1
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Lorenzo JP, Molla L, Amro EM, Ibarra IL, Ruf S, Neber C, Gkougkousis C, Ridani J, Subramani PG, Boulais J, Harjanto D, Vonica A, Di Noia JM, Dieterich C, Zaugg JB, Papavasiliou FN. APOBEC2 safeguards skeletal muscle cell fate through binding chromatin and regulating transcription of non-muscle genes during myoblast differentiation. Proc Natl Acad Sci U S A 2024; 121:e2312330121. [PMID: 38625936 PMCID: PMC11047093 DOI: 10.1073/pnas.2312330121] [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: 07/25/2023] [Accepted: 03/07/2024] [Indexed: 04/18/2024] Open
Abstract
The apolipoprotein B messenger RNA editing enzyme, catalytic polypeptide (APOBEC) family is composed of nucleic acid editors with roles ranging from antibody diversification to RNA editing. APOBEC2, a member of this family with an evolutionarily conserved nucleic acid-binding cytidine deaminase domain, has neither an established substrate nor function. Using a cellular model of muscle differentiation where APOBEC2 is inducibly expressed, we confirmed that APOBEC2 does not have the attributed molecular functions of the APOBEC family, such as RNA editing, DNA demethylation, and DNA mutation. Instead, we found that during muscle differentiation APOBEC2 occupied a specific motif within promoter regions; its removal from those regions resulted in transcriptional changes. Mechanistically, these changes reflect the direct interaction of APOBEC2 with histone deacetylase (HDAC) transcriptional corepressor complexes. We also found that APOBEC2 could bind DNA directly, in a sequence-specific fashion, suggesting that it functions as a recruiter of HDAC to specific genes whose promoters it occupies. These genes are normally suppressed during muscle cell differentiation, and their suppression may contribute to the safeguarding of muscle cell fate. Altogether, our results reveal a unique role for APOBEC2 within the APOBEC family.
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Affiliation(s)
- J. Paulo Lorenzo
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg69120, Germany
| | - Linda Molla
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY10065
| | - Elias Moris Amro
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
| | - Ignacio L. Ibarra
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg69117, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg85764, Germany
| | - Sandra Ruf
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
| | - Cedrik Neber
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
| | - Christos Gkougkousis
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
| | - Jana Ridani
- Institut de Recherches Cliniques de Montréal, Montréal, QCH2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QCH4A 3J1, Canada
| | - Poorani Ganesh Subramani
- Institut de Recherches Cliniques de Montréal, Montréal, QCH2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QCH4A 3J1, Canada
| | - Jonathan Boulais
- Institut de Recherches Cliniques de Montréal, Montréal, QCH2W 1R7, Canada
| | - Dewi Harjanto
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY10065
| | - Alin Vonica
- Department of Biology, Nazareth University, Rochester, NY14618
| | - Javier M. Di Noia
- Institut de Recherches Cliniques de Montréal, Montréal, QCH2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QCH4A 3J1, Canada
- Department of Medicine, Université de Montréal, Montréal, QCH3C 3J7, Canada
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg69120, Germany
- German Center for Cardiovascular Research (DZHK) - Partner site Heidelberg/Mannheim, Heidelberg69120, Germany
| | - Judith B. Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg69117, Germany
| | - F. Nina Papavasiliou
- Division of Immune Diversity, German Cancer Research Center, Heidelberg69120, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg69120, Germany
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY10065
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2
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Mathioudaki A, Wang X, Sedloev D, Huth R, Kamal A, Hundemer M, Liu Y, Vasileiou S, Lulla P, Müller-Tidow C, Dreger P, Luft T, Sauer T, Schmitt M, Zaugg JB, Pabst C. The remission status of AML patients after allo-HCT is associated with a distinct single-cell bone marrow T-cell signature. Blood 2024; 143:1269-1281. [PMID: 38197505 PMCID: PMC10997908 DOI: 10.1182/blood.2023021815] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/14/2023] [Accepted: 11/28/2023] [Indexed: 01/11/2024] Open
Abstract
ABSTRACT Acute myeloid leukemia (AML) is a hematologic malignancy for which allogeneic hematopoietic cell transplantation (allo-HCT) often remains the only curative therapeutic approach. However, incapability of T cells to recognize and eliminate residual leukemia stem cells might lead to an insufficient graft-versus-leukemia (GVL) effect and relapse. Here, we performed single-cell RNA-sequencing (scRNA-seq) on bone marrow (BM) T lymphocytes and CD34+ cells of 6 patients with AML 100 days after allo-HCT to identify T-cell signatures associated with either imminent relapse (REL) or durable complete remission (CR). We observed a higher frequency of cytotoxic CD8+ effector and gamma delta (γδ) T cells in CR vs REL samples. Pseudotime and gene regulatory network analyses revealed that CR CD8+ T cells were more advanced in maturation and had a stronger cytotoxicity signature, whereas REL samples were characterized by inflammatory tumor necrosis factor/NF-κB signaling and an immunosuppressive milieu. We identified ADGRG1/GPR56 as a surface marker enriched in CR CD8+ T cells and confirmed in a CD33-directed chimeric antigen receptor T cell/AML coculture model that GPR56 becomes upregulated on T cells upon antigen encounter and elimination of AML cells. We show that GPR56 continuously increases at the protein level on CD8+ T cells after allo-HCT and confirm faster interferon gamma (IFN-γ) secretion upon re-exposure to matched, but not unmatched, recipient AML cells in the GPR56+ vs GPR56- CD8+ T-cell fraction. Together, our data provide a single-cell reference map of BM-derived T cells after allo-HCT and propose GPR56 expression dynamics as a surrogate for antigen encounter after allo-HCT.
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Affiliation(s)
- Anna Mathioudaki
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Xizhe Wang
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - David Sedloev
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Richard Huth
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Aryan Kamal
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Hundemer
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Yi Liu
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Spyridoula Vasileiou
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital-Texas Children's Hospital, Houston, TX
| | - Premal Lulla
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital-Texas Children's Hospital, Houston, TX
| | - Carsten Müller-Tidow
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Peter Dreger
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Luft
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Tim Sauer
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Schmitt
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Judith B. Zaugg
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Caroline Pabst
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
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3
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Hauth A, Panten J, Kneuss E, Picard C, Servant N, Rall I, Pérez-Rico YA, Clerquin L, Servaas N, Villacorta L, Jung F, Luong C, Chang HY, Zaugg JB, Stegle O, Odom DT, Loda A, Heard E. Escape from X inactivation is directly modulated by levels of Xist non-coding RNA. bioRxiv 2024:2024.02.22.581559. [PMID: 38559194 PMCID: PMC10979913 DOI: 10.1101/2024.02.22.581559] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
In placental females, one copy of the two X chromosomes is largely silenced during a narrow developmental time window, in a process mediated by the non-coding RNA Xist1. Here, we demonstrate that Xist can initiate X-chromosome inactivation (XCI) well beyond early embryogenesis. By modifying its endogenous level, we show that Xist has the capacity to actively silence genes that escape XCI both in neuronal progenitor cells (NPCs) and in vivo, in mouse embryos. We also show that Xist plays a direct role in eliminating TAD-like structures associated with clusters of escapee genes on the inactive X chromosome, and that this is dependent on Xist's XCI initiation partner, SPEN2. We further demonstrate that Xist's function in suppressing gene expression of escapees and topological domain formation is reversible for up to seven days post-induction, but that sustained Xist up-regulation leads to progressively irreversible silencing and CpG island DNA methylation of facultative escapees. Thus, the distinctive transcriptional and regulatory topologies of the silenced X chromosome is actively, directly - and reversibly - controlled by Xist RNA throughout life.
