1
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Schweingruber C, Nijssen J, Mechtersheimer J, Reber S, Lebœuf M, O'Brien NL, Mei I, Hedges E, Keuper M, Benitez JA, Radoi V, Jastroch M, Ruepp MD, Hedlund E. Single-cell RNA-sequencing reveals early mitochondrial dysfunction unique to motor neurons shared across FUS- and TARDBP-ALS. Nat Commun 2025; 16:4633. [PMID: 40389397 PMCID: PMC12089458 DOI: 10.1038/s41467-025-59679-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 04/30/2025] [Indexed: 05/21/2025] Open
Abstract
Mutations in FUS and TARDBP cause amyotrophic lateral sclerosis (ALS), but the precise mechanisms of selective motor neuron degeneration remain unresolved. To address if pathomechanisms are shared across mutations and related to either gain- or loss-of-function, we performed single-cell RNA sequencing across isogenic induced pluripotent stem cell-derived neuron types, harbouring FUS P525L, FUS R495X, TARDBP M337V mutations or FUS knockout. Transcriptional changes were far more pronounced in motor neurons than interneurons. About 20% of uniquely dysregulated motor neuron transcripts were shared across FUS mutations, half from gain-of-function. Most indicated mitochondrial impairments, with attenuated pathways shared with mutant TARDBP M337V as well as C9orf72-ALS patient motor neurons. Mitochondrial motility was impaired in ALS motor axons, even with nuclear localized FUS mutants, demonstrating shared toxic gain-of-function mechanisms across FUS- and TARDBP-ALS, uncoupled from protein mislocalization. These early mitochondrial dysfunctions unique to motor neurons may affect survival and represent therapeutic targets in ALS.
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Affiliation(s)
- Christoph Schweingruber
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius v. 16C, 106 91, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Solna v. 9, 171 77, Stockholm, Sweden
| | - Jik Nijssen
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Solna v. 9, 171 77, Stockholm, Sweden
- Department of Neuroscience, Karolinska Institutet, Biomedicum, Solna v. 9, 171 77, Stockholm, Sweden
| | - Jonas Mechtersheimer
- UK Dementia Research Institute Centre at King's College London, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, 5 Cutcombe Rd, SE5 9RX, London, United Kingdom
| | - Stefan Reber
- UK Dementia Research Institute Centre at King's College London, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, 5 Cutcombe Rd, SE5 9RX, London, United Kingdom
| | - Mélanie Lebœuf
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius v. 16C, 106 91, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Solna v. 9, 171 77, Stockholm, Sweden
| | - Niamh L O'Brien
- UK Dementia Research Institute Centre at King's College London, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, 5 Cutcombe Rd, SE5 9RX, London, United Kingdom
| | - Irene Mei
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius v. 16C, 106 91, Stockholm, Sweden
| | - Erin Hedges
- UK Dementia Research Institute Centre at King's College London, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, 5 Cutcombe Rd, SE5 9RX, London, United Kingdom
| | - Michaela Keuper
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius v. 20C, 106 91, Stockholm, Sweden
| | - Julio Aguila Benitez
- Department of Neuroscience, Karolinska Institutet, Biomedicum, Solna v. 9, 171 77, Stockholm, Sweden
| | - Vlad Radoi
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius v. 16C, 106 91, Stockholm, Sweden
| | - Martin Jastroch
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius v. 20C, 106 91, Stockholm, Sweden
| | - Marc-David Ruepp
- UK Dementia Research Institute Centre at King's College London, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, 5 Cutcombe Rd, SE5 9RX, London, United Kingdom.
| | - Eva Hedlund
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius v. 16C, 106 91, Stockholm, Sweden.
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Solna v. 9, 171 77, Stockholm, Sweden.
- Department of Neuroscience, Karolinska Institutet, Biomedicum, Solna v. 9, 171 77, Stockholm, Sweden.
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2
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Blotenburg M, Suurenbroek L, Bax D, de Visser J, Bhardwaj V, Braccioli L, de Wit E, van Boxtel A, Marks H, Zeller P. Stem cell culture conditions affect in vitro differentiation potential and mouse gastruloid formation. PLoS One 2025; 20:e0317309. [PMID: 40138371 PMCID: PMC11940422 DOI: 10.1371/journal.pone.0317309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 12/24/2024] [Indexed: 03/29/2025] Open
Abstract
Aggregating low numbers of mouse embryonic stem cells (mESCs) and inducing Wnt signalling generates 'gastruloids', self-organising complex structures that display an anteroposterior organisation of cell types derived from all three germ layers. Current gastruloid protocols display considerable heterogeneity between experiments in terms of morphology, elongation efficiency, and cell type composition. We therefore investigated whether altering the mESC pluripotency state would provide more consistent results. By growing three mESC lines from two different genetic backgrounds in different intervals of ESLIF and 2i medium the pluripotency state of cells was modulated, and mESC culture as well as the resulting gastruloids were analysed. Microscopic analysis showed a pre-culture-specific effect on gastruloid formation, in terms of aspect ratio and reproducibility. RNA-seq analysis of the mESC start population confirmed that short-term pulses of 2i and ESLIF modulate the pluripotency state, and result in different cellular states. Since multiple epigenetic regulators were detected among the top differentially expressed genes, we further analysed genome-wide DNA methylation and H3K27me3 distributions. We observed epigenetic differences between conditions, most dominantly in the promoter regions of developmental regulators. Lastly, when we investigated the cell type composition of gastruloids grown from these different pre-cultures, we observed that mESCs subjected to 2i-ESLIF preceding aggregation generated gastruloids more consistently, including more complex mesodermal contributions as compared to the ESLIF-only control. These results indicate that optimisation of the mESCs pluripotency state allows the modulation of cell differentiation during gastruloid formation.
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Affiliation(s)
- Marloes Blotenburg
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Oncode Institute, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lianne Suurenbroek
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Oncode Institute, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Danique Bax
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Joëlle de Visser
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Vivek Bhardwaj
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Oncode Institute, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Luca Braccioli
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Elzo de Wit
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Antonius van Boxtel
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Peter Zeller
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Oncode Institute, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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3
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Ding M, Wang D, Chen H, Kesner B, Grimm NB, Weissbein U, Lappala A, Jiang J, Rivera C, Lou J, Li P, Lee JT. A biophysical basis for the spreading behavior and limited diffusion of Xist. Cell 2025; 188:978-997.e25. [PMID: 39824183 PMCID: PMC11863002 DOI: 10.1016/j.cell.2024.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 11/04/2024] [Accepted: 12/06/2024] [Indexed: 01/20/2025]
Abstract
Xist RNA initiates X inactivation as it spreads in cis across the chromosome. Here, we reveal a biophysical basis for its cis-limited diffusion. Xist RNA and HNRNPK together drive a liquid-liquid phase separation (LLPS) that encapsulates the chromosome. HNRNPK droplets pull on Xist and internalize the RNA. Once internalized, Xist induces a further phase transition and "softens" the HNRNPK droplet. Xist alters the condensate's deformability, adhesiveness, and wetting properties in vitro. Other Xist-interacting proteins are internalized and entrapped within the droplet, resulting in a concentration of Xist and protein partners within the condensate. We attribute LLPS to HNRNPK's RGG and Xist's repeat B (RepB) motifs. Mutating these motifs causes Xist diffusion, disrupts polycomb recruitment, and precludes the required mixing of chromosomal compartments for Xist's migration. Thus, we hypothesize that phase transitions in HNRNPK condensates allow Xist to locally concentrate silencing factors and to spread through internal channels of the HNRNPK-encapsulated chromosome.
