific criteria, we selected four lncRNAs expressed in the mouse cochlea, which are conserved in the human transcriptome and are relevant for inner ear function. Bioinformatic characterization demonstrated a lack of coding potential and an absence of evolutionary conservation that represent properties commonly shared by their class members. RNAscope® analysis of the spatial and temporal expression profiles revealed specific localization to inner ear cells. Sub-cellular localization analysis presented a distinct pattern for each lncRNA and mouse tissue expression evaluation displayed a large variability in terms of level and location. Our findings establish the expression of specific lncRNAs in different cell types of the auditory system and present a potential pathway by which the lncRNA Gas5 acts in the inner ear. Studying lncRNAs and deciphering their functions may deepen our knowledge of inner ear physiology and morphology and may reveal the basis of as yet unresolved genetic hearing loss-related pathologies. Moreover, our experimental design may be employed as a reference for studying other inner ear-related lncRNAs, as well as lncRNAs expressed in other sensory systems.
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Affiliation(s)
- Tal Koffler-Brill
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Taiber
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Alejandro Anaya
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Mor Bordeynik-Cohen
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Einat Rosen
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Likhitha Kolla
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Naama Messika-Gold
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Matthew W Kelley
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, Maryland, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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36
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Hezroni H, Ben-Tov Perry R, Gil N, Degani N, Ulitsky I. Regulation of neuronal commitment in mouse embryonic stem cells by the Reno1/Bahcc1 locus. EMBO Rep 2020; 21:e51264. [PMID: 32969152 DOI: 10.15252/embr.202051264] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 11/09/2022] Open
Abstract
Mammalian genomes encode thousands of long noncoding RNAs (lncRNAs), yet the biological functions of most of them remain unknown. A particularly rich repertoire of lncRNAs found in mammalian brain and in the early embryo. We used RNA-seq and computational analysis to prioritize lncRNAs that may regulate commitment of pluripotent cells to a neuronal fate and perturbed their expression prior to neuronal differentiation. Knockdown by RNAi of two highly conserved and well-expressed lncRNAs, Reno1 (2810410L24Rik) and lnc-Nr2f1, decreased the expression of neuronal markers and led to massive changes in gene expression in the differentiated cells. We further show that the Reno1 locus forms increasing spatial contacts during neurogenesis with its adjacent protein-coding gene Bahcc1. Loss of either Reno1 or Bahcc1 leads to an early arrest in neuronal commitment, failure to induce a neuronal gene expression program, and to global reduction in chromatin accessibility at regions that are marked by the H3K4me3 chromatin mark at the onset of differentiation. Reno1 and Bahcc1 thus form a previously uncharacterized circuit required for the early steps of neuronal commitment.
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Affiliation(s)
| | | | - Noa Gil
- Weizmann Institute of Science, Rehovot, Israel
| | - Neta Degani
- Weizmann Institute of Science, Rehovot, Israel
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37
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Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJ, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJ, Rackham OJ, Rizzu P, Martinez DFS, Sandelin A, Sanjana P, Semple CA, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest AR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJ, Shin JW, Carninci P. Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res 2020. [DOI: 10.1101/gr.270330.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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38
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Keshet R, Lee JS, Adler L, Iraqi M, Ariav Y, Lim LQJ, Lerner S, Rabinovich S, Oren R, Katzir R, Weiss Tishler H, Stettner N, Goldman O, Landesman H, Galai S, Kuperman Y, Kuznetsov Y, Brandis A, Mehlman T, Malitsky S, Itkin M, Koehler SE, Zhao Y, Talsania K, Shen TW, Peled N, Ulitsky I, Porgador A, Ruppin E, Erez A. Targeting purine synthesis in ASS1-expressing tumors enhances the response to immune checkpoint inhibitors. Nat Cancer 2020; 1:894-908. [PMID: 35121952 DOI: 10.1038/s43018-020-0106-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 07/21/2020] [Indexed: 06/14/2023]
Abstract
Argininosuccinate synthase (ASS1) downregulation in different tumors has been shown to support cell proliferation and yet, in several common cancer subsets ASS1 expression associates with poor patient prognosis. Here we demonstrate that ASS1 expression under glucose deprivation is induced by c-MYC, providing survival benefit by increasing nitric oxide synthesis and activating the gluconeogenic enzymes pyruvate carboxylase and phosphoenolpyruvate carboxykinase by S-nitrosylation. The resulting increased flux through gluconeogenesis enhances serine, glycine and subsequently purine synthesis. Notably, high ASS1-expressing breast cancer mice do not respond to immune checkpoint inhibitors and patients with breast cancer with high ASS1 have more metastases. We further find that inhibiting purine synthesis increases pyrimidine to purine ratio, elevates expression of the immunoproteasome and significantly enhances the response of autologous primary CD8+ T cells to anti-PD-1. These results suggest that treating patients with high-ASS1 cancers with purine synthesis inhibition is beneficial and may also sensitize them to immune checkpoint inhibition therapy.