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Affiliation(s)
- Antonia Hauth
- European Molecular Biology Laboratory, Directors' Research, 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Germany
| | - Jasper Panten
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany
| | - Emma Kneuss
- European Molecular Biology Laboratory, Directors' Research, 69117 Heidelberg, Germany
| | - Christel Picard
- European Molecular Biology Laboratory, Directors' Research, 69117 Heidelberg, Germany
- Present address: Institute of Molecular Genetics of Montpellier University of Montpellier, CNRS, 34090 Montpellier, France
| | - Nicolas Servant
- Bioinformatics and Computational Systems Biology of Cancer, INSERM U900, Paris 75005, France
| | - Isabell Rall
- European Molecular Biology Laboratory, Directors' Research, 69117 Heidelberg, Germany
- Present address: Institute of Human Biology (IHB), Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Yuvia A Pérez-Rico
- European Molecular Biology Laboratory, Directors' Research, 69117 Heidelberg, Germany
| | - Lena Clerquin
- European Molecular Biology Laboratory, Directors' Research, 69117 Heidelberg, Germany
| | - Nila Servaas
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Laura Villacorta
- European Molecular Biology Laboratory, Genomics Core Facility, 69117 Heidelberg, Germany
| | - Ferris Jung
- European Molecular Biology Laboratory, Genomics Core Facility, 69117 Heidelberg, Germany
| | - Christy Luong
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Judith B Zaugg
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, EMBL-University of Heidelberg, Heidelberg, Germany
| | - Oliver Stegle
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - Duncan T Odom
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Agnese Loda
- European Molecular Biology Laboratory, Directors' Research, 69117 Heidelberg, Germany
| | - Edith Heard
- European Molecular Biology Laboratory, Directors' Research, 69117 Heidelberg, Germany
- Collège de France, Paris 75005, France
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4
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Kamal A, Arnold C, Claringbould A, Moussa R, Servaas NH, Kholmatov M, Daga N, Nogina D, Mueller‐Dott S, Reyes‐Palomares A, Palla G, Sigalova O, Bunina D, Pabst C, Zaugg JB. GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks. Mol Syst Biol 2023; 19:e11627. [PMID: 37073532 PMCID: PMC10258561 DOI: 10.15252/msb.202311627] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 02/27/2023] [Revised: 04/01/2023] [Accepted: 04/03/2023] [Indexed: 04/20/2023] Open
Abstract
Enhancers play a vital role in gene regulation and are critical in mediating the impact of noncoding genetic variants associated with complex traits. Enhancer activity is a cell-type-specific process regulated by transcription factors (TFs), epigenetic mechanisms and genetic variants. Despite the strong mechanistic link between TFs and enhancers, we currently lack a framework for jointly analysing them in cell-type-specific gene regulatory networks (GRN). Equally important, we lack an unbiased way of assessing the biological significance of inferred GRNs since no complete ground truth exists. To address these gaps, we present GRaNIE (Gene Regulatory Network Inference including Enhancers) and GRaNPA (Gene Regulatory Network Performance Analysis). GRaNIE (https://git.embl.de/grp-zaugg/GRaNIE) builds enhancer-mediated GRNs based on covariation of chromatin accessibility and RNA-seq across samples (e.g. individuals), while GRaNPA (https://git.embl.de/grp-zaugg/GRaNPA) assesses the performance of GRNs for predicting cell-type-specific differential expression. We demonstrate their power by investigating gene regulatory mechanisms underlying the response of macrophages to infection, cancer and common genetic traits including autoimmune diseases. Finally, our methods identify the TF PURA as a putative regulator of pro-inflammatory macrophage polarisation.
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Affiliation(s)
- Aryan Kamal
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
- Faculty of BiosciencesCollaboration for Joint PhD Degree between EMBL and Heidelberg UniversityHeidelbergGermany
| | - Christian Arnold
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Annique Claringbould
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Rim Moussa
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Nila H Servaas
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Maksim Kholmatov
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Neha Daga
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Daria Nogina
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Sophia Mueller‐Dott
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Armando Reyes‐Palomares
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
- Present address:
Department of Biochemistry and Molecular BiologyComplutense University of MadridMadridSpain
| | - Giovanni Palla
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
- Present address:
Institute of Computational BiologyHelmholtz Center MunichOberschleißheimGermany
| | - Olga Sigalova
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
- Faculty of BiosciencesCollaboration for Joint PhD Degree between EMBL and Heidelberg UniversityHeidelbergGermany
| | - Daria Bunina
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
| | - Caroline Pabst
- Department of Medicine V, Hematology, Oncology and RheumatologyUniversity Hospital HeidelbergHeidelbergGermany
- Molecular Medicine Partnership UnitUniversity of HeidelbergHeidelbergGermany
| | - Judith B Zaugg
- European Molecular Biology Laboratory, Structural and Computational Biology UnitHeidelbergGermany
- Molecular Medicine Partnership UnitUniversity of HeidelbergHeidelbergGermany
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5
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Weigel B, Tegethoff JF, Grieder SD, Lim B, Nagarajan B, Liu YC, Truberg J, Papageorgiou D, Adrian-Segarra JM, Schmidt LK, Kaspar J, Poisel E, Heinzelmann E, Saraswat M, Christ M, Arnold C, Ibarra IL, Campos J, Krijgsveld J, Monyer H, Zaugg JB, Acuna C, Mall M. MYT1L haploinsufficiency in human neurons and mice causes autism-associated phenotypes that can be reversed by genetic and pharmacologic intervention. Mol Psychiatry 2023; 28:2122-2135. [PMID: 36782060 PMCID: PMC10575775 DOI: 10.1038/s41380-023-01959-7] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 12/30/2022] [Accepted: 01/11/2023] [Indexed: 02/15/2023]
Abstract
MYT1L is an autism spectrum disorder (ASD)-associated transcription factor that is expressed in virtually all neurons throughout life. How MYT1L mutations cause neurological phenotypes and whether they can be targeted remains enigmatic. Here, we examine the effects of MYT1L deficiency in human neurons and mice. Mutant mice exhibit neurodevelopmental delays with thinner cortices, behavioural phenotypes, and gene expression changes that resemble those of ASD patients. MYT1L target genes, including WNT and NOTCH, are activated upon MYT1L depletion and their chemical inhibition can rescue delayed neurogenesis in vitro. MYT1L deficiency also causes upregulation of the main cardiac sodium channel, SCN5A, and neuronal hyperactivity, which could be restored by shRNA-mediated knockdown of SCN5A or MYT1L overexpression in postmitotic neurons. Acute application of the sodium channel blocker, lamotrigine, also rescued electrophysiological defects in vitro and behaviour phenotypes in vivo. Hence, MYT1L mutation causes both developmental and postmitotic neurological defects. However, acute intervention can normalise resulting electrophysiological and behavioural phenotypes in adulthood.
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Affiliation(s)
- Bettina Weigel
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Jana F Tegethoff
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Sarah D Grieder
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Bryce Lim
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Bhuvaneswari Nagarajan
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Yu-Chao Liu
- Department of Clinical Neurobiology, University Hospital Heidelberg and DKFZ, Heidelberg, Germany
| | - Jule Truberg
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Dimitris Papageorgiou
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Medical Faculty, Heidelberg University, 69120, Heidelberg, Germany
| | - Juan M Adrian-Segarra
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Laura K Schmidt
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Janina Kaspar
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Eric Poisel
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Elisa Heinzelmann
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Manu Saraswat
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Marleen Christ
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Christian Arnold
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69115, Heidelberg, Germany
| | - Ignacio L Ibarra
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69115, Heidelberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Joaquin Campos
- Chica and Heinz Schaller Research Group, Institute for Anatomy and Cell Biology, Heidelberg University, 69120, Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Medical Faculty, Heidelberg University, 69120, Heidelberg, Germany
| | - Hannah Monyer
- Department of Clinical Neurobiology, University Hospital Heidelberg and DKFZ, Heidelberg, Germany
| | - Judith B Zaugg
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69115, Heidelberg, Germany
| | - Claudio Acuna
- Chica and Heinz Schaller Research Group, Institute for Anatomy and Cell Biology, Heidelberg University, 69120, Heidelberg, Germany
| | - Moritz Mall
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany.
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany.
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany.
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6
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de Teresa-Trueba I, Goetz SK, Mattausch A, Stojanovska F, Zimmerli CE, Toro-Nahuelpan M, Cheng DWC, Tollervey F, Pape C, Beck M, Diz-Muñoz A, Kreshuk A, Mahamid J, Zaugg JB. Convolutional networks for supervised mining of molecular patterns within cellular context. Nat Methods 2023; 20:284-294. [PMID: 36690741 PMCID: PMC9911354 DOI: 10.1038/s41592-022-01746-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [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: 04/12/2022] [Accepted: 12/02/2022] [Indexed: 01/24/2023]
Abstract
Cryo-electron tomograms capture a wealth of structural information on the molecular constituents of cells and tissues. We present DeePiCt (deep picker in context), an open-source deep-learning framework for supervised segmentation and macromolecular complex localization in cryo-electron tomography. To train and benchmark DeePiCt on experimental data, we comprehensively annotated 20 tomograms of Schizosaccharomyces pombe for ribosomes, fatty acid synthases, membranes, nuclear pore complexes, organelles, and cytosol. By comparing DeePiCt to state-of-the-art approaches on this dataset, we show its unique ability to identify low-abundance and low-density complexes. We use DeePiCt to study compositionally distinct subpopulations of cellular ribosomes, with emphasis on their contextual association with mitochondria and the endoplasmic reticulum. Finally, applying pre-trained networks to a HeLa cell tomogram demonstrates that DeePiCt achieves high-quality predictions in unseen datasets from different biological species in a matter of minutes. The comprehensively annotated experimental data and pre-trained networks are provided for immediate use by the community.