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Affiliation(s)
- Mingrui Ding
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Danni Wang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Hui Chen
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Barry Kesner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Niklas-Benedikt Grimm
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Uri Weissbein
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Anna Lappala
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jiying Jiang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Carlos Rivera
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jizhong Lou
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Pilong Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
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Meurs R, De Matos M, Bothe A, Guex N, Weber T, Teleman AA, Ban N, Gatfield D. MCTS2 and distinct eIF2D roles in uORF-dependent translation regulation revealed by in vitro re-initiation assays. EMBO J 2025; 44:854-876. [PMID: 39748120 PMCID: PMC11790910 DOI: 10.1038/s44318-024-00347-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2024] [Revised: 11/28/2024] [Accepted: 12/10/2024] [Indexed: 01/04/2025] Open
Abstract
Ribosomes scanning from the mRNA 5' cap to the start codon may initiate at upstream open reading frames (uORFs), decreasing protein biosynthesis. Termination at a uORF can lead to re-initiation, where 40S subunits resume scanning and initiate another translation event downstream. The noncanonical translation factors MCTS1-DENR participate in re-initiation at specific uORFs, but knowledge of other trans-acting factors or uORF features influencing re-initiation is limited. Here, we establish a cell-free re-initiation assay using HeLa lysates to address this question. Comparing in vivo and in vitro re-initiation on uORF-containing reporters, we validate MCTS1-DENR-dependent re-initiation in vitro. Using this system and ribosome profiling in cells, we found that knockdown of the MCTS1-DENR homolog eIF2D causes widespread gene deregulation unrelated to uORF translation, and thus distinct to MCTS1-DENR-dependent re-initiation regulation. Additionally, we identified MCTS2, encoded by an Mcts1 retrogene, as a DENR partner promoting re-initiation in vitro, providing a plausible explanation for clinical differences associated with DENR vs. MCTS1 mutations in humans.
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Affiliation(s)
- Romane Meurs
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland
| | - Mara De Matos
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland
| | - Adrian Bothe
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, 1015, Lausanne, Switzerland
| | - Tobias Weber
- Division of Signal Transduction in Cancer and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aurelio A Teleman
- Division of Signal Transduction in Cancer and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093, Zurich, Switzerland
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland.
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5
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Gridina M, Orlova P, Serov O. Targeted correction of megabase-scale CNTN6 duplication in induced pluripotent stem cells and impacts on gene expression. PeerJ 2025; 13:e18567. [PMID: 39850828 PMCID: PMC11756360 DOI: 10.7717/peerj.18567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Accepted: 10/31/2024] [Indexed: 01/25/2025] Open
Abstract
Copy number variations of the human CNTN6 gene, resulting from megabase-scale microdeletions or microduplications in the 3p26.3 region, are frequently implicated in neurodevelopmental disorders such as intellectual disability and developmental delay. However, duplication of the full-length human CNTN6 gene presents with variable penetrance, resulting in phenotypes that range from neurodevelopmental disorders to no visible pathologies, even within the same family. Previously, we obtained a set of induced pluripotent stem cell lines derived from a patient with a CNTN6 gene duplication and from two healthy donors. Our findings demonstrated that CNTN6 expression in neurons carrying the duplication was significantly reduced. Additionally, the expression from the CNTN6 duplicated allele was markedly lower compared to the wild-type allele. Here, we first introduce a system for correcting megabase-scale duplications in induced pluripotent stem cells and secondly analyze the impact of this correction on CNTN6 gene expression. We showed that the deletion of one copy of the CNTN6 duplication did not affect the expression levels of the remaining allele in the neuronal cells.
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Affiliation(s)
- Maria Gridina
- Genomic Mechanisms of Ontogenesis, Institute of Cytology and Genetics, Novosibirsk, Novosibirsk, Russia
- Ontogenetics, Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
- Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Polina Orlova
- Genomic Mechanisms of Ontogenesis, Institute of Cytology and Genetics, Novosibirsk, Novosibirsk, Russia
- Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Oleg Serov
- Genomic Mechanisms of Ontogenesis, Institute of Cytology and Genetics, Novosibirsk, Novosibirsk, Russia
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Goolab S, Scholefield J. Making gene editing accessible in resource limited environments: recommendations to guide a first-time user. Front Genome Ed 2024; 6:1464531. [PMID: 39386178 PMCID: PMC11461239 DOI: 10.3389/fgeed.2024.1464531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Accepted: 09/05/2024] [Indexed: 10/12/2024] Open
Abstract
The designer nuclease, CRISPR-Cas9 system has advanced the field of genome engineering owing to its programmability and ease of use. The application of these molecular scissors for genome engineering earned the developing researchers the Nobel prize in Chemistry in the year 2020. At present, the potential of this technology to improve global challenges continues to grow exponentially. CRISPR-Cas9 shows promise in the recent advances made in the Global North such as the FDA-approved gene therapy for the treatment of sickle cell anaemia and β-thalassemia and the gene editing of porcine kidney for xenotransplantation into humans affected by end-stage kidney failure. Limited resources, low government investment with an allocation of 1% of gross domestic production to research and development including a shortage of skilled professionals and lack of knowledge may preclude the use of this revolutionary technology in the Global South where the countries involved have reduced science and technology budgets. Focusing on the practical application of genome engineering, successful genetic manipulation is not easily accomplishable and is influenced by the chromatin landscape of the target locus, guide RNA selection, the experimental design including the profiling of the gene edited cells, which impacts the overall outcome achieved. Our assessment primarily delves into economical approaches of performing efficient genome engineering to support the first-time user restricted by limited resources with the aim of democratizing the use of the technology across low- and middle-income countries. Here we provide a comprehensive overview on existing experimental techniques, the significance for target locus analysis and current pitfalls such as the underrepresentation of global genetic diversity. Several perspectives of genome engineering approaches are outlined, which can be adopted in a resource limited setting to enable a higher success rate of genome editing-based innovations in low- and middle-income countries.