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Affiliation(s)
- Rom Keshet
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
- The Bert W. Strassburger Lipid Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Joo Sang Lee
- Cancer Data Science Lab, National Cancer Institutes of Health, Bethesda, MD, USA
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University, Suwon, Republic of Korea
| | - Lital Adler
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Muhammed Iraqi
- Faculty of Health Sciences, The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Yarden Ariav
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Lisha Qiu Jin Lim
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Shaul Lerner
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Shiran Rabinovich
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Roni Oren
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Katzir
- Cancer Data Science Lab, National Cancer Institutes of Health, Bethesda, MD, USA
| | - Hila Weiss Tishler
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Stettner
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Omer Goldman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Landesman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Sivan Galai
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Kuperman
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Yuri Kuznetsov
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Brandis
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Tevi Mehlman
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Malitsky
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Maxim Itkin
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - S Eleonore Koehler
- Department Anatomy & Embryology, Maastricht University, Maastricht, the Netherlands
| | - Yongmei Zhao
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Keyur Talsania
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tsai-Wei Shen
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nir Peled
- The Legacy Heritage Oncology Center and Dr. Larry Norton Institute, Soroka Medical Center and Ben-Gurion University, Beer-Sheva, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Angel Porgador
- Faculty of Health Sciences, The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Eytan Ruppin
- Cancer Data Science Lab, National Cancer Institutes of Health, Bethesda, MD, USA.
| | - Ayelet Erez
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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39
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Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJF, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJC, Rackham OJL, Rizzu P, Sánchez Martinez DF, Sandelin A, Sanjana P, Semple CAM, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest ARR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJL, Shin JW, Carninci P. Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res 2020; 30:1060-1072. [PMID: 32718982 PMCID: PMC7397864 DOI: 10.1101/gr.254219.119] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 06/24/2020] [Indexed: 12/12/2022]
Abstract
Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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Affiliation(s)
- Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jen-Chien Chang
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yari Ciani
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy
| | - Ivan V Kulakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Mickaël Mendez
- Department of Computer Science, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | | | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
| | - Andreas Petri
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 9220, Denmark
| | - Leonie Roos
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kayoko Yasuzawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Altuna Akalin
- Berlin Institute for Medical Systems Biology, Max Delbrük Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Ivan V Antonov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Alessandro Bonetti
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hidemasa Bono
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima City 739-0046, Japan
| | - Beatrice Borsari
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Frank Brombacher
- International Centre for Genetic Engineering and Biotechnology (ICGEB), University of Cape Town, Cape Town 7925, South Africa.,Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Christopher JF Cameron
- School of Computer Science, McGill University, Montréal, Québec H3G 1Y6, Canada.,Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, USA
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden 01062, Germany.,Center for Complex Network Intelligence (CCNI) at the Tsinghua Laboratory of Brain and Intelligence (THBI), Department of Bioengineering, Tsinghua University, Beijing 100084, China
| | - Ryan Cardenas
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Melissa Cardon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Howard Chang
- Center for Personal Dynamic Regulome, Stanford University, Stanford, California 94305, USA
| | - Josée Dostie
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Luca Ducoli
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, Zurich 8093, Switzerland
| | - Alexander Favorov
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Alexandre Fort
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Diego Garrido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Noa Gil
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Juliette Gimenez
- Epigenetics and Genome Reprogramming Laboratory, IRCCS Fondazione Santa Lucia, Rome 00179, Italy
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology (ICGEB), University of Cape Town, Cape Town 7925, South Africa.,Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lusy Handoko
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jayson Harshbarger