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Affiliation(s)
- Irene de Teresa-Trueba
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,Present Address: Computer Science and Artificial Intelligence Lab, ENGIE Lab Crigen, Stains, France
| | - Sara K. Goetz
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Alexander Mattausch
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Frosina Stojanovska
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Christian E. Zimmerli
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.419494.50000 0001 1018 9466Present Address: Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Mauricio Toro-Nahuelpan
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,Present Address: Santiago GmbH & Co. KG, Willich, Germany
| | - Dorothy W. C. Cheng
- grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Fergus Tollervey
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Constantin Pape
- grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7450.60000 0001 2364 4210Present Address: Institute for Computer Science, Universität Göttingen, Göttingen, Germany
| | - Martin Beck
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.419494.50000 0001 1018 9466Present Address: Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Alba Diz-Muñoz
- grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anna Kreshuk
- grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Judith B. Zaugg
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XGenome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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7
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Serina Secanechia YN, Bergiers I, Rogon M, Arnold C, Descostes N, Le S, López-Anguita N, Ganter K, Kapsali C, Bouilleau L, Gut A, Uzuotaite A, Aliyeva A, Zaugg JB, Lancrin C. Identifying a novel role for the master regulator Tal1 in the Endothelial to Hematopoietic Transition. Sci Rep 2022; 12:16974. [PMID: 36217016 PMCID: PMC9550822 DOI: 10.1038/s41598-022-20906-0] [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: 10/27/2021] [Accepted: 09/20/2022] [Indexed: 12/29/2022] Open
Abstract
Progress in the generation of Hematopoietic Stem and Progenitor Cells (HSPCs) in vitro and ex vivo has been built on the knowledge of developmental hematopoiesis, underscoring the importance of understanding this process. HSPCs emerge within the embryonic vasculature through an Endothelial-to-Hematopoietic Transition (EHT). The transcriptional regulator Tal1 exerts essential functions in the earliest stages of blood development, but is considered dispensable for the EHT. Nevertheless, Tal1 is expressed with its binding partner Lmo2 and it homologous Lyl1 in endothelial and transitioning cells at the time of EHT. Here, we investigated the function of these genes using a mouse embryonic-stem cell (mESC)-based differentiation system to model hematopoietic development. We showed for the first time that the expression of TAL1 in endothelial cells is crucial to ensure the efficiency of the EHT process and a sustained hematopoietic output. Our findings uncover an important function of Tal1 during the EHT, thus filling the current gap in the knowledge of the role of this master gene throughout the whole process of hematopoietic development.
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Affiliation(s)
- Yasmin Natalia Serina Secanechia
- grid.418924.20000 0004 0627 3632European Molecular Biology Laboratory, EMBL Rome - Epigenetics and Neurobiology Unit, via E. Ramarini 32, 00015 Monterotondo, Italy
| | - Isabelle Bergiers
- grid.418924.20000 0004 0627 3632European Molecular Biology Laboratory, EMBL Rome - Epigenetics and Neurobiology Unit, via E. Ramarini 32, 00015 Monterotondo, Italy ,grid.419619.20000 0004 0623 0341Present Address: Therapeutics Discovery, Pharmaceutical Companies of Johnson & Johnson, Janssen Research & Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Matt Rogon
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Centre for Biomolecular Network Analysis, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Christian Arnold
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Nicolas Descostes
- grid.418924.20000 0004 0627 3632European Molecular Biology Laboratory, EMBL Rome - Epigenetics and Neurobiology Unit, Bioinformatics Services, via E. Ramarini 32, 00015 Monterotondo, Italy
| | - Stephanie Le
- grid.418924.20000 0004 0627 3632European Molecular Biology Laboratory, EMBL Rome - Epigenetics and Neurobiology Unit, via E. Ramarini 32, 00015 Monterotondo, Italy
| | - Natalia López-Anguita
- grid.418924.20000 0004 0627 3632European Molecular Biology Laboratory, EMBL Rome - Epigenetics and Neurobiology Unit, via E. Ramarini 32, 00015 Monterotondo, Italy ,grid.419538.20000 0000 9071 0620Present Address: Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Kerstin Ganter
- grid.418924.20000 0004 0627 3632European Molecular Biology Laboratory, EMBL Rome - Epigenetics and Neurobiology Unit, via E. Ramarini 32, 00015 Monterotondo, Italy
| | - Chrysi Kapsali
- grid.418924.20000 0004 0627 3632European Molecular Biology Laboratory, EMBL Rome - Epigenetics and Neurobiology Unit, via E. Ramarini 32, 00015 Monterotondo, Italy
| | - Lea Bouilleau
- grid.418924.20000 0004 0627 3632European Molecular Biology Laboratory, EMBL Rome - Epigenetics and Neurobiology Unit, via E. Ramarini 32, 00015 Monterotondo, Italy
| | - Aaron Gut
- grid.418924.20000 0004 0627 3632European Molecular Biology Laboratory, EMBL Rome - Epigenetics and Neurobiology Unit, via E. Ramarini 32, 00015 Monterotondo, Italy
| | - Auguste Uzuotaite
- grid.418924.20000 0004 0627 3632European Molecular Biology Laboratory, EMBL Rome - Epigenetics and Neurobiology Unit, via E. Ramarini 32, 00015 Monterotondo, Italy
| | - Ayshan Aliyeva
- grid.418924.20000 0004 0627 3632European Molecular Biology Laboratory, EMBL Rome - Epigenetics and Neurobiology Unit, via E. Ramarini 32, 00015 Monterotondo, Italy
| | - Judith B. Zaugg
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Christophe Lancrin
- grid.418924.20000 0004 0627 3632European Molecular Biology Laboratory, EMBL Rome - Epigenetics and Neurobiology Unit, via E. Ramarini 32, 00015 Monterotondo, Italy
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8
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Kafkia E, Andres-Pons A, Ganter K, Seiler M, Smith TS, Andrejeva A, Jouhten P, Pereira F, Franco C, Kuroshchenkova A, Leone S, Sawarkar R, Boston R, Thaventhiran J, Zaugg JB, Lilley KS, Lancrin C, Beck M, Patil KR. Operation of a TCA cycle subnetwork in the mammalian nucleus. Sci Adv 2022; 8:eabq5206. [PMID: 36044572 PMCID: PMC9432838 DOI: 10.1126/sciadv.abq5206] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/14/2022] [Indexed: 05/23/2023]
Abstract
Nucleic acid and histone modifications critically depend on the tricarboxylic acid (TCA) cycle for substrates and cofactors. Although a few TCA cycle enzymes have been reported in the nucleus, the corresponding pathways are considered to operate in mitochondria. Here, we show that a part of the TCA cycle is operational also in the nucleus. Using 13C-tracer analysis, we identified activity of glutamine-to-fumarate, citrate-to-succinate, and glutamine-to-aspartate routes in the nuclei of HeLa cells. Proximity labeling mass spectrometry revealed a spatial vicinity of the involved enzymes with core nuclear proteins. We further show nuclear localization of aconitase 2 and 2-oxoglutarate dehydrogenase in mouse embryonic stem cells. Nuclear localization of the latter enzyme, which produces succinyl-CoA, changed from pluripotency to a differentiated state with accompanying changes in the nuclear protein succinylation. Together, our results demonstrate operation of an extended metabolic pathway in the nucleus, warranting a revision of the canonical view on metabolic compartmentalization.
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Affiliation(s)
- Eleni Kafkia
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Amparo Andres-Pons
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Kerstin Ganter
- European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Markus Seiler
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Tom S. Smith
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Anna Andrejeva
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Paula Jouhten
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- VTT Technical Research Center of Finland, Helsinki, Finland
| | - Filipa Pereira
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Catarina Franco
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Anna Kuroshchenkova
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Sergio Leone
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Ritwick Sawarkar
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Rebecca Boston
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - James Thaventhiran
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Judith B. Zaugg
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | | | - Martin Beck
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Kiran Raosaheb Patil
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
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9
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Bruch PM, Giles HA, Kolb C, Herbst SA, Becirovic T, Roider T, Lu J, Scheinost S, Wagner L, Huellein J, Berest I, Kriegsmann M, Kriegsmann K, Zgorzelski C, Dreger P, Zaugg JB, Müller-Tidow C, Zenz T, Huber W, Dietrich S. Drug-microenvironment perturbations reveal resistance mechanisms and prognostic subgroups in CLL. Mol Syst Biol 2022; 18:e10855. [PMID: 35959629 PMCID: PMC9372727 DOI: 10.15252/msb.202110855] [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: 12/06/2021] [Revised: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 11/25/2022] Open
Abstract
The tumour microenvironment and genetic alterations collectively influence drug efficacy in cancer, but current evidence is limited and systematic analyses are lacking. Using chronic lymphocytic leukaemia (CLL) as a model disease, we investigated the influence of 17 microenvironmental stimuli on 12 drugs in 192 genetically characterised patient samples. Based on microenvironmental response, we identified four subgroups with distinct clinical outcomes beyond known prognostic markers. Response to multiple microenvironmental stimuli was amplified in trisomy 12 samples. Trisomy 12 was associated with a distinct epigenetic signature. Bromodomain inhibition reversed this epigenetic profile and could be used to target microenvironmental signalling in trisomy 12 CLL. We quantified the impact of microenvironmental stimuli on drug response and their dependence on genetic alterations, identifying interleukin 4 (IL4) and Toll‐like receptor (TLR) stimulation as the strongest actuators of drug resistance. IL4 and TLR signalling activity was increased in CLL‐infiltrated lymph nodes compared with healthy samples. High IL4 activity correlated with faster disease progression. The publicly available dataset can facilitate the investigation of cell‐extrinsic mechanisms of drug resistance and disease progression.