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Affiliation(s)
- Shivani Goolab
- Bioengineering and Integrated Genomics Group, Future Production Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Janine Scholefield
- Bioengineering and Integrated Genomics Group, Future Production Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Human Genetics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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7
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Roučová K, Vopálenský V, Mašek T, Del Llano E, Provazník J, Landry JJM, Azevedo N, Ehler E, Beneš V, Pospíšek M. Loss of ADAR1 protein induces changes in small RNA landscape in hepatocytes. RNA (NEW YORK, N.Y.) 2024; 30:1164-1183. [PMID: 38844344 PMCID: PMC11331409 DOI: 10.1261/rna.080097.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 08/18/2024]
Abstract
In recent years, numerous evidence has been accumulated about the extent of A-to-I editing in human RNAs and the key role ADAR1 plays in the cellular editing machinery. It has been shown that A-to-I editing occurrence and frequency are tissue-specific and essential for some tissue development, such as the liver. To study the effect of ADAR1 function in hepatocytes, we have created Huh7.5 ADAR1 KO cell lines. Upon IFN treatment, the Huh7.5 ADAR1 KO cells show rapid arrest of growth and translation, from which they do not recover. We analyzed translatome changes by using a method based on sequencing of separate polysome profile RNA fractions. We found significant changes in the transcriptome and translatome of the Huh7.5 ADAR1 KO cells. The most prominent changes include negatively affected transcription by RNA polymerase III and the deregulation of snoRNA and Y RNA levels. Furthermore, we observed that ADAR1 KO polysomes are enriched in mRNAs coding for proteins pivotal in a wide range of biological processes such as RNA localization and RNA processing, whereas the unbound fraction is enriched mainly in mRNAs coding for ribosomal proteins and translational factors. This indicates that ADAR1 plays a more relevant role in small RNA metabolism and ribosome biogenesis.
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Affiliation(s)
- Kristina Roučová
- Laboratory of RNA Biochemistry, Department of Genetics and Microbiology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - Václav Vopálenský
- Laboratory of RNA Biochemistry, Department of Genetics and Microbiology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - Tomáš Mašek
- Laboratory of RNA Biochemistry, Department of Genetics and Microbiology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | - Edgar Del Llano
- Laboratory of RNA Biochemistry, Department of Genetics and Microbiology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, 277 21 Liběchov, Czech Republic
| | | | | | | | - Edvard Ehler
- Department of Biology and Environmental Studies, Faculty of Education, Charles University, 116 39 Prague, Czech Republic
| | | | - Martin Pospíšek
- Laboratory of RNA Biochemistry, Department of Genetics and Microbiology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
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8
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Lee YW, Weissbein U, Blum R, Lee JT. G-quadruplex folding in Xist RNA antagonizes PRC2 activity for stepwise regulation of X chromosome inactivation. Mol Cell 2024; 84:1870-1885.e9. [PMID: 38759625 PMCID: PMC11505738 DOI: 10.1016/j.molcel.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/25/2023] [Accepted: 04/19/2024] [Indexed: 05/19/2024]
Abstract
How Polycomb repressive complex 2 (PRC2) is regulated by RNA remains an unsolved problem. Although PRC2 binds G-tracts with the potential to form RNA G-quadruplexes (rG4s), whether rG4s fold extensively in vivo and whether PRC2 binds folded or unfolded rG4 are unknown. Using the X-inactivation model in mouse embryonic stem cells, here we identify multiple folded rG4s in Xist RNA and demonstrate that PRC2 preferentially binds folded rG4s. High-affinity rG4 binding inhibits PRC2's histone methyltransferase activity, and stabilizing rG4 in vivo antagonizes H3 at lysine 27 (H3K27me3) enrichment on the inactive X chromosome. Surprisingly, mutagenizing the rG4 does not affect PRC2 recruitment but promotes its release and catalytic activation on chromatin. H3K27me3 marks are misplaced, however, and gene silencing is compromised. Xist-PRC2 complexes become entrapped in the S1 chromosome compartment, precluding the required translocation into the S2 compartment. Thus, Xist rG4 folding controls PRC2 activity, H3K27me3 enrichment, and the stepwise regulation of chromosome-wide gene silencing.
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Affiliation(s)
- Yong Woo Lee
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Uri Weissbein
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Roy Blum
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.
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9
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Sulimenko V, Sládková V, Sulimenko T, Dráberová E, Vosecká V, Dráberová L, Skalli O, Dráber P. Regulation of microtubule nucleation in mouse bone marrow-derived mast cells by ARF GTPase-activating protein GIT2. Front Immunol 2024; 15:1321321. [PMID: 38370406 PMCID: PMC10870779 DOI: 10.3389/fimmu.2024.1321321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/16/2024] [Indexed: 02/20/2024] Open
Abstract
Aggregation of high-affinity IgE receptors (FcϵRIs) on granulated mast cells triggers signaling pathways leading to a calcium response and release of inflammatory mediators from secretory granules. While microtubules play a role in the degranulation process, the complex molecular mechanisms regulating microtubule remodeling in activated mast cells are only partially understood. Here, we demonstrate that the activation of bone marrow mast cells induced by FcϵRI aggregation increases centrosomal microtubule nucleation, with G protein-coupled receptor kinase-interacting protein 2 (GIT2) playing a vital role in this process. Both endogenous and exogenous GIT2 were associated with centrosomes and γ-tubulin complex proteins. Depletion of GIT2 enhanced centrosomal microtubule nucleation, and phenotypic rescue experiments revealed that GIT2, unlike GIT1, acts as a negative regulator of microtubule nucleation in mast cells. GIT2 also participated in the regulation of antigen-induced degranulation and chemotaxis. Further experiments showed that phosphorylation affected the centrosomal localization of GIT2 and that during antigen-induced activation, GIT2 was phosphorylated by conventional protein kinase C, which promoted microtubule nucleation. We propose that GIT2 is a novel regulator of microtubule organization in activated mast cells by modulating centrosomal microtubule nucleation.
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Affiliation(s)
- Vadym Sulimenko
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Vladimíra Sládková
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Tetyana Sulimenko
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Eduarda Dráberová
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Věra Vosecká
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Lubica Dráberová
- Laboratory of Signal Transduction, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Omar Skalli
- Department of Biological Sciences, The University of Memphis, Memphis, TN, United States
| | - Pavel Dráber
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
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10
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Sun Y, Wiese M, Hmadi R, Karayol R, Seyfferth J, Martinez Greene JA, Erdogdu NU, Deboutte W, Arrigoni L, Holz H, Renschler G, Hirsch N, Foertsch A, Basilicata MF, Stehle T, Shvedunova M, Bella C, Pessoa Rodrigues C, Schwalb B, Cramer P, Manke T, Akhtar A. MSL2 ensures biallelic gene expression in mammals. Nature 2023; 624:173-181. [PMID: 38030723 PMCID: PMC10700137 DOI: 10.1038/s41586-023-06781-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
In diploid organisms, biallelic gene expression enables the production of adequate levels of mRNA1,2. This is essential for haploinsufficient genes, which require biallelic expression for optimal function to prevent the onset of developmental disorders1,3. Whether and how a biallelic or monoallelic state is determined in a cell-type-specific manner at individual loci remains unclear. MSL2 is known for dosage compensation of the male X chromosome in flies. Here we identify a role of MSL2 in regulating allelic expression in mammals. Allele-specific bulk and single-cell analyses in mouse neural progenitor cells revealed that, in addition to the targets showing biallelic downregulation, a class of genes transitions from biallelic to monoallelic expression after MSL2 loss. Many of these genes are haploinsufficient. In the absence of MSL2, one allele remains active, retaining active histone modifications and transcription factor binding, whereas the other allele is silenced, exhibiting loss of promoter-enhancer contacts and the acquisition of DNA methylation. Msl2-knockout mice show perinatal lethality and heterogeneous phenotypes during embryonic development, supporting a role for MSL2 in regulating gene dosage. The role of MSL2 in preserving biallelic expression of specific dosage-sensitive genes sets the stage for further investigation of other factors that are involved in allelic dosage compensation in mammalian cells, with considerable implications for human disease.