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yuki Hasegawa
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Norihito Hayatsu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Peter Heutink
- Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Eddie L Imada
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Masayoshi Itoh
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Bogumil Kaczkowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Aditi Kanhere
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Emily Kawabata
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Tsugumi Kawashima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - S Thomas Kelly
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Miki Kojima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Naoto Kondo
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Anton Kratz
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Mariola Kurowska-Stolarska
- Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, Scotland G12 8QQ, United Kingdom
| | - Andrew Tae Jun Kwon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jeffrey Leek
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden
| | - Marina Lizio
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Fernando López-Redondo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Shiori Maeda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Vsevolod J Makeev
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Luigi Marchionni
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Aki Minoda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Manuel Muñoz-Aguirre
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hiromi Nishiyori
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kazuhiro R Nitta
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yukihiko Noro
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ramil Nurtdinov
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Yasushi Okazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Valerio Orlando
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Denis Paquette
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Callum J C Parr
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Patrizia Rizzu
- Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany
| | | | - Albin Sandelin
- Department of Biology and BRIC, University of Copenhagen, Denmark, Copenhagen N DK2200, Denmark
| | - Pillay Sanjana
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Colin A M Semple
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Youtaro Shibayama
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Divya M Sivaraman
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Takahiro Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | | | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Martin S Taylor
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Malte Thodberg
- Department of Biology and BRIC, University of Copenhagen, Denmark, Copenhagen N DK2200, Denmark
| | - Supat Thongjuea
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Vidisha Tripathi
- National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Roberto Verardo
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy
| | - Ilya E Vorontsov
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Chinatsu Yamamoto
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Robert S Young
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
| | - Alistair R R Forrest
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, Western Australia 6009, Australia
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia 08002, Spain
| | | | - Chung Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 9220, Denmark
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki and Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Boris Lenhard
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen N-5008, Norway
| | - Claudio Schneider
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy.,Department of Medicine and Consorzio Interuniversitario Biotecnologie p.zle Kolbe 1 University of Udine, Udine 33100, Italy
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ken Yagi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Michiel J L de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
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40
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Geirsdottir L, David E, Keren-Shaul H, Weiner A, Bohlen SC, Neuber J, Balic A, Giladi A, Sheban F, Dutertre CA, Pfeifle C, Peri F, Raffo-Romero A, Vizioli J, Matiasek K, Scheiwe C, Meckel S, Mätz-Rensing K, van der Meer F, Thormodsson FR, Stadelmann C, Zilkha N, Kimchi T, Ginhoux F, Ulitsky I, Erny D, Amit I, Prinz M. Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program. Cell 2020; 179:1609-1622.e16. [PMID: 31835035 DOI: 10.1016/j.cell.2019.11.010] [Citation(s) in RCA: 225] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/30/2019] [Accepted: 11/06/2019] [Indexed: 02/08/2023]
Abstract
Microglia, the brain-resident immune cells, are critically involved in many physiological and pathological brain processes, including neurodegeneration. Here we characterize microglia morphology and transcriptional programs across ten species spanning more than 450 million years of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to humans, including ligands and receptors associated with interactions between glia and neurons. In most species, microglia show a single dominant transcriptional state, whereas human microglia display significant heterogeneity. In addition, we observed notable differences in several gene modules of rodents compared with primate microglia, including complement, phagocytic, and susceptibility genes to neurodegeneration, such as Alzheimer's and Parkinson's disease. Our study provides an essential resource of conserved and divergent microglia pathways across evolution, with important implications for future development of microglia-based therapies in humans.