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Affiliation(s)
- Peter-Martin Bruch
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Holly Ar Giles
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.,EMBL Heidelberg, Heidelberg, Germany.,Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Carolin Kolb
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Sophie A Herbst
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.,EMBL Heidelberg, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tina Becirovic
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Tobias Roider
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.,EMBL Heidelberg, Heidelberg, Germany
| | - Junyan Lu
- EMBL Heidelberg, Heidelberg, Germany
| | - Sebastian Scheinost
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumour Diseases, Heidelberg, Germany
| | - Lena Wagner
- German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumour Diseases, Heidelberg, Germany
| | | | | | - Mark Kriegsmann
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | | | | | - Peter Dreger
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Judith B Zaugg
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.,EMBL Heidelberg, Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany
| | - Thorsten Zenz
- Department of Hematology, University of Zürich, Zürich, Switzerland
| | - Wolfgang Huber
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.,EMBL Heidelberg, Heidelberg, Germany
| | - Sascha Dietrich
- Department of Medicine V, Heidelberg University Hospital, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.,EMBL Heidelberg, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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10
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Ibarra IL, Ratnu VS, Gordillo L, Hwang IY, Mariani L, Weinand K, Hammarén HM, Heck J, Bulyk ML, Savitski MM, Zaugg JB, Noh KM. Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements. Mol Syst Biol 2022; 18:e10473. [PMID: 35996956 PMCID: PMC9396287 DOI: 10.15252/msb.202110473] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 05/27/2021] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 12/30/2022] Open
Abstract
Neuronal stimulation induced by the brain-derived neurotrophic factor (BDNF) triggers gene expression, which is crucial for neuronal survival, differentiation, synaptic plasticity, memory formation, and neurocognitive health. However, its role in chromatin regulation is unclear. Here, using temporal profiling of chromatin accessibility and transcription in mouse primary cortical neurons upon either BDNF stimulation or depolarization (KCl), we identify features that define BDNF-specific chromatin-to-gene expression programs. Enhancer activation is an early event in the regulatory control of BDNF-treated neurons, where the bZIP motif-binding Fos protein pioneered chromatin opening and cooperated with co-regulatory transcription factors (Homeobox, EGRs, and CTCF) to induce transcription. Deleting cis-regulatory sequences affect BDNF-mediated Arc expression, a regulator of synaptic plasticity. BDNF-induced accessible regions are linked to preferential exon usage by neurodevelopmental disorder-related genes and the heritability of neuronal complex traits, which were validated in human iPSC-derived neurons. Thus, we provide a comprehensive view of BDNF-mediated genome regulatory features using comparative genomic approaches to dissect mammalian neuronal stimulation.
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Affiliation(s)
- Ignacio L Ibarra
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany.,Institute of Computational Biology, Helmholtz Center Munich, Oberschleißheim, Germany
| | - Vikram S Ratnu
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Lucia Gordillo
- Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - In-Young Hwang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Luca Mariani
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kathryn Weinand
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Henrik M Hammarén
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jennifer Heck
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Kyung-Min Noh
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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11
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He L, Arnold C, Thoma J, Rohde C, Kholmatov M, Garg S, Hsiao CC, Viol L, Zhang K, Sun R, Schmidt C, Janssen M, MacRae T, Huber K, Thiede C, Hébert J, Sauvageau G, Spratte J, Fluhr H, Aust G, Müller-Tidow C, Niehrs C, Pereira G, Hamann J, Tanaka M, Zaugg JB, Pabst C. CDK7/12/13 inhibition targets an oscillating leukemia stem cell network and synergizes with venetoclax in acute myeloid leukemia. EMBO Mol Med 2022; 14:e14990. [PMID: 35253392 PMCID: PMC8988201 DOI: 10.15252/emmm.202114990] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
The heterogeneous response of acute myeloid leukemia (AML) to current anti‐leukemic therapies is only partially explained by mutational heterogeneity. We previously identified GPR56 as a surface marker associated with poor outcome across genetic groups, which characterizes two leukemia stem cell (LSC)‐enriched compartments with different self‐renewal capacities. How these compartments self‐renew remained unclear. Here, we show that GPR56+ LSC compartments are promoted in a complex network involving epithelial‐to‐mesenchymal transition (EMT) regulators besides Rho, Wnt, and Hedgehog (Hh) signaling. Unexpectedly, Wnt pathway inhibition increased the more immature, slowly cycling GPR56+CD34+ fraction and Hh/EMT gene expression, while Wnt activation caused opposite effects. Our data suggest that the crucial role of GPR56 lies in its ability to co‐activate these opposing signals, thus ensuring the constant supply of both LSC subsets. We show that CDK7 inhibitors suppress both LSC‐enriched subsets in vivo and synergize with the Bcl‐2 inhibitor venetoclax. Our data establish reciprocal transition between LSC compartments as a novel concept underlying the poor outcome in GPR56high AML and propose combined CDK7 and Bcl‐2 inhibition as LSC‐directed therapy in this disease.
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Affiliation(s)
- Lixiazi He
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Christian Arnold
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Judith Thoma
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Christian Rohde
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Maksim Kholmatov
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Swati Garg
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Cheng-Chih Hsiao
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Linda Viol
- Centre for Organismal Studies (COS)/Centre for Cell and Molecular Biology (ZMBH), University of Heidelberg, Heidelberg, Germany.,German Cancer Research Centre (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Kaiqing Zhang
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Rui Sun
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Christina Schmidt
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Maike Janssen
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Tara MacRae
- Laboratory of Molecular Genetics of Stem Cells, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
| | - Karin Huber
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christian Thiede
- Department of Internal Medicine I, University Hospital of Dresden Carl Gustav Carus, Dresden, Germany
| | - Josée Hébert
- The Quebec Leukemia Cell Bank and Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montréal, Canada.,Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada.,Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
| | - Guy Sauvageau
- Laboratory of Molecular Genetics of Stem Cells, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada.,Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada.,Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
| | - Julia Spratte
- Department of Gynecology and Obstetrics, University Hospital Heidelberg, Heidelberg, Germany
| | - Herbert Fluhr
- Department of Gynecology and Obstetrics, University Hospital Heidelberg, Heidelberg, Germany
| | - Gabriela Aust
- Department of Surgery, Research Laboratories, Leipzig University, Leipzig, Germany
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Christof Niehrs
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany.,Institute of Molecular Biology (IMB), Mainz, Germany
| | - Gislene Pereira
- Centre for Organismal Studies (COS)/Centre for Cell and Molecular Biology (ZMBH), University of Heidelberg, Heidelberg, Germany.,German Cancer Research Centre (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Jörg Hamann
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Motomu Tanaka
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany.,Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto, Japan
| | - Judith B Zaugg
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Caroline Pabst
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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12
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Claringbould A, Zaugg JB. Enhancers in disease: molecular basis and emerging treatment strategies. Trends Mol Med 2021; 27:1060-1073. [PMID: 34420874 DOI: 10.1016/j.molmed.2021.07.012] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [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: 05/21/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
Enhancers are genomic sequences that play a key role in regulating tissue-specific gene expression levels. An increasing number of diseases are linked to impaired enhancer function through chromosomal rearrangement, genetic variation within enhancers, or epigenetic modulation. Here, we review how these enhancer disruptions have recently been implicated in congenital disorders, cancers, and common complex diseases and address the implications for diagnosis and treatment. Although further fundamental research into enhancer function, target genes, and context is required, enhancer-targeting drugs and gene editing approaches show great therapeutic promise for a range of diseases.
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Affiliation(s)
- Annique Claringbould
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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13
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Weidemüller P, Kholmatov M, Petsalaki E, Zaugg JB. Transcription factors: Bridge between cell signaling and gene regulation. Proteomics 2021; 21:e2000034. [PMID: 34314098 DOI: 10.1002/pmic.202000034] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/05/2021] [Accepted: 07/16/2021] [Indexed: 01/17/2023]
Abstract
Transcription factors (TFs) are key regulators of intrinsic cellular processes, such as differentiation and development, and of the cellular response to external perturbation through signaling pathways. In this review we focus on the role of TFs as a link between signaling pathways and gene regulation. Cell signaling tends to result in the modulation of a set of TFs that then lead to changes in the cell's transcriptional program. We highlight the molecular layers at which TF activity can be measured and the associated technical and conceptual challenges. These layers include post-translational modifications (PTMs) of the TF, regulation of TF binding to DNA through chromatin accessibility and epigenetics, and expression of target genes. We highlight that a large number of TFs are understudied in both signaling and gene regulation studies, and that our knowledge about known TF targets has a strong literature bias. We argue that TFs serve as a perfect bridge between the fields of gene regulation and signaling, and that separating these fields hinders our understanding of cell functions. Multi-omics approaches that measure multiple dimensions of TF activity are ideally suited to study the interplay of cell signaling and gene regulation using TFs as the anchor to link the two fields.