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Affiliation(s)
- Yidan Sun
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Meike Wiese
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Raed Hmadi
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Remzi Karayol
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Janine Seyfferth
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Juan Alfonso Martinez Greene
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Niyazi Umut Erdogdu
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ward Deboutte
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Laura Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Herbert Holz
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Gina Renschler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Naama Hirsch
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Arion Foertsch
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Thomas Stehle
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Maria Shvedunova
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Chiara Bella
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Bjoern Schwalb
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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11
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Pánek J, Roithová A, Radivojević N, Sýkora M, Prusty AB, Huston N, Wan H, Pyle AM, Fischer U, Staněk D. The SMN complex drives structural changes in human snRNAs to enable snRNP assembly. Nat Commun 2023; 14:6580. [PMID: 37852981 PMCID: PMC10584915 DOI: 10.1038/s41467-023-42324-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
Spliceosomal snRNPs are multicomponent particles that undergo a complex maturation pathway. Human Sm-class snRNAs are generated as 3'-end extended precursors, which are exported to the cytoplasm and assembled together with Sm proteins into core RNPs by the SMN complex. Here, we provide evidence that these pre-snRNA substrates contain compact, evolutionarily conserved secondary structures that overlap with the Sm binding site. These structural motifs in pre-snRNAs are predicted to interfere with Sm core assembly. We model structural rearrangements that lead to an open pre-snRNA conformation compatible with Sm protein interaction. The predicted rearrangement pathway is conserved in Metazoa and requires an external factor that initiates snRNA remodeling. We show that the essential helicase Gemin3, which is a component of the SMN complex, is crucial for snRNA structural rearrangements during snRNP maturation. The SMN complex thus facilitates ATP-driven structural changes in snRNAs that expose the Sm site and enable Sm protein binding.
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Affiliation(s)
- Josef Pánek
- Laboratory of Bioinformatics, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic.
| | - Adriana Roithová
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
- Laboratory of Regulation of Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Nenad Radivojević
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Sýkora
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | | | - Nicholas Huston
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, USA
| | - Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, USA
- Department of Chemistry, Yale University, New Haven, USA
- Howard Hughes Medical Institute, Chevy Chase, USA
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | - David Staněk
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic.
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12
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Flemr M, Schwaiger M, Hess D, Iesmantavicius V, Ahel J, Tuck AC, Mohn F, Bühler M. Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites. RNA (NEW YORK, N.Y.) 2023; 29:1140-1165. [PMID: 37137667 PMCID: PMC10351895 DOI: 10.1261/rna.079465.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/19/2023] [Indexed: 05/05/2023]
Abstract
Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing of U1 snRNA with a 5' splice site (5'SS). In mammals, many introns contain weak 5'SSs that are not efficiently recognized by the canonical U1 snRNP, suggesting alternative mechanisms exist. Here, we develop a cross-linking immunoprecipitation coupled to a high-throughput sequencing method, BCLIP-seq, to identify NRDE2 (nuclear RNAi-defective 2), and CCDC174 (coiled-coil domain-containing 174) as novel RNA-binding proteins in mouse ES cells that associate with U1 snRNA and 5'SSs. Both proteins bind directly to U1 snRNA independently of canonical U1 snRNP-specific proteins, and they are required for the selection and effective processing of weak 5'SSs. Our results reveal that mammalian cells use noncanonical splicing factors bound directly to U1 snRNA to effectively select suboptimal 5'SS sequences in hundreds of genes, promoting proper splice site choice, and accurate pre-mRNA splicing.
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Affiliation(s)
- Matyas Flemr
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Michaela Schwaiger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | | | - Josip Ahel
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Alex Charles Tuck
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Fabio Mohn
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- University of Basel, 4003 Basel, Switzerland
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13
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Mikkelsen NS, Bak RO. Enrichment strategies to enhance genome editing. J Biomed Sci 2023; 30:51. [PMID: 37393268 PMCID: PMC10315055 DOI: 10.1186/s12929-023-00943-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023] Open
Abstract
Genome editing technologies hold great promise for numerous applications including the understanding of cellular and disease mechanisms and the development of gene and cellular therapies. Achieving high editing frequencies is critical to these research areas and to achieve the overall goal of being able to manipulate any target with any desired genetic outcome. However, gene editing technologies sometimes suffer from low editing efficiencies due to several challenges. This is often the case for emerging gene editing technologies, which require assistance for translation into broader applications. Enrichment strategies can support this goal by selecting gene edited cells from non-edited cells. In this review, we elucidate the different enrichment strategies, their many applications in non-clinical and clinical settings, and the remaining need for novel strategies to further improve genome research and gene and cellular therapy studies.
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Affiliation(s)
- Nanna S Mikkelsen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, Bldg. 1115, 8000, Aarhus C., Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, Bldg. 1115, 8000, Aarhus C., Denmark.
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14
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Schmolka N, Karemaker ID, Cardoso da Silva R, Recchia DC, Spegg V, Bhaskaran J, Teske M, de Wagenaar NP, Altmeyer M, Baubec T. Dissecting the roles of MBD2 isoforms and domains in regulating NuRD complex function during cellular differentiation. Nat Commun 2023; 14:3848. [PMID: 37385984 PMCID: PMC10310694 DOI: 10.1038/s41467-023-39551-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/19/2023] [Indexed: 07/01/2023] Open
Abstract
The Nucleosome Remodeling and Deacetylation (NuRD) complex is a crucial regulator of cellular differentiation. Two members of the Methyl-CpG-binding domain (MBD) protein family, MBD2 and MBD3, are known to be integral, but mutually exclusive subunits of the NuRD complex. Several MBD2 and MBD3 isoforms are present in mammalian cells, resulting in distinct MBD-NuRD complexes. Whether these different complexes serve distinct functional activities during differentiation is not fully explored. Based on the essential role of MBD3 in lineage commitment, we systematically investigated a diverse set of MBD2 and MBD3 variants for their potential to rescue the differentiation block observed for mouse embryonic stem cells (ESCs) lacking MBD3. While MBD3 is indeed crucial for ESC differentiation to neuronal cells, it functions independently of its MBD domain. We further identify that MBD2 isoforms can replace MBD3 during lineage commitment, however with different potential. Full-length MBD2a only partially rescues the differentiation block, while MBD2b, an isoform lacking an N-terminal GR-rich repeat, fully rescues the Mbd3 KO phenotype. In case of MBD2a, we further show that removing the methylated DNA binding capacity or the GR-rich repeat enables full redundancy to MBD3, highlighting the synergistic requirements for these domains in diversifying NuRD complex function.