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Affiliation(s)
- Laufey Geirsdottir
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Keren-Shaul
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel; Life Science Core Facility-Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Weiner
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Jana Neuber
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Adam Balic
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, United Kingdom
| | - Amir Giladi
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Fadi Sheban
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Charles-Antoine Dutertre
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore; Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, Singapore, Singapore
| | - Christine Pfeifle
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Ploen, Germany
| | - Francesca Peri
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Antonella Raffo-Romero
- Universite Lille, Inserm, U-1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille, France
| | - Jacopo Vizioli
- Universite Lille, Inserm, U-1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille, France
| | - Kaspar Matiasek
- Section of Clinical & Comparative Neuropathology, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christian Scheiwe
- Clinic for Neurosurgery, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stephan Meckel
- Department of Neuroradiology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kerstin Mätz-Rensing
- German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | | | | | - Christine Stadelmann
- Institute of Neuropathology, University Medical Center Göttingen, Göttingen, Germany
| | - Noga Zilkha
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Tali Kimchi
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore; Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai, China; Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the Academia, Singapore, Singapore
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel Erny
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Berta-Ottenstein-Programme, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
| | - Marco Prinz
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Signaling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany; Center for NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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41
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Slobodin B, Bahat A, Sehrawat U, Becker-Herman S, Zuckerman B, Weiss AN, Han R, Elkon R, Agami R, Ulitsky I, Shachar I, Dikstein R. Transcription Dynamics Regulate Poly(A) Tails and Expression of the RNA Degradation Machinery to Balance mRNA Levels. Mol Cell 2020; 78:434-444.e5. [PMID: 32294471 DOI: 10.1016/j.molcel.2020.03.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/25/2020] [Accepted: 03/14/2020] [Indexed: 02/02/2023]
Abstract
Gene expression is regulated by the rates of synthesis and degradation of mRNAs, but how these processes are coordinated is poorly understood. Here, we show that reduced transcription dynamics of specific genes leads to enhanced m6A deposition, preferential activity of the CCR4-Not complex, shortened poly(A) tails, and reduced stability of the respective mRNAs. These effects are also exerted by internal ribosome entry site (IRES) elements, which we found to be transcriptional pause sites. However, when transcription dynamics, and subsequently poly(A) tails, are globally altered, cells buffer mRNA levels by adjusting the expression of mRNA degradation machinery. Stress-provoked global impediment of transcription elongation leads to a dramatic inhibition of the mRNA degradation machinery and massive mRNA stabilization. Accordingly, globally enhanced transcription, such as following B cell activation or glucose stimulation, has the opposite effects. This study uncovers two molecular pathways that maintain balanced gene expression in mammalian cells by linking transcription to mRNA stability.
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Affiliation(s)
- Boris Slobodin
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Anat Bahat
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Urmila Sehrawat
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shirly Becker-Herman
- Department of Immunology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Binyamin Zuckerman
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Amanda N Weiss
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ruiqi Han
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Igor Ulitsky
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Idit Shachar
- Department of Immunology, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rivka Dikstein
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.
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42
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Geirsdottir L, David E, Keren-Shaul H, Weiner A, Bohlen SC, Neuber J, Balic A, Giladi A, Sheban F, Dutertre CA, Pfeifle C, Peri F, Raffo-Romero A, Vizioli J, Matiasek K, Scheiwe C, Meckel S, Mätz-Rensing K, van der Meer F, Thormodsson FR, Stadelmann C, Zilkha N, Kimchi T, Ginhoux F, Ulitsky I, Erny D, Amit I, Prinz M. Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program. Cell 2020; 181:746. [PMID: 32359440 DOI: 10.1016/j.cell.2020.04.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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43
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Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA. A guide to naming human non-coding RNA genes. EMBO J 2020; 39:e103777. [PMID: 32090359 PMCID: PMC7073466 DOI: 10.15252/embj.2019103777] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 12/15/2022] Open
Abstract
Research on non-coding RNA (ncRNA) is a rapidly expanding field. Providing an official gene symbol and name to ncRNA genes brings order to otherwise potential chaos as it allows unambiguous communication about each gene. The HUGO Gene Nomenclature Committee (HGNC, www.genenames.org) is the only group with the authority to approve symbols for human genes. The HGNC works with specialist advisors for different classes of ncRNA to ensure that ncRNA nomenclature is accurate and informative, where possible. Here, we review each major class of ncRNA that is currently annotated in the human genome and describe how each class is assigned a standardised nomenclature.