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Affiliation(s)
- Paula Weidemüller
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Maksim Kholmatov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg, 69117, Germany
| | - Evangelia Petsalaki
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg, 69117, Germany
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14
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Kim KP, Li C, Bunina D, Jeong HW, Ghelman J, Yoon J, Shin B, Park H, Han DW, Zaugg JB, Kim J, Kuhlmann T, Adams RH, Noh KM, Goldman SA, Schöler HR. Donor cell memory confers a metastable state of directly converted cells. Cell Stem Cell 2021; 28:1291-1306.e10. [PMID: 33848472 DOI: 10.1016/j.stem.2021.02.023] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/29/2021] [Accepted: 02/16/2021] [Indexed: 12/24/2022]
Abstract
Generation of induced oligodendrocyte progenitor cells (iOPCs) from somatic fibroblasts is a strategy for cell-based therapy of myelin diseases. However, iOPC generation is inefficient, and the resulting iOPCs exhibit limited expansion and differentiation competence. Here we overcome these limitations by transducing an optimized transcription factor combination into a permissive donor phenotype, the pericyte. Pericyte-derived iOPCs (PC-iOPCs) are stably expandable and functionally myelinogenic with high differentiation competence. Unexpectedly, however, we found that PC-iOPCs are metastable so that they can produce myelination-competent oligodendrocytes or revert to their original identity in a context-dependent fashion. Phenotypic reversion of PC-iOPCs is tightly linked to memory of their original transcriptome and epigenome. Phenotypic reversion can be disconnected from this donor cell memory effect, and in vivo myelination can eventually be achieved by transplantation of O4+ pre-oligodendrocytes. Our data show that donor cell source and memory can contribute to the fate and stability of directly converted cells.
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Affiliation(s)
- Kee-Pyo Kim
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany; Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul 06591, Republic of Korea
| | - Cui Li
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Daria Bunina
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hyun-Woo Jeong
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany
| | - Julia Ghelman
- Institute of Neuropathology, University Hospital Münster, Münster 48149, Germany
| | - Juyong Yoon
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany
| | - Borami Shin
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany
| | - Hongryeol Park
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany
| | - Dong Wook Han
- School of Biotechnology and Healthcare, Wuyi University, Jiangmen 529020, China
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Johnny Kim
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Tanja Kuhlmann
- Institute of Neuropathology, University Hospital Münster, Münster 48149, Germany
| | - Ralf H Adams
- Department of Tissue Morphogenesis, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany
| | - Kyung-Min Noh
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Steven A Goldman
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, USA; Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany; Faculty of Medicine, University of Münster, Münster 48149, Germany.
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15
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Ranzoni AM, Tangherloni A, Berest I, Riva SG, Myers B, Strzelecka PM, Xu J, Panada E, Mohorianu I, Zaugg JB, Cvejic A. Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis. Cell Stem Cell 2021; 28:472-487.e7. [PMID: 33352111 PMCID: PMC7939551 DOI: 10.1016/j.stem.2020.11.015] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/18/2020] [Accepted: 11/19/2020] [Indexed: 02/08/2023]
Abstract
Regulation of hematopoiesis during human development remains poorly defined. Here we applied single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) to over 8,000 human immunophenotypic blood cells from fetal liver and bone marrow. We inferred their differentiation trajectory and identified three highly proliferative oligopotent progenitor populations downstream of hematopoietic stem cells (HSCs)/multipotent progenitors (MPPs). Along this trajectory, we observed opposing patterns of chromatin accessibility and differentiation that coincided with dynamic changes in the activity of distinct lineage-specific transcription factors. Integrative analysis of chromatin accessibility and gene expression revealed extensive epigenetic but not transcriptional priming of HSCs/MPPs prior to their lineage commitment. Finally, we refined and functionally validated the sorting strategy for the HSCs/MPPs and achieved around 90% enrichment. Our study provides a useful framework for future investigation of human developmental hematopoiesis in the context of blood pathologies and regenerative medicine.
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Affiliation(s)
- Anna Maria Ranzoni
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Andrea Tangherloni
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Ivan Berest
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69115 Heidelberg, Germany
| | - Simone Giovanni Riva
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Brynelle Myers
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Paulina M Strzelecka
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Jiarui Xu
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Elisa Panada
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Irina Mohorianu
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK
| | - Judith B Zaugg
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69115 Heidelberg, Germany
| | - Ana Cvejic
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
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16
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Sigalova OM, Shaeiri A, Forneris M, Furlong EEM, Zaugg JB. Predictive features of gene expression variation reveal mechanistic link with differential expression. Mol Syst Biol 2020; 16:e9539. [PMID: 32767663 PMCID: PMC7411568 DOI: 10.15252/msb.20209539] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 02/25/2020] [Revised: 06/26/2020] [Accepted: 06/30/2020] [Indexed: 12/22/2022] Open
Abstract
For most biological processes, organisms must respond to extrinsic cues, while maintaining essential gene expression programmes. Although studied extensively in single cells, it is still unclear how variation is controlled in multicellular organisms. Here, we used a machine-learning approach to identify genomic features that are predictive of genes with high versus low variation in their expression across individuals, using bulk data to remove stochastic cell-to-cell variation. Using embryonic gene expression across 75 Drosophila isogenic lines, we identify features predictive of expression variation (controlling for expression level), many of which are promoter-related. Genes with low variation fall into two classes reflecting different mechanisms to maintain robust expression, while genes with high variation seem to lack both types of stabilizing mechanisms. Applying this framework to humans revealed similar predictive features, indicating that promoter architecture is an ancient mechanism to control expression variation. Remarkably, expression variation features could also partially predict differential expression after diverse perturbations in both Drosophila and humans. Differential gene expression signatures may therefore be partially explained by genetically encoded gene-specific features, unrelated to the studied treatment.
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Affiliation(s)
- Olga M Sigalova
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Amirreza Shaeiri
- Structures and Computational Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Mattia Forneris
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Eileen EM Furlong
- Genome Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Judith B Zaugg
- Structures and Computational Biology UnitEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
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17
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Grubert F, Srivas R, Spacek DV, Kasowski M, Ruiz-Velasco M, Sinnott-Armstrong N, Greenside P, Narasimha A, Liu Q, Geller B, Sanghi A, Kulik M, Sa S, Rabinovitch M, Kundaje A, Dalton S, Zaugg JB, Snyder M. Landscape of cohesin-mediated chromatin loops in the human genome. Nature 2020; 583:737-743. [PMID: 32728247 PMCID: PMC7410831 DOI: 10.1038/s41586-020-2151-x] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [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: 09/08/2017] [Accepted: 11/11/2019] [Indexed: 01/14/2023]
Abstract
Physical interactions between distal regulatory elements have a key role in regulating gene expression, but the extent to which these interactions vary between cell types and contribute to cell-type-specific gene expression remains unclear. Here, to address these questions as part of phase III of the Encyclopedia of DNA Elements (ENCODE), we mapped cohesin-mediated chromatin loops, using chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), and analysed gene expression in 24 diverse human cell types, including core ENCODE cell lines. Twenty-eight per cent of all chromatin loops vary across cell types; these variations modestly correlate with changes in gene expression and are effective at grouping cell types according to their tissue of origin. The connectivity of genes corresponds to different functional classes, with housekeeping genes having few contacts, and dosage-sensitive genes being more connected to enhancer elements. This atlas of chromatin loops complements the diverse maps of regulatory architecture that comprise the ENCODE Encyclopedia, and will help to support emerging analyses of genome structure and function.
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Affiliation(s)
- Fabian Grubert
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Rohith Srivas
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Damek V Spacek
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Maya Kasowski
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Mariana Ruiz-Velasco
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Peyton Greenside
- Biomedical Informatics Graduate Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Anil Narasimha
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Qing Liu
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Benjamin Geller
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Akshay Sanghi
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Michael Kulik
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Silin Sa
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Palo Alto, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Marlene Rabinovitch
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Palo Alto, CA, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Stephen Dalton
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Judith B Zaugg
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA, USA.
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18
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Bunina D, Abazova N, Diaz N, Noh KM, Krijgsveld J, Zaugg JB. Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons. Cell Syst 2020; 10:480-494.e8. [PMID: 32553182 PMCID: PMC7322528 DOI: 10.1016/j.cels.2020.05.003] [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] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 03/19/2020] [Accepted: 05/15/2020] [Indexed: 02/08/2023]
Abstract
Cellular differentiation requires dramatic changes in chromatin organization, transcriptional regulation, and protein production. To understand the regulatory connections between these processes, we generated proteomic, transcriptomic, and chromatin accessibility data during differentiation of mouse embryonic stem cells (ESCs) into postmitotic neurons and found extensive associations between different molecular layers within and across differentiation time points. We observed that SOX2, as a regulator of pluripotency and neuronal genes, redistributes from pluripotency enhancers to neuronal promoters during differentiation, likely driven by changes in its protein interaction network. We identified ATRX as a major SOX2 partner in neurons, whose co-localization correlated with an increase in active enhancer marks and increased expression of nearby genes, which we experimentally confirmed for three loci. Collectively, our data provide key insights into the regulatory transformation of SOX2 during neuronal differentiation, and we highlight the significance of multi-omic approaches in understanding gene regulation in complex systems. Complex interplay of RNA, protein, and chromatin during neuronal differentiation Multi-omic profiling reveals divergent roles of SOX2 in stem cells and neurons SOX2 on-chromatin interaction network changes from pluripotent to neuronal factors ATRX interacts with SOX2 in neurons and co-binds highly expressed neuronal genes
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Affiliation(s)
- Daria Bunina
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany; Genome Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany
| | - Nade Abazova
- Genome Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany; Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Collaboration for joint PhD degree between the European Molecular Biology Laboratory and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Nichole Diaz
- Genome Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany
| | - Kyung-Min Noh
- Genome Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany.
| | - Jeroen Krijgsveld
- Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Heidelberg University, Medical Faculty Heidelberg University, Faculty of Biosciences, Heidelberg, Germany.