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Affiliation(s)
- Nina Schmolka
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Ino D Karemaker
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Richard Cardoso da Silva
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Davide C Recchia
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands
- Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Jahnavi Bhaskaran
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- MRC London Institute of Medical Sciences, London, UK
| | - Michael Teske
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Nathalie P de Wagenaar
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, Utrecht, The Netherlands.
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15
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Flury V, Reverón-Gómez N, Alcaraz N, Stewart-Morgan KR, Wenger A, Klose RJ, Groth A. Recycling of modified H2A-H2B provides short-term memory of chromatin states. Cell 2023; 186:1050-1065.e19. [PMID: 36750094 PMCID: PMC9994263 DOI: 10.1016/j.cell.2023.01.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/11/2022] [Accepted: 01/06/2023] [Indexed: 02/08/2023]
Abstract
Chromatin landscapes are disrupted during DNA replication and must be restored faithfully to maintain genome regulation and cell identity. The histone H3-H4 modification landscape is restored by parental histone recycling and modification of new histones. How DNA replication impacts on histone H2A-H2B is currently unknown. Here, we measure H2A-H2B modifications and H2A.Z during DNA replication and across the cell cycle using quantitative genomics. We show that H2AK119ub1, H2BK120ub1, and H2A.Z are recycled accurately during DNA replication. Modified H2A-H2B are segregated symmetrically to daughter strands via POLA1 on the lagging strand, but independent of H3-H4 recycling. Post-replication, H2A-H2B modification and variant landscapes are quickly restored, and H2AK119ub1 guides accurate restoration of H3K27me3. This work reveals epigenetic transmission of parental H2A-H2B during DNA replication and identifies cross talk between H3-H4 and H2A-H2B modifications in epigenome propagation. We propose that rapid short-term memory of recycled H2A-H2B modifications facilitates restoration of stable H3-H4 chromatin states.
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Affiliation(s)
- Valentin Flury
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nazaret Reverón-Gómez
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nicolas Alcaraz
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kathleen R Stewart-Morgan
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Alice Wenger
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, 2200 Copenhagen, Denmark.
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16
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Bademosi AT, Decet M, Kuenen S, Calatayud C, Swerts J, Gallego SF, Schoovaerts N, Karamanou S, Louros N, Martin E, Sibarita JB, Vints K, Gounko NV, Meunier FA, Economou A, Versées W, Rousseau F, Schymkowitz J, Soukup SF, Verstreken P. EndophilinA-dependent coupling between activity-induced calcium influx and synaptic autophagy is disrupted by a Parkinson-risk mutation. Neuron 2023; 111:1402-1422.e13. [PMID: 36827984 PMCID: PMC10166451 DOI: 10.1016/j.neuron.2023.02.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 11/09/2022] [Accepted: 01/31/2023] [Indexed: 02/26/2023]
Abstract
Neuronal activity causes use-dependent decline in protein function. However, it is unclear how this is coupled to local quality control mechanisms. We show in Drosophila that the endocytic protein Endophilin-A (EndoA) connects activity-induced calcium influx to synaptic autophagy and neuronal survival in a Parkinson disease-relevant fashion. Mutations in the disordered loop, including a Parkinson disease-risk mutation, render EndoA insensitive to neuronal stimulation and affect protein dynamics: when EndoA is more flexible, its mobility in membrane nanodomains increases, making it available for autophagosome formation. Conversely, when EndoA is more rigid, its mobility reduces, blocking stimulation-induced autophagy. Balanced stimulation-induced autophagy is required for dopagminergic neuron survival, and a variant in the human ENDOA1 disordered loop conferring risk to Parkinson disease also blocks nanodomain protein mobility and autophagy both in vivo and in human-induced dopaminergic neurons. Thus, we reveal a mechanism that neurons use to connect neuronal activity to local autophagy and that is critical for neuronal survival.
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Affiliation(s)
- Adekunle T Bademosi
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium; Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St Lucia Campus, Brisbane, QLD 4072, Australia
| | - Marianna Decet
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium
| | - Sabine Kuenen
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium
| | - Carles Calatayud
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium
| | - Jef Swerts
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium
| | - Sandra F Gallego
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium
| | - Nils Schoovaerts
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium
| | - Spyridoula Karamanou
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven 3000, Belgium
| | - Nikolaos Louros
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Ella Martin
- VIB-VUB Center for Structural Biology, Brussels 1050, Belgium; Department of Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Jean-Baptiste Sibarita
- Interdisciplinary Institute for Neuroscience, University of Bordeaux, F-33000 Bordeaux, France
| | - Katlijn Vints
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium; VIB Bio Core, KU Leuven, Leuven 3000, Belgium
| | - Natalia V Gounko
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium; VIB Bio Core, KU Leuven, Leuven 3000, Belgium
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, St Lucia Campus, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, St Lucia Campus, Brisbane, QLD 4072, Australia
| | - Anastassios Economou
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven 3000, Belgium
| | - Wim Versées
- VIB-VUB Center for Structural Biology, Brussels 1050, Belgium; Department of Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Frederic Rousseau
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Joost Schymkowitz
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | | | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven 3000, Belgium.
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17
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Molenaar TM, Malik M, Silva J, Liu NQ, Haarhuis JHI, Ambrosi C, Kwesi-Maliepaard EM, van Welsem T, Baubec T, Faller WJ, van Leeuwen F. The histone methyltransferase SETD2 negatively regulates cell size. J Cell Sci 2022; 135:jcs259856. [PMID: 36052643 PMCID: PMC9659392 DOI: 10.1242/jcs.259856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 08/23/2022] [Indexed: 11/20/2022] Open
Abstract
Cell size varies between cell types but is tightly regulated by cell intrinsic and extrinsic mechanisms. Cell size control is important for cell function, and changes in cell size are frequently observed in cancer. Here, we uncover a role for SETD2 in regulating cell size. SETD2 is a lysine methyltransferase and a tumor suppressor protein involved in transcription, RNA processing and DNA repair. At the molecular level, SETD2 is best known for associating with RNA polymerase II through its Set2-Rbp1 interacting (SRI) domain and methylating histone H3 on lysine 36 (H3K36) during transcription. Using multiple independent perturbation strategies, we identify SETD2 as a negative regulator of global protein synthesis rates and cell size. We provide evidence that overexpression of the H3K36 demethylase KDM4A or the oncohistone H3.3K36M also increase cell size. In addition, ectopic overexpression of a decoy SRI domain increased cell size, suggesting that the relevant substrate is engaged by SETD2 via its SRI domain. These data add a central role of SETD2 in regulating cellular physiology and warrant further studies on separating the different functions of SETD2 in cancer development.