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Affiliation(s)
- Ruth L Seal
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai, China
| | - Sam Griffiths-Jones
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Michael B Mathews
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Dawn O'Reilly
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Andrew J Pierce
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia.,Santa Fe Institute, Santa Fe, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Sandra L Wolin
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
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44
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Pradas-Juni M, Hansmeier NR, Link JC, Schmidt E, Larsen BD, Klemm P, Meola N, Topel H, Loureiro R, Dhaouadi I, Kiefer CA, Schwarzer R, Khani S, Oliverio M, Awazawa M, Frommolt P, Heeren J, Scheja L, Heine M, Dieterich C, Büning H, Yang L, Cao H, Jesus DFD, Kulkarni RN, Zevnik B, Tröder SE, Knippschild U, Edwards PA, Lee RG, Yamamoto M, Ulitsky I, Fernandez-Rebollo E, Vallim TQDA, Kornfeld JW. A MAFG-lncRNA axis links systemic nutrient abundance to hepatic glucose metabolism. Nat Commun 2020; 11:644. [PMID: 32005828 PMCID: PMC6994702 DOI: 10.1038/s41467-020-14323-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/27/2019] [Indexed: 02/07/2023] Open
Abstract
Obesity and type 2 diabetes mellitus are global emergencies and long noncoding RNAs (lncRNAs) are regulatory transcripts with elusive functions in metabolism. Here we show that a high fraction of lncRNAs, but not protein-coding mRNAs, are repressed during diet-induced obesity (DIO) and refeeding, whilst nutrient deprivation induced lncRNAs in mouse liver. Similarly, lncRNAs are lost in diabetic humans. LncRNA promoter analyses, global cistrome and gain-of-function analyses confirm that increased MAFG signaling during DIO curbs lncRNA expression. Silencing Mafg in mouse hepatocytes and obese mice elicits a fasting-like gene expression profile, improves glucose metabolism, de-represses lncRNAs and impairs mammalian target of rapamycin (mTOR) activation. We find that obesity-repressed LincIRS2 is controlled by MAFG and observe that genetic and RNAi-mediated LincIRS2 loss causes elevated blood glucose, insulin resistance and aberrant glucose output in lean mice. Taken together, we identify a MAFG-lncRNA axis controlling hepatic glucose metabolism in health and metabolic disease. Despite widespread transcription of LncRNA in mammalian systems, their contribution to metabolic homeostasis at the cellular and tissue level remains elusive. Here Pradas-Juni et al. describe a transcription factor–LncRNA pathway that couples hepatocyte nutrient sensing to regulation of glucose metabolism in mice.
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Affiliation(s)
- Marta Pradas-Juni
- Functional Genomics and Metabolism Unit, Department for Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.,Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931, Cologne, Germany.,Cologne Cluster of Excellence-Cellular Stress Responses in Ageing-associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Nils R Hansmeier
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931, Cologne, Germany.,Cologne Cluster of Excellence-Cellular Stress Responses in Ageing-associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Jenny C Link
- Department of Biological Chemistry, University of California, Los Angeles (UCLA), 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.,Department of Medicine, Division of Cardiology, UCLA, 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
| | - Elena Schmidt
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931, Cologne, Germany.,Cologne Cluster of Excellence-Cellular Stress Responses in Ageing-associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Bjørk Ditlev Larsen
- Functional Genomics and Metabolism Unit, Department for Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Paul Klemm
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931, Cologne, Germany.,Cologne Cluster of Excellence-Cellular Stress Responses in Ageing-associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Nicola Meola
- Functional Genomics and Metabolism Unit, Department for Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Hande Topel
- Functional Genomics and Metabolism Unit, Department for Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.,Izmir Biomedicine and Genome Center (IBG), Mithatpasa Ave. 58/5, 35340, Izmir, Turkey.,Department of Medical Biology and Genetics, Graduate School of Health Sciences, Dokuz Eylul University, Mithatpasa Ave. 1606, 35330, Izmir, Turkey
| | - Rute Loureiro
- Functional Genomics and Metabolism Unit, Department for Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.,Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931, Cologne, Germany.,Cologne Cluster of Excellence-Cellular Stress Responses in Ageing-associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Ines Dhaouadi
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931, Cologne, Germany.,Cologne Cluster of Excellence-Cellular Stress Responses in Ageing-associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Christoph A Kiefer
- Functional Genomics and Metabolism Unit, Department for Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Robin Schwarzer
- Cologne Cluster of Excellence-Cellular Stress Responses in Ageing-associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Sajjad Khani
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931, Cologne, Germany.,Cologne Cluster of Excellence-Cellular Stress Responses in Ageing-associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Matteo Oliverio
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931, Cologne, Germany.,Cologne Cluster of Excellence-Cellular Stress Responses in Ageing-associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Motoharu Awazawa
- Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931, Cologne, Germany.,Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Peter Frommolt
- Cologne Cluster of Excellence-Cellular Stress Responses in Ageing-associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Joerg Heeren
- Department of Biochemistry and Molecular Cell Biology, Martinistraße 52, 20246, Hamburg, Germany
| | - Ludger Scheja
- Department of Biochemistry and Molecular Cell Biology, Martinistraße 52, 20246, Hamburg, Germany
| | - Markus Heine
- Department of Biochemistry and Molecular Cell Biology, Martinistraße 52, 20246, Hamburg, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
| | - Hildegard Büning
- Institute of Experimental Hematology, Hanover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Ling Yang
- Cardiovascular Branch, National Heart Lung and Blood Institute, Bethesda, MD, 20892, USA.,Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Haiming Cao
- Cardiovascular Branch, National Heart Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Dario F De Jesus
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, 02215, MA, USA
| | - Rohit N Kulkarni
- Islet Cell and Regenerative Biology, Joslin Diabetes Center, Department of Medicine, Brigham and Women's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, 02215, MA, USA
| | - Branko Zevnik
- CECAD in vivo Research Facility, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Simon E Tröder
- CECAD in vivo Research Facility, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Uwe Knippschild
- Department of General and Visceral Surgery, University Hospital Ulm, Albert-Einstein Allee 93, 89081, Ulm, Germany
| | - Peter A Edwards
- Department of Biological Chemistry, University of California, Los Angeles (UCLA), 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.,Department of Medicine, Division of Cardiology, UCLA, 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
| | | | - Masayuki Yamamoto
- Department of Medical Biochemistry, Tohoku Medical Megabank Organization, Sendai, 980-8573, Japan
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Eduardo Fernandez-Rebollo
- Functional Genomics and Metabolism Unit, Department for Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Thomas Q de Aguiar Vallim
- Department of Biological Chemistry, University of California, Los Angeles (UCLA), 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA. .,Department of Medicine, Division of Cardiology, UCLA, 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.
| | - Jan-Wilhelm Kornfeld
- Functional Genomics and Metabolism Unit, Department for Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark. .,Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931, Cologne, Germany. .,Cologne Cluster of Excellence-Cellular Stress Responses in Ageing-associated Diseases (CECAD), Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany.
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45
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Hezroni H, Perry RBT, Ulitsky I. Long Noncoding RNAs in Development and Regeneration of the Neural Lineage. Cold Spring Harb Symp Quant Biol 2020; 84:165-177. [PMID: 31900326 DOI: 10.1101/sqb.2019.84.039347] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) are gathering increasing attention toward their roles in different biological systems. In mammals, the richest repertoires of lncRNAs are expressed in the brain and in the testis, and the diversity of lncRNAs in the nervous system is thought to be related to the diversity and the complexity of its cell types. Supporting this notion, many lncRNAs are differentially expressed between different regions of the brain or in particular cell types, and many lncRNAs are dynamically expressed during embryonic or postnatal neurogenesis. Less is known about the functions of these genes, if any, but they are increasingly implicated in diverse processes in health and disease. Here, we review the current knowledge about the roles and importance of lncRNAs in the central and peripheral nervous systems and discuss the specific niches within gene regulatory networks that might be preferentially occupied by lncRNAs.
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Affiliation(s)
- Hadas Hezroni
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Ben Tov Perry
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
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46
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47
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Rom A, Melamed L, Gil N, Goldrich MJ, Kadir R, Golan M, Biton I, Perry RBT, Ulitsky I. Regulation of CHD2 expression by the Chaserr long noncoding RNA gene is essential for viability. Nat Commun 2019; 10:5092. [PMID: 31704914 PMCID: PMC6841665 DOI: 10.1038/s41467-019-13075-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022] Open
Abstract
Chromodomain helicase DNA binding protein 2 (Chd2) is a chromatin remodeller implicated in neurological disease. Here we show that Chaserr, a highly conserved long noncoding RNA transcribed from a region near the transcription start site of Chd2 and on the same strand, acts in concert with the CHD2 protein to maintain proper Chd2 expression levels. Loss of Chaserr in mice leads to early postnatal lethality in homozygous mice, and severe growth retardation in heterozygotes. Mechanistically, loss of Chaserr leads to substantially increased Chd2 mRNA and protein levels, which in turn lead to transcriptional interference by inhibiting promoters found downstream of highly expressed genes. We further show that Chaserr production represses Chd2 expression solely in cis, and that the phenotypic consequences of Chaserr loss are rescued when Chd2 is perturbed as well. Targeting Chaserr is thus a potential strategy for increasing CHD2 levels in haploinsufficient individuals.