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany.
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19
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Gehre M, Bunina D, Sidoli S, Lübke MJ, Diaz N, Trovato M, Garcia BA, Zaugg JB, Noh KM. Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy. Nat Genet 2020; 52:273-282. [PMID: 32139906 DOI: 10.1038/s41588-020-0586-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 01/29/2020] [Indexed: 12/26/2022]
Abstract
Mutations in enzymes that modify histone H3 at lysine 4 (H3K4) or lysine 36 (H3K36) have been linked to human disease, yet the role of these residues in mammals is unclear. We mutated K4 or K36 to alanine in the histone variant H3.3 and showed that the K4A mutation in mouse embryonic stem cells (ESCs) impaired differentiation and induced widespread gene expression changes. K4A resulted in substantial H3.3 depletion, especially at ESC promoters; it was accompanied by reduced remodeler binding and increased RNA polymerase II (Pol II) activity. Regulatory regions depleted of H3.3K4A showed histone modification alterations and changes in enhancer activity that correlated with gene expression. In contrast, the K36A mutation did not alter H3.3 deposition and affected gene expression at the later stages of differentiation. Thus, H3K4 is required for nucleosome deposition, histone turnover and chromatin remodeler binding at regulatory regions, where tight regulation of Pol II activity is necessary for proper ESC differentiation.
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Affiliation(s)
- Maja Gehre
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Collaboration for joint PhD degree between the European Molecular Biology Laboratory and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Daria Bunina
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Simone Sidoli
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Marlena J Lübke
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Nichole Diaz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Matteo Trovato
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Collaboration for joint PhD degree between the European Molecular Biology Laboratory and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Judith B Zaugg
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Kyung-Min Noh
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
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20
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Ibarra IL, Hollmann NM, Klaus B, Augsten S, Velten B, Hennig J, Zaugg JB. Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions. Nat Commun 2020; 11:124. [PMID: 31913281 PMCID: PMC6949242 DOI: 10.1038/s41467-019-13888-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [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: 05/16/2019] [Accepted: 11/28/2019] [Indexed: 11/25/2022] Open
Abstract
Recent high-throughput transcription factor (TF) binding assays revealed that TF cooperativity is a widespread phenomenon. However, a global mechanistic and functional understanding of TF cooperativity is still lacking. To address this, here we introduce a statistical learning framework that provides structural insight into TF cooperativity and its functional consequences based on next generation sequencing data. We identify DNA shape as driver for cooperativity, with a particularly strong effect for Forkhead-Ets pairs. Follow-up experiments reveal a local shape preference at the Ets-DNA-Forkhead interface and decreased cooperativity upon loss of the interaction. Additionally, we discover many functional associations for cooperatively bound TFs. Examination of the link between FOXO1:ETV6 and lymphomas reveals that their joint expression levels improve patient clinical outcome stratification. Altogether, our results demonstrate that inter-family cooperative TF binding is driven by position-specific DNA readout mechanisms, which provides an additional regulatory layer for downstream biological functions. Although transcription factor (TF) cooperativity is widespread, a global mechanistic understanding of the role of TF cooperativity is still lacking. Here the authors introduce a statistical learning framework that provides structural insight into TF cooperativity and its functional consequences based on next generation sequencing data and provide mechanistic insights into TF cooperativity and its impact on protein-phenotype interactions.
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Affiliation(s)
- Ignacio L Ibarra
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Nele M Hollmann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Bernd Klaus
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sandra Augsten
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Britta Velten
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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21
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Berest I, Arnold C, Reyes-Palomares A, Palla G, Rasmussen KD, Giles H, Bruch PM, Huber W, Dietrich S, Helin K, Zaugg JB. Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF. Cell Rep 2019; 29:3147-3159.e12. [DOI: 10.1016/j.celrep.2019.10.106] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 09/20/2019] [Accepted: 10/28/2019] [Indexed: 12/26/2022] Open
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22
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Rasmussen KD, Berest I, Keβler S, Nishimura K, Simón-Carrasco L, Vassiliou GS, Pedersen MT, Christensen J, Zaugg JB, Helin K. TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells. Genome Res 2019; 29:564-575. [PMID: 30796038 PMCID: PMC6442383 DOI: 10.1101/gr.239277.118] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [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: 05/07/2018] [Accepted: 02/19/2019] [Indexed: 12/17/2022]
Abstract
The epigenetic regulator TET2 is frequently mutated in hematological diseases. Mutations have been shown to arise in hematopoietic stem cells early in disease development and lead to altered DNA methylation landscapes and an increased risk of hematopoietic malignancy. Here, we show by genome-wide mapping of TET2 binding sites in different cell types that TET2 localizes to regions of open chromatin and cell-type-specific enhancers. We find that deletion of Tet2 in native hematopoiesis as well as fully transformed acute myeloid leukemia (AML) results in changes in transcription factor (TF) activity within these regions, and we provide evidence that loss of TET2 leads to attenuation of chromatin binding of members of the basic helix-loop-helix (bHLH) TF family. Together, these findings demonstrate that TET2 activity shapes the local chromatin environment at enhancers to facilitate TF binding and provides an example of how epigenetic dysregulation can affect gene expression patterns and drive disease development.
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Affiliation(s)
- Kasper D Rasmussen
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ivan Berest
- European Molecular Biology Institute, Structural and Computational Unit, 69115 Heidelberg, Germany
| | - Sandra Keβler
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Koutarou Nishimura
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Lucía Simón-Carrasco
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - George S Vassiliou
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB2 0XY, United Kingdom
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge CB2 0PT, United Kingdom
| | - Marianne T Pedersen
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jesper Christensen
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Judith B Zaugg
- European Molecular Biology Institute, Structural and Computational Unit, 69115 Heidelberg, Germany
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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23
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Ruiz-Velasco M, Kumar M, Lai MC, Bhat P, Solis-Pinson AB, Reyes A, Kleinsorg S, Noh KM, Gibson TJ, Zaugg JB. CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals. Cell Syst 2017; 5:628-637.e6. [DOI: 10.1016/j.cels.2017.10.018] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 08/02/2017] [Accepted: 10/27/2017] [Indexed: 12/20/2022]
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24
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Lai MC, Bechy AL, Denk F, Collins E, Gavriliouk M, Zaugg JB, Ryan BJ, Wade-Martins R, Caffrey TM. Haplotype-specific MAPT exon 3 expression regulated by common intronic polymorphisms associated with Parkinsonian disorders. Mol Neurodegener 2017; 12:79. [PMID: 29084565 PMCID: PMC5663040 DOI: 10.1186/s13024-017-0224-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 05/24/2017] [Accepted: 10/23/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome wide association studies have identified microtubule associated protein tau (MAPT) H1 haplotype single nucleotide polymorphisms (SNPs) as leading common risk variants for Parkinson's disease, progressive supranuclear palsy and corticobasal degeneration. The MAPT risk variants fall within a large 1.8 Mb region of high linkage disequilibrium, making it difficult to discern the functionally important risk variants. Here, we leverage the strong haplotype-specific expression of MAPT exon 3 to investigate the functionality of SNPs that fall within this H1 haplotype region of linkage disequilibrium. METHODS In this study, we dissect the molecular mechanisms by which haplotype-specific SNPs confer allele-specific effects on the alternative splicing of MAPT exon 3. Firstly, we use haplotype-hybrid whole-locus genomic MAPT vectors studies to identify functional SNPs. Next, we characterise the RNA-protein interactions at two loci by mass spectrometry. Lastly, we knockdown candidate splice factors to determine their effect on MAPT exon 3 using a novel allele-specific qPCR assay. RESULTS Using whole-locus genomic DNA expression vectors to express MAPT haplotype variants, we demonstrate that rs17651213 regulates exon 3 inclusion in a haplotype-specific manner. We further investigated the functionality of this region using RNA-electrophoretic mobility shift assays to show differential RNA-protein complex formation at the H1 and H2 sequence variants of SNP rs17651213 and rs1800547 and subsequently identified candidate trans-acting splicing factors interacting with these functional SNPs sequences by RNA-protein pull-down experiment and mass spectrometry. Finally, gene knockdown of candidate splice factors identified by mass spectrometry demonstrate a role for hnRNP F and hnRNP Q in the haplotype-specific regulation of exon 3 inclusion. CONCLUSIONS We identified common splice factors hnRNP F and hnRNP Q regulating the haplotype-specific splicing of MAPT exon 3 through intronic variants rs1800547 and rs17651213. This work demonstrates an integrated approach to characterise the functionality of risk variants in large regions of linkage disequilibrium.