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Affiliation(s)
- Thom M. Molenaar
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Muddassir Malik
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Joana Silva
- Division of Oncogenomics, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Ning Qing Liu
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Judith H. I. Haarhuis
- Division of Cell Biology, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Christina Ambrosi
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
- Life Science Zurich Graduate School, University of Zurich and ETH Zurich, CH-8057 Zurich, Switzerland
| | | | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - William J. Faller
- Division of Oncogenomics, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
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18
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Suzuki T, Takagi S, Hara T. Multiple Gene Transfer and All-In-One Conditional Knockout Systems in Mouse Embryonic Stem Cells for Analysis of Gene Function. Front Cell Dev Biol 2022; 10:870629. [PMID: 35419367 PMCID: PMC8995969 DOI: 10.3389/fcell.2022.870629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Mouse embryonic stem cells (ESCs) are powerful tools for functional analysis of stem cell-related genes; however, complex gene manipulations, such as locus-targeted introduction of multiple genes and conditional gene knockout conditional knockout, are technically difficult. Here, we review recent advances in technologies aimed at generating cKO clones in ESCs, including two new methods developed in our laboratory: the simultaneous or sequential integration of multiple genes system for introducing an unlimited number of gene cassettes into a specific chromosomal locus using reciprocal recombinases; and the all-in-one cKO system, which enables introduction of an EGFP reporter expression cassette and FLAG-tagged gene of interest under an endogenous promoter. In addition, methods developed in other laboratories, including conventional approaches to establishment of cKO cell clones, inducible Cas9-mediated cKO generation, and cKO assisted by reporter construct, invertible gene-trap cassette, and conditional protein degradation. Finally, we discuss the advantages of each approach, as well as the remaining issues and challenges.
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Affiliation(s)
- Teruhiko Suzuki
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Satoko Takagi
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahiko Hara
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Graduate School of Science, Department of Biological Science, Tokyo Metropolitan University, Tokyo, Japan
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19
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Klebanovych A, Vinopal S, Dráberová E, Sládková V, Sulimenko T, Sulimenko V, Vosecká V, Macůrek L, Legido A, Dráber P. C53 Interacting with UFM1-Protein Ligase 1 Regulates Microtubule Nucleation in Response to ER Stress. Cells 2022; 11:cells11030555. [PMID: 35159364 PMCID: PMC8834445 DOI: 10.3390/cells11030555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 02/01/2023] Open
Abstract
ER distribution depends on microtubules, and ER homeostasis disturbance activates the unfolded protein response resulting in ER remodeling. CDK5RAP3 (C53) implicated in various signaling pathways interacts with UFM1-protein ligase 1 (UFL1), which mediates the ufmylation of proteins in response to ER stress. Here we find that UFL1 and C53 associate with γ-tubulin ring complex proteins. Knockout of UFL1 or C53 in human osteosarcoma cells induces ER stress and boosts centrosomal microtubule nucleation accompanied by γ-tubulin accumulation, microtubule formation, and ER expansion. C53, which is stabilized by UFL1, associates with the centrosome and rescues microtubule nucleation in cells lacking UFL1. Pharmacological induction of ER stress by tunicamycin also leads to increased microtubule nucleation and ER expansion. Furthermore, tunicamycin suppresses the association of C53 with the centrosome. These findings point to a novel mechanism for the relief of ER stress by stimulation of centrosomal microtubule nucleation.
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Affiliation(s)
- Anastasiya Klebanovych
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, CZ 142 20 Prague, Czech Republic; (A.K.); (S.V.); (E.D.); (V.S.); (T.S.); (V.S.); (V.V.); (L.M.)
| | - Stanislav Vinopal
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, CZ 142 20 Prague, Czech Republic; (A.K.); (S.V.); (E.D.); (V.S.); (T.S.); (V.S.); (V.V.); (L.M.)
| | - Eduarda Dráberová
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, CZ 142 20 Prague, Czech Republic; (A.K.); (S.V.); (E.D.); (V.S.); (T.S.); (V.S.); (V.V.); (L.M.)
| | - Vladimíra Sládková
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, CZ 142 20 Prague, Czech Republic; (A.K.); (S.V.); (E.D.); (V.S.); (T.S.); (V.S.); (V.V.); (L.M.)
| | - Tetyana Sulimenko
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, CZ 142 20 Prague, Czech Republic; (A.K.); (S.V.); (E.D.); (V.S.); (T.S.); (V.S.); (V.V.); (L.M.)
| | - Vadym Sulimenko
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, CZ 142 20 Prague, Czech Republic; (A.K.); (S.V.); (E.D.); (V.S.); (T.S.); (V.S.); (V.V.); (L.M.)
| | - Věra Vosecká
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, CZ 142 20 Prague, Czech Republic; (A.K.); (S.V.); (E.D.); (V.S.); (T.S.); (V.S.); (V.V.); (L.M.)
| | - Libor Macůrek
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, CZ 142 20 Prague, Czech Republic; (A.K.); (S.V.); (E.D.); (V.S.); (T.S.); (V.S.); (V.V.); (L.M.)
| | - Agustin Legido
- Section of Neurology, St. Christopher’s Hospital for Children, Department of Pediatrics, Drexel University College of Medicine, Philadelphia, PA 19134, USA;
| | - Pavel Dráber
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, CZ 142 20 Prague, Czech Republic; (A.K.); (S.V.); (E.D.); (V.S.); (T.S.); (V.S.); (V.V.); (L.M.)
- Correspondence: ; Tel.: +420-241-062-632
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20
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Butz S, Schmolka N, Karemaker ID, Villaseñor R, Schwarz I, Domcke S, Uijttewaal ECH, Jude J, Lienert F, Krebs AR, de Wagenaar NP, Bao X, Zuber J, Elling U, Schübeler D, Baubec T. DNA sequence and chromatin modifiers cooperate to confer epigenetic bistability at imprinting control regions. Nat Genet 2022; 54:1702-1710. [PMID: 36333500 PMCID: PMC9649441 DOI: 10.1038/s41588-022-01210-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/19/2022] [Indexed: 11/06/2022]
Abstract
Genomic imprinting is regulated by parental-specific DNA methylation of imprinting control regions (ICRs). Despite an identical DNA sequence, ICRs can exist in two distinct epigenetic states that are memorized throughout unlimited cell divisions and reset during germline formation. Here, we systematically study the genetic and epigenetic determinants of this epigenetic bistability. By iterative integration of ICRs and related DNA sequences to an ectopic location in the mouse genome, we first identify the DNA sequence features required for maintenance of epigenetic states in embryonic stem cells. The autonomous regulatory properties of ICRs further enabled us to create DNA-methylation-sensitive reporters and to screen for key components involved in regulating their epigenetic memory. Besides DNMT1, UHRF1 and ZFP57, we identify factors that prevent switching from methylated to unmethylated states and show that two of these candidates, ATF7IP and ZMYM2, are important for the stability of DNA and H3K9 methylation at ICRs in embryonic stem cells.