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Affiliation(s)
- Aviv Rom
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Liliya Melamed
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Gil
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | | | - Rotem Kadir
- National Institute for Biotechnology in the Negev and Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Matan Golan
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Inbal Biton
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Ben-Tov Perry
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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48
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Ciolli Mattioli C, Rom A, Franke V, Imami K, Arrey G, Terne M, Woehler A, Akalin A, Ulitsky I, Chekulaeva M. Alternative 3' UTRs direct localization of functionally diverse protein isoforms in neuronal compartments. Nucleic Acids Res 2019; 47:2560-2573. [PMID: 30590745 PMCID: PMC6411841 DOI: 10.1093/nar/gky1270] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/27/2018] [Accepted: 12/13/2018] [Indexed: 01/01/2023] Open
Abstract
The proper subcellular localization of RNAs and local translational regulation is crucial in highly compartmentalized cells, such as neurons. RNA localization is mediated by specific cis-regulatory elements usually found in mRNA 3′UTRs. Therefore, processes that generate alternative 3′UTRs—alternative splicing and polyadenylation—have the potential to diversify mRNA localization patterns in neurons. Here, we performed mapping of alternative 3′UTRs in neurites and soma isolated from mESC-derived neurons. Our analysis identified 593 genes with differentially localized 3′UTR isoforms. In particular, we have shown that two isoforms of Cdc42 gene with distinct functions in neuronal polarity are differentially localized between neurites and soma of mESC-derived and mouse primary cortical neurons, at both mRNA and protein level. Using reporter assays and 3′UTR swapping experiments, we have identified the role of alternative 3′UTRs and mRNA transport in differential localization of alternative CDC42 protein isoforms. Moreover, we used SILAC to identify isoform-specific Cdc42 3′UTR-bound proteome with potential role in Cdc42 localization and translation. Our analysis points to usage of alternative 3′UTR isoforms as a novel mechanism to provide for differential localization of functionally diverse alternative protein isoforms.
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Affiliation(s)
- Camilla Ciolli Mattioli
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Aviv Rom
- Weizmann Institute of Science, Rehovot, Israel
| | - Vedran Franke
- BIMSB Bioinformatics platform, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Koshi Imami
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Gerard Arrey
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Mandy Terne
- Developmental Biology / Signal Transduction, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Andrew Woehler
- BIMSB Light Microscopy platform, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Altuna Akalin
- BIMSB Bioinformatics platform, Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | | | - Marina Chekulaeva
- Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
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49
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Monteiro JP, Bennett M, Rodor J, Caudrillier A, Ulitsky I, Baker AH. Endothelial function and dysfunction in the cardiovascular system: the long non-coding road. Cardiovasc Res 2019; 115:1692-1704. [PMID: 31214683 PMCID: PMC6755355 DOI: 10.1093/cvr/cvz154] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/23/2019] [Accepted: 06/05/2019] [Indexed: 12/18/2022] Open
Abstract
Present throughout the vasculature, endothelial cells (ECs) are essential for blood vessel function and play a central role in the pathogenesis of diverse cardiovascular diseases. Understanding the intricate molecular determinants governing endothelial function and dysfunction is essential to develop novel clinical breakthroughs and improve knowledge. An increasing body of evidence demonstrates that long non-coding RNAs (lncRNAs) are active regulators of the endothelial transcriptome and function, providing emerging insights into core questions surrounding EC contributions to pathology, and perhaps the emergence of novel therapeutic opportunities. In this review, we discuss this class of non-coding transcripts and their role in endothelial biology during cardiovascular development, homeostasis, and disease, highlighting challenges during discovery and characterization and how these have been overcome to date. We further discuss the translational therapeutic implications and the challenges within the field, highlighting lncRNA that support endothelial phenotypes prevalent in cardiovascular disease.