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Affiliation(s)
- Mang Ching Lai
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX UK
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Anne-Laure Bechy
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX UK
| | - Franziska Denk
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX UK
| | - Emma Collins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX UK
| | - Maria Gavriliouk
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX UK
| | - Judith B. Zaugg
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Brent J. Ryan
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX UK
- Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, OX1 3QX UK
| | - Richard Wade-Martins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX UK
- Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, OX1 3QX UK
| | - Tara M. Caffrey
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX UK
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25
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26
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Cakiroglu SA, Zaugg JB, Luscombe NM. Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation. Nucleic Acids Res 2016; 44:8065-72. [PMID: 27492286 PMCID: PMC5041482 DOI: 10.1093/nar/gkw683] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 01/11/2016] [Revised: 07/20/2016] [Accepted: 07/24/2016] [Indexed: 01/04/2023] Open
Abstract
Backmasking is a recording technique used to hide a sound or message in a music track in reverse, meaning that it is only audible when the record is played backwards. Analogously, the compact yeast genome encodes for diverse sources of information such as overlapping coding and non-coding transcripts, and protein-binding sites on the two complementary DNA strands. Examples are the consensus binding site sequences of the RNA-binding proteins Nrd1 and Nab3 that target non-coding transcripts for degradation. Here, by examining the overlap of stable (SUTs, stable unannotated transcripts) and unstable (CUTs, cryptic unstable transcripts) transcripts with protein-coding genes, we show that the predicted Nrd1 and Nab3-binding site sequences occur at differing frequencies. They are always depleted in the sense direction of protein-coding genes, thus avoiding degradation of the transcript. However in the antisense direction, predicted binding sites occur at high frequencies in genes with overlapping unstable ncRNAs (CUTs), so limiting the availability of non-functional transcripts. In contrast they are depleted in genes with overlapping stable ncRNAs (SUTs), presumably to avoid degrading the non-coding transcript. The protein-coding genes maintain similar amino-acid contents, but they display distinct codon usages so that Nrd1 and Nab3-binding sites can arise at differing frequencies in antisense depending on the overlapping transcript type. Our study demonstrates how yeast has evolved to encode multiple layers of information-protein-coding genes in one strand and the relative chance of degrading antisense RNA in the other strand-in the same regions of a compact genome.
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Affiliation(s)
- S Aylin Cakiroglu
- The Francis Crick Institute, 44 Lincoln's Inn Fields Laboratory, London WC2A 3LY, UK
| | - Judith B Zaugg
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Nicholas M Luscombe
- The Francis Crick Institute, 44 Lincoln's Inn Fields Laboratory, London WC2A 3LY, UK UCL Genetics Institute, University College London, London WC1E 6BT, UK Okinawa Institute of Science & Technology Graduate University, Okinawa 904-0495, Japan
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27
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Arnold C, Bhat P, Zaugg JB. SNPhood: investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data. ACTA ACUST UNITED AC 2016; 32:2359-60. [PMID: 27153574 PMCID: PMC4965630 DOI: 10.1093/bioinformatics/btw127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 12/08/2015] [Accepted: 03/01/2016] [Indexed: 11/12/2022]
Abstract
MOTIVATION The vast majority of the many thousands of disease-associated single nucleotide polymorphisms (SNPs) lie in the non-coding part of the genome. They are likely to affect regulatory elements, such as enhancers and promoters, rather than the function of a protein. To understand the molecular mechanisms underlying genetic diseases, it is therefore increasingly important to study the effect of a SNP on nearby molecular traits such as chromatin or transcription factor binding. RESULTS We developed SNPhood, a user-friendly Bioconductor R package to investigate, quantify and visualise the local epigenetic neighbourhood of a set of SNPs in terms of chromatin marks or TF binding sites using data from NGS experiments. AVAILABILITY AND IMPLEMENTATION SNPhood is publicly available and maintained as an R Bioconductor package at http://bioconductor.org/packages/SNPhood/ CONTACT judith.zaugg@embl.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Christian Arnold
- European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany
| | - Pooja Bhat
- European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany
| | - Judith B Zaugg
- European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany
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28
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Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR, Greenside P, Srivas R, Phanstiel DH, Pekowska A, Heidari N, Euskirchen G, Huber W, Pritchard JK, Bustamante CD, Steinmetz LM, Kundaje A, Snyder M. Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. Cell 2015; 162:1051-65. [PMID: 26300125 PMCID: PMC4556133 DOI: 10.1016/j.cell.2015.07.048] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [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: 10/16/2014] [Revised: 03/05/2015] [Accepted: 07/21/2015] [Indexed: 01/12/2023]
Abstract
Deciphering the impact of genetic variants on gene regulation is fundamental to understanding human disease. Although gene regulation often involves long-range interactions, it is unknown to what extent non-coding genetic variants influence distal molecular phenotypes. Here, we integrate chromatin profiling for three histone marks in lymphoblastoid cell lines (LCLs) from 75 sequenced individuals with LCL-specific Hi-C and ChIA-PET-based chromatin contact maps to uncover one of the largest collections of local and distal histone quantitative trait loci (hQTLs). Distal QTLs are enriched within topologically associated domains and exhibit largely concordant variation of chromatin state coordinated by proximal and distal non-coding genetic variants. Histone QTLs are enriched for common variants associated with autoimmune diseases and enable identification of putative target genes of disease-associated variants from genome-wide association studies. These analyses provide insights into how genetic variation can affect human disease phenotypes by coordinated changes in chromatin at interacting regulatory elements.
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Affiliation(s)
- Fabian Grubert
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Judith B Zaugg
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; The European Molecular Biology Laboratory Heidelberg, 69117 Heidelberg, Germany
| | - Maya Kasowski
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Oana Ursu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Damek V Spacek
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alicia R Martin
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peyton Greenside
- Biomedical Informatics Graduate Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rohith Srivas
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Doug H Phanstiel
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aleksandra Pekowska
- The European Molecular Biology Laboratory Heidelberg, 69117 Heidelberg, Germany
| | - Nastaran Heidari
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ghia Euskirchen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wolfgang Huber
- The European Molecular Biology Laboratory Heidelberg, 69117 Heidelberg, Germany
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Carlos D Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lars M Steinmetz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; The European Molecular Biology Laboratory Heidelberg, 69117 Heidelberg, Germany
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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29
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Zaugg LK, Lenherr P, Zaugg JB, Weiger R, Krastl G. Influence of the bleaching interval on the luminosity of long-term discolored enamel-dentin discs. Clin Oral Investig 2015; 20:451-8. [PMID: 26254597 DOI: 10.1007/s00784-015-1545-x] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 07/20/2015] [Indexed: 11/28/2022]
Abstract
OBJECTIVES The aim of this study is to investigate the influence of changing the sodium perborate-tetrahydrate (PBS-4) at a 4-day interval versus no change after 16 days of internal bleaching. MATERIALS AND METHODS Two hundred and ten bovine enamel-dentin discs were discolored for 3.5 years with 14 different endodontic materials. All groups with a discoloring index of ∆E (mean) ≥ 5.5 were included in the present investigation: ApexCal (APCA), MTA white + blood (WMTA+BL), Portland cement + blood (PC+BL), blood (BL), MTA gray (GMTA), MTA gray + blood (GMTA+BL), Ledermix (LED), and triple antibiotic paste containing minocycline (3Mix). Fourteen specimens of each group were randomly assigned into two treatment groups: (1) no change of the PBS-4 (n = 7); (2) change of the PBS-4 every 4 days (n = 7). Color measurements were taken at 10 different time intervals and the L*a*b* values were recorded with a spectrophotometer (VITA Easyshade® compact). RESULTS In the group 3Mix, significantly better results were achieved by changing the bleaching agent every 4 days (P = 0.0049; q = 0.04), while the group WMTA+BL indicated better results by no change of the bleaching agent (P = 0.0222, q = 0.09). All remaining groups showed no statistical difference between the two treatment procedures. CONCLUSIONS Moderate discolorations can be successfully treated without changing the bleaching agent over a period of 16 days. Changing the sodium perborate-tetrahydrate every 4 days is preferred in case of severe discolored enamel-dentin discs only. CLINICAL RELEVANCE This approach may offer a reduced number of clinical appointments and a secondary cost reduction to the patient.
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Affiliation(s)
- Lucia K Zaugg
- Department of Periodontology, Endodontology and Cariology, University of Basel, Hebelstrasse 3, 4056, Basel, Switzerland.
| | - Patrik Lenherr
- Department of Reconstructive Dentistry and Temporomandibular Disorders, University of Basel, Hebelstrasse 3, 4056, Basel, Switzerland
| | - Judith B Zaugg
- European Molecular Biology Laboratory, Computational and Structural Biology Unit, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Roland Weiger
- Department of Periodontology, Endodontology and Cariology, University of Basel, Hebelstrasse 3, 4056, Basel, Switzerland
| | - Gabriel Krastl
- Department of Conservative Dentistry and Periodontology, University of Würzburg, Pleicherwall 2, 97070, Würzburg, Germany
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30
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Castelnuovo M, Zaugg JB, Guffanti E, Maffioletti A, Camblong J, Xu Z, Clauder-Münster S, Steinmetz LM, Luscombe NM, Stutz F. Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast. Nucleic Acids Res 2014; 42:4348-62. [PMID: 24497191 PMCID: PMC3985671 DOI: 10.1093/nar/gku100] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [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: 02/05/2013] [Revised: 01/09/2014] [Accepted: 01/12/2014] [Indexed: 12/15/2022] Open
Abstract
Most genomes, including yeast Saccharomyces cerevisiae, are pervasively transcribed producing numerous non-coding RNAs, many of which are unstable and eliminated by nuclear or cytoplasmic surveillance pathways. We previously showed that accumulation of PHO84 antisense RNA (asRNA), in cells lacking the nuclear exosome component Rrp6, is paralleled by repression of sense transcription in a process dependent on the Hda1 histone deacetylase (HDAC) and the H3K4 histone methyl transferase Set1. Here we investigate this process genome-wide and measure the whole transcriptome of various histone modification mutants in a Δrrp6 strain using tiling arrays. We confirm widespread occurrence of potentially antisense-dependent gene regulation and identify three functionally distinct classes of genes that accumulate asRNAs in the absence of Rrp6. These classes differ in whether the genes are silenced by the asRNA and whether the silencing is HDACs and histone methyl transferase-dependent. Among the distinguishing features of asRNAs with regulatory potential, we identify weak early termination by Nrd1/Nab3/Sen1, extension of the asRNA into the open reading frame promoter and dependence of the silencing capacity on Set1 and the HDACs Hda1 and Rpd3 particularly at promoters undergoing extensive chromatin remodelling. Finally, depending on the efficiency of Nrd1/Nab3/Sen1 early termination, asRNA levels are modulated and their capability of silencing is changed.