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Affiliation(s)
- Stefan Butz
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Nina Schmolka
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Present Address: Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Ino D. Karemaker
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Rodrigo Villaseñor
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland ,grid.5252.00000 0004 1936 973XPresent Address: Division of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Isabel Schwarz
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Silvia Domcke
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Faculty of Science, University of Basel, Basel, Switzerland ,grid.34477.330000000122986657Present Address: Department of Genome Sciences, University of Washington, Seattle, WA USA
| | - Esther C. H. Uijttewaal
- grid.473822.80000 0005 0375 3232Institute of Molecular Biotechnology Austria (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Julian Jude
- grid.14826.390000 0000 9799 657XResearch Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Florian Lienert
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Faculty of Science, University of Basel, Basel, Switzerland
| | - Arnaud R. Krebs
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.4709.a0000 0004 0495 846XPresent Address: European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Nathalie P. de Wagenaar
- grid.5477.10000000120346234Division of Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands
| | - Xue Bao
- grid.5477.10000000120346234Division of Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands
| | - Johannes Zuber
- grid.14826.390000 0000 9799 657XResearch Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria ,grid.22937.3d0000 0000 9259 8492Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Ulrich Elling
- grid.473822.80000 0005 0375 3232Institute of Molecular Biotechnology Austria (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Dirk Schübeler
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Faculty of Science, University of Basel, Basel, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland. .,Division of Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands.
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21
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Perez-Leal O, Nixon-Abell J, Barrero CA, Gordon JC, Oesterling J, Rico MC. Multiplex Gene Tagging with CRISPR-Cas9 for Live-Cell Microscopy and Application to Study the Role of SARS-CoV-2 Proteins in Autophagy, Mitochondrial Dynamics, and Cell Growth. CRISPR J 2021; 4:854-871. [PMID: 34847745 PMCID: PMC8742308 DOI: 10.1089/crispr.2021.0041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The lack of efficient tools to label multiple endogenous targets in cell lines without staining or fixation has limited our ability to track physiological and pathological changes in cells over time via live-cell studies. Here, we outline the FAST-HDR vector system to be used in combination with CRISPR-Cas9 to allow visual live-cell studies of up to three endogenous proteins within the same cell line. Our approach utilizes a novel set of advanced donor plasmids for homology-directed repair and a streamlined workflow optimized for microscopy-based cell screening to create genetically modified cell lines that do not require staining or fixation to accommodate microscopy-based studies. We validated this new methodology by developing two advanced cell lines with three fluorescent-labeled endogenous proteins that support high-content imaging without using antibodies or exogenous staining. We applied this technology to study seven severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/COVID-19) viral proteins to understand better their effects on autophagy, mitochondrial dynamics, and cell growth. Using these two cell lines, we were able to identify the protein ORF3a successfully as a potent inhibitor of autophagy, inducer of mitochondrial relocalization, and a growth inhibitor, which highlights the effectiveness of live-cell studies using this technology.
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Affiliation(s)
- Oscar Perez-Leal
- Department of Pharmaceutical Sciences, Moulder Center for Drug Discovery, School of Pharmacy, Temple University, Philadelphia, Pennsylvania, USA
| | - Jonathon Nixon-Abell
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, Virginia, USA
| | - Carlos A Barrero
- Department of Pharmaceutical Sciences, Moulder Center for Drug Discovery, School of Pharmacy, Temple University, Philadelphia, Pennsylvania, USA
| | - John C Gordon
- Department of Pharmaceutical Sciences, Moulder Center for Drug Discovery, School of Pharmacy, Temple University, Philadelphia, Pennsylvania, USA
| | - James Oesterling
- Flow Cytometry and Cell Sorting Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
| | - Mario C Rico
- Department of Pharmaceutical Sciences, Moulder Center for Drug Discovery, School of Pharmacy, Temple University, Philadelphia, Pennsylvania, USA
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22
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Sherstyuk VV, Zakian SM. Generation of Transgenic Rat Embryonic Stem Cells Using the CRISPR/Cpf1 System for Inducible Gene Knockout. BIOCHEMISTRY (MOSCOW) 2021; 86:843-851. [PMID: 34284709 DOI: 10.1134/s0006297921070051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Rat embryonic stem cells (ESCs) play an important role in the studies of genes involved in maintaining of pluripotent state and early development of this model organism. To study functions of the essential genes, as well as the processes of cell differentiation, the method of induced knockout is widely used. The CreERT2/loxP system allows obtaining an inducible knockout in cells expressing tamoxifen-inducible Cre recombinase (CreERT2) and containing loxP sites flanking the target gene by adding 4-hydroxy tamoxifen to the culture medium. However, the rat ESC lines expressing CreERT2 are absent. In this work, we tested three CRISPR/Cas systems for introduction of double-strand breaks into the Rosa26 locus in the rat ESCs and inserted tamoxifen-dependent Cre recombinase into this locus using the CRISPR/Cpf1 system. It was shown that the obtained transgenic rat ESC lines retained the characteristics of pluripotent cells. Tamoxifen-inducible Cre recombinase activity was analyzed using a reporter vector.
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Affiliation(s)
- Vladimir V Sherstyuk
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Suren M Zakian
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
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23
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Suzuki T, Katada E, Mizuoka Y, Takagi S, Kazuki Y, Oshimura M, Shindo M, Hara T. A novel all-in-one conditional knockout system uncovered an essential role of DDX1 in ribosomal RNA processing. Nucleic Acids Res 2021; 49:e40. [PMID: 33503245 PMCID: PMC8053084 DOI: 10.1093/nar/gkaa1296] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/09/2020] [Accepted: 01/04/2021] [Indexed: 11/13/2022] Open
Abstract
Generation of conditional knockout (cKO) and various gene-modified cells is laborious and time-consuming. Here, we established an all-in-one cKO system, which enables highly efficient generation of cKO cells and simultaneous gene modifications, including epitope tagging and reporter gene knock-in. We applied this system to mouse embryonic stem cells (ESCs) and generated RNA helicase Ddx1 cKO ESCs. The targeted cells displayed endogenous promoter-driven EGFP and FLAG-tagged DDX1 expression, and they were converted to Ddx1 KO via FLP recombinase. We further established TetFE ESCs, which carried a reverse tetracycline transactivator (rtTA) expression cassette and a tetracycline response element (TRE)-regulated FLPERT2 cassette in the Gt(ROSA26)Sor locus for instant and tightly regulated induction of gene KO. By utilizing TetFE Ddx1F/F ESCs, we isolated highly pure Ddx1F/F and Ddx1−/− ESCs and found that loss of Ddx1 caused rRNA processing defects, thereby activating the ribosome stress–p53 pathway. We also demonstrated cKO of various genes in ESCs and homologous recombination-non-proficient human HT1080 cells. The frequency of cKO clones was remarkably high for both cell types and reached up to 96% when EGFP-positive clones were analyzed. This all-in-one cKO system will be a powerful tool for rapid and precise analyses of gene functions.