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Affiliation(s)
- João P Monteiro
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Matthew Bennett
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Julie Rodor
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Axelle Caudrillier
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Andrew H Baker
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK
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50
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Mahmoud AD, Ballantyne MD, Miscianinov V, Pinel K, Hung J, Scanlon JP, Iyinikkel J, Kaczynski J, Tavares AS, Bradshaw AC, Mills NL, Newby DE, Caporali A, Gould GW, George SJ, Ulitsky I, Sluimer JC, Rodor J, Baker AH. The Human-Specific and Smooth Muscle Cell-Enriched LncRNA SMILR Promotes Proliferation by Regulating Mitotic CENPF mRNA and Drives Cell-Cycle Progression Which Can Be Targeted to Limit Vascular Remodeling. Circ Res 2019; 125:535-551. [PMID: 31339449 PMCID: PMC6693924 DOI: 10.1161/circresaha.119.314876] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 07/05/2019] [Accepted: 07/19/2019] [Indexed: 12/20/2022]
Abstract
RATIONALE In response to blood vessel wall injury, aberrant proliferation of vascular smooth muscle cells (SMCs) causes pathological remodeling. However, the controlling mechanisms are not completely understood. OBJECTIVE We recently showed that the human long noncoding RNA, SMILR, promotes vascular SMCs proliferation by a hitherto unknown mechanism. Here, we assess the therapeutic potential of SMILR inhibition and detail the molecular mechanism of action. METHODS AND RESULTS We used deep RNA-sequencing of human saphenous vein SMCs stimulated with IL (interleukin)-1α and PDGF (platelet-derived growth factor)-BB with SMILR knockdown (siRNA) or overexpression (lentivirus), to identify SMILR-regulated genes. This revealed a SMILR-dependent network essential for cell cycle progression. In particular, we found using the fluorescent ubiquitination-based cell cycle indicator viral system that SMILR regulates the late mitotic phase of the cell cycle and cytokinesis with SMILR knockdown resulting in ≈10% increase in binucleated cells. SMILR pulldowns further revealed its potential molecular mechanism, which involves an interaction with the mRNA of the late mitotic protein CENPF (centromere protein F) and the regulatory Staufen1 RNA-binding protein. SMILR and this downstream axis were also found to be activated in the human ex vivo vein graft pathological model and in primary human coronary artery SMCs and atherosclerotic plaques obtained at carotid endarterectomy. Finally, to assess the therapeutic potential of SMILR, we used a novel siRNA approach in the ex vivo vein graft model (within the 30 minutes clinical time frame that would occur between harvest and implant) to assess the reduction of proliferation by EdU incorporation. SMILR knockdown led to a marked decrease in proliferation from ≈29% in controls to ≈5% with SMILR depletion. CONCLUSIONS Collectively, we demonstrate that SMILR is a critical mediator of vascular SMC proliferation via direct regulation of mitotic progression. Our data further reveal a potential SMILR-targeting intervention to limit atherogenesis and adverse vascular remodeling.
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MESH Headings
- Cell Cycle/physiology
- Cell Proliferation/physiology
- Cells, Cultured
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Humans
- Microfilament Proteins/genetics
- Microfilament Proteins/metabolism
- Mitosis/physiology
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/metabolism
- Myocytes, Smooth Muscle/metabolism
- Organ Culture Techniques
- RNA, Long Noncoding/biosynthesis
- RNA, Long Noncoding/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Saphenous Vein/cytology
- Saphenous Vein/metabolism
- Vascular Remodeling/physiology
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Affiliation(s)
- Amira D. Mahmoud
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Margaret D. Ballantyne
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Vladislav Miscianinov
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Karine Pinel
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - John Hung
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Jessica P. Scanlon
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Jean Iyinikkel
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Jakub Kaczynski
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Adriana S. Tavares
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Angela C. Bradshaw
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, United Kingdom (A.C.B.)
| | - Nicholas L. Mills
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - David E. Newby
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Andrea Caporali
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Gwyn W. Gould
- Institute of Molecular Cell and Systems Biology, College of Medicine, Veterinary and Life Sciences, University of Glasgow, United Kingdom (G.W.G.)
| | - Sarah J. George
- School of Clinical Sciences, University of Bristol, Research Floor Level Seven, Bristol Royal Infirmary, United Kingdom (S.J.G.)
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel (I.U.)
| | - Judith C. Sluimer
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
- Department of Pathology, Maastricht University Medical Center, the Netherlands (J.C.S., A.H.B.)
| | - Julie Rodor
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Andrew H. Baker
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
- Department of Pathology, Maastricht University Medical Center, the Netherlands (J.C.S., A.H.B.)
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