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Affiliation(s)
- Manuele Castelnuovo
- Department of Cell Biology and NCCR "Frontiers in Genetics", iGE3, University of Geneva, 1211 Geneva, Switzerland, EBI-EMBL Hinxton, Cambridge CB101SD, England, European Molecular Biology Laboratory, 69117 Heidelberg, Germany, Department of Genetics, Stanford University, Stanford, CA 94395 USA and Stanford Genome Technology Center, Palo Alto, CA 94303, USA
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31
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Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, Kellis M, Batzoglou S, Snyder M. Extensive variation in chromatin states across humans. Science 2013; 342:750-2. [PMID: 24136358 PMCID: PMC4075767 DOI: 10.1126/science.1242510] [Citation(s) in RCA: 306] [Impact Index Per Article: 27.8] [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] [Indexed: 11/02/2022]
Abstract
The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.
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Affiliation(s)
- Maya Kasowski
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | | | - Fabian Grubert
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Judith B. Zaugg
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
- Department of Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yuling Liu
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Alan P. Boyle
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Qiangfeng Cliff Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Fouad Zakharia
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Damek V. Spacek
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jingjing Li
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dan Xie
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Lars M. Steinmetz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Genome Biology, The European Molecular Biology Laboratory Heidelberg, 69117 Heidelberg, Germany
| | - John B. Hogenesch
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Manolis Kellis
- Department of Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Serafim Batzoglou
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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32
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Tan-Wong SM, Zaugg JB, Camblong J, Xu Z, Zhang DW, Mischo HE, Ansari AZ, Luscombe NM, Steinmetz LM, Proudfoot NJ. Gene loops enhance transcriptional directionality. Science 2012; 338:671-5. [PMID: 23019609 PMCID: PMC3563069 DOI: 10.1126/science.1224350] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [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] [Indexed: 02/04/2023]
Abstract
Eukaryotic genomes are extensively transcribed, forming both messenger RNAs (mRNAs) and noncoding RNAs (ncRNAs). ncRNAs made by RNA polymerase II often initiate from bidirectional promoters (nucleosome-depleted chromatin) that synthesize mRNA and ncRNA in opposite directions. We demonstrate that, by adopting a gene-loop conformation, actively transcribed mRNA encoding genes restrict divergent transcription of ncRNAs. Because gene-loop formation depends on a protein factor (Ssu72) that coassociates with both the promoter and the terminator, the inactivation of Ssu72 leads to increased synthesis of promoter-associated divergent ncRNAs, referred to as Ssu72-restricted transcripts (SRTs). Similarly, inactivation of individual gene loops by gene mutation enhances SRT synthesis. We demonstrate that gene-loop conformation enforces transcriptional directionality on otherwise bidirectional promoters.
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MESH Headings
- Exosome Multienzyme Ribonuclease Complex/metabolism
- Genes, Fungal
- Genome, Fungal
- Mutation
- Nucleic Acid Conformation
- Phosphoprotein Phosphatases/metabolism
- Promoter Regions, Genetic
- RNA Polymerase II/metabolism
- RNA Stability
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/metabolism
- Transcription, Genetic
- mRNA Cleavage and Polyadenylation Factors/metabolism
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Affiliation(s)
- Sue Mei Tan-Wong
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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Zaugg JB, Luscombe NM. A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast. Genome Res 2012; 22:84-94. [PMID: 21930892 PMCID: PMC3246209 DOI: 10.1101/gr.124099.111] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [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: 03/30/2011] [Accepted: 09/12/2011] [Indexed: 02/04/2023]
Abstract
Nucleosomes play an important role in gene regulation. Molecular studies observed that nucleosome binding in promoters tends to be repressive. In contrast, genomic studies have delivered conflicting results: An analysis of yeast grown on diverse carbon sources reported that nucleosome occupancies remain largely unchanged between conditions, whereas a study of the heat-shock response suggested that nucleosomes get evicted at promoters of genes with increased expression. Consequently, there are few general principles that capture the relationship between chromatin organization and transcriptional regulation. Here, we present a qualitative model for nucleosome positioning in Saccharomyces cerevisiae that helps explain important properties of gene expression. By integrating publicly available data sets, we observe that promoter-bound nucleosomes assume one of four discrete configurations that determine the active and silent transcriptional states of a gene, but not its expression level. In TATA-box-containing promoters, nucleosome architecture indicates the amount of transcriptional noise. We show that >20% of genes switch promoter states upon changes in cellular conditions. The data suggest that DNA-binding transcription factors together with chromatin-remodeling enzymes are primarily responsible for the nucleosome architecture. Our model for promoter nucleosome architecture reconciles genome-scale findings with molecular studies; in doing so, we establish principles for nucleosome positioning and gene expression that apply not only to individual genes, but across the entire genome. The study provides a stepping stone for future models of transcriptional regulation that encompass the intricate interplay between cis- and trans-acting factors, chromatin, and the core transcriptional machinery.
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Affiliation(s)
- Judith B. Zaugg
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, United Kingdom
| | - Nicholas M. Luscombe
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, United Kingdom
- Genome Biology Unit, EMBL Heidelberg, Heidelberg D-69117, Germany
- Okinawa Institute of Science & Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0412, Japan
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Hoskins AA, Morar M, Kappock TJ, Mathews II, Zaugg JB, Barder TE, Peng P, Okamoto A, Ealick SE, Stubbe J. N5-CAIR mutase: role of a CO2 binding site and substrate movement in catalysis. Biochemistry 2007; 46:2842-55. [PMID: 17298082 PMCID: PMC2569195 DOI: 10.1021/bi602436g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [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] [Indexed: 11/28/2022]
Abstract
N5-Carboxyaminoimidazole ribonucleotide mutase (N5-CAIR mutase or PurE) from Escherichia coli catalyzes the reversible interconversion of N5-CAIR to carboxyaminoimidazole ribonucleotide (CAIR) with direct CO2 transfer. Site-directed mutagenesis, a pH-rate profile, DFT calculations, and X-ray crystallography together provide new insight into the mechanism of this unusual transformation. These studies suggest that a conserved, protonated histidine (His45) plays an essential role in catalysis. The importance of proton transfers is supported by DFT calculations on CAIR and N5-CAIR analogues in which the ribose 5'-phosphate is replaced with a methyl group. The calculations suggest that the nonaromatic tautomer of CAIR (isoCAIR) is only 3.1 kcal/mol higher in energy than its aromatic counterpart, implicating this species as a potential intermediate in the PurE-catalyzed reaction. A structure of wild-type PurE cocrystallized with 4-nitroaminoimidazole ribonucleotide (NO2-AIR, a CAIR analogue) and structures of H45N and H45Q PurEs soaked with CAIR have been determined and provide the first insight into the binding of an intact PurE substrate. A comparison of 19 available structures of PurE and PurE mutants in apo and nucleotide-bound forms reveals a common, buried carboxylate or CO2 binding site for CAIR and N5-CAIR in a hydrophobic pocket in which the carboxylate or CO2 interacts with backbone amides. This work has led to a mechanistic proposal in which the carboxylate orients the substrate for proton transfer from His45 to N5-CAIR to form an enzyme-bound aminoimidazole ribonucleotide (AIR) and CO2 intermediate. Subsequent movement of the aminoimidazole moiety of AIR reorients it for addition of CO2 at C4 to generate isoCAIR. His45 is now in a position to remove a C4 proton to produce CAIR.
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Affiliation(s)
| | | | | | | | | | | | - Paul Peng
- Massachusetts Institute of Technology, Chemistry
| | | | - Steven E. Ealick
- Cornell University
- To whom correspondence should be addressed: SEE: Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850. Telephone: (607) 255-7961. Fax: (607) 255-1227. . JS: Department of Chemistry, MIT, Cambridge, MA 02139. Telephone: (617) 253-1814. Fax: (617) 258-7247.
| | - JoAnne Stubbe
- Massachusetts Institute of Technology, Chemistry
- Massachusetts Institute of Technology, Biology
- To whom correspondence should be addressed: SEE: Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850. Telephone: (607) 255-7961. Fax: (607) 255-1227. . JS: Department of Chemistry, MIT, Cambridge, MA 02139. Telephone: (617) 253-1814. Fax: (617) 258-7247.
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