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Affiliation(s)
- Teruhiko Suzuki
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Eiji Katada
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yuki Mizuoka
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Satoko Takagi
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yasuhiro Kazuki
- Chromosome Engineering Research Center (CERC), Tottori University, 86 Nishicho, Yonago 683-8503, Japan.,Division of Genome and Cellular Functions, Department of Molecular and Cellular Biology, School of Life Science, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan
| | - Mitsuo Oshimura
- Chromosome Engineering Research Center (CERC), Tottori University, 86 Nishicho, Yonago 683-8503, Japan
| | - Mayumi Shindo
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Takahiko Hara
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.,Graduate School of Science, Department of Biological Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji-shi, Tokyo 192-0397, Japan
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24
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Kriz AJ, Colognori D, Sunwoo H, Nabet B, Lee JT. Balancing cohesin eviction and retention prevents aberrant chromosomal interactions, Polycomb-mediated repression, and X-inactivation. Mol Cell 2021; 81:1970-1987.e9. [PMID: 33725485 PMCID: PMC8106664 DOI: 10.1016/j.molcel.2021.02.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 12/18/2020] [Accepted: 02/22/2021] [Indexed: 12/17/2022]
Abstract
Depletion of architectural factors globally alters chromatin structure but only modestly affects gene expression. We revisit the structure-function relationship using the inactive X chromosome (Xi) as a model. We investigate cohesin imbalances by forcing its depletion or retention using degron-tagged RAD21 (cohesin subunit) or WAPL (cohesin release factor). Cohesin loss disrupts the Xi superstructure, unveiling superloops between escapee genes with minimal effect on gene repression. By contrast, forced cohesin retention markedly affects Xi superstructure, compromises spreading of Xist RNA-Polycomb complexes, and attenuates Xi silencing. Effects are greatest at distal chromosomal ends, where looping contacts with the Xist locus are weakened. Surprisingly, cohesin loss creates an Xi superloop, and cohesin retention creates Xi megadomains on the active X chromosome. Across the genome, a proper cohesin balance protects against aberrant inter-chromosomal interactions and tempers Polycomb-mediated repression. We conclude that a balance of cohesin eviction and retention regulates X inactivation and inter-chromosomal interactions across the genome.
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Affiliation(s)
- Andrea J Kriz
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - David Colognori
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Hongjae Sunwoo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Behnam Nabet
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.
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25
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Halloy F, Iyer PS, Ghidini A, Lysenko V, Barman-Aksözen J, Grubenmann CP, Jucker J, Wildner-Verhey van Wijk N, Ruepp MD, Minder EI, Minder AE, Schneider-Yin X, Theocharides APA, Schümperli D, Hall J. Repurposing of glycine transport inhibitors for the treatment of erythropoietic protoporphyria. Cell Chem Biol 2021; 28:1221-1234.e6. [PMID: 33756123 DOI: 10.1016/j.chembiol.2021.02.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/19/2021] [Accepted: 02/23/2021] [Indexed: 12/16/2022]
Abstract
Erythropoietic protoporphyria (EPP) is a rare disease in which patients experience severe light sensitivity. It is caused by a deficiency of ferrochelatase (FECH), the last enzyme in heme biosynthesis (HBS). The lack of FECH causes accumulation of its photoreactive substrate protoporphyrin IX (PPIX) in patients' erythrocytes. Here, we explored an approach for the treatment of EPP by decreasing PPIX synthesis using small-molecule inhibitors directed to factors in the HBS pathway. We generated a FECH-knockout clone from K562 erythroleukemia cells, which accumulates PPIX and undergoes oxidative stress upon light exposure. We used these matched cell lines to screen a set of publicly available inhibitors of factors in the HBS pathway. Inhibitors of the glycine transporters GlyT1 and GlyT2 lowered levels of PPIX and markers of oxidative stress selectively in K56211B4 cells, and in primary erythroid cultures from an EPP patient. Our findings open the door to investigation of glycine transport inhibitors for HBS disorders.
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Affiliation(s)
- François Halloy
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Pavithra S Iyer
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Alice Ghidini
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Veronika Lysenko
- Department of Medical Oncology and Hematology, University Hospital and University of Zurich, 8091 Zurich, Switzerland
| | - Jasmin Barman-Aksözen
- Institute of Laboratory Medicine, Municipal Hospital Waid and Triemli, 8063 Zurich, Switzerland
| | - Chia-Pei Grubenmann
- Institute of Laboratory Medicine, Municipal Hospital Waid and Triemli, 8063 Zurich, Switzerland
| | - Jessica Jucker
- Institute of Laboratory Medicine, Municipal Hospital Waid and Triemli, 8063 Zurich, Switzerland
| | | | - Marc-David Ruepp
- UK Dementia Research Institute at King's College London, SE5 9RT London, UK; Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE5 8AF London, UK
| | - Elisabeth I Minder
- Department for Endocrinology, Diabetology, Porphyria, Municipal Hospital Waid and Triemli, 8063 Zurich, Switzerland
| | - Anna-Elisabeth Minder
- Department for Endocrinology, Diabetology, Porphyria, Municipal Hospital Waid and Triemli, 8063 Zurich, Switzerland
| | - Xiaoye Schneider-Yin
- Institute of Laboratory Medicine, Municipal Hospital Waid and Triemli, 8063 Zurich, Switzerland
| | - Alexandre P A Theocharides
- Department of Medical Oncology and Hematology, University Hospital and University of Zurich, 8091 Zurich, Switzerland
| | - Daniel Schümperli
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland.
| | - Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland.
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26
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Rosenberg M, Blum R, Kesner B, Aeby E, Garant JM, Szanto A, Lee JT. Motif-driven interactions between RNA and PRC2 are rheostats that regulate transcription elongation. Nat Struct Mol Biol 2021; 28:103-117. [PMID: 33398172 PMCID: PMC8050941 DOI: 10.1038/s41594-020-00535-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 10/20/2020] [Indexed: 01/30/2023]
Abstract
Although Polycomb repressive complex 2 (PRC2) is now recognized as an RNA-binding complex, the full range of binding motifs and why PRC2-RNA complexes often associate with active genes have not been elucidated. Here we identify high-affinity RNA motifs whose mutations weaken PRC2 binding and attenuate its repressive function in mouse embryonic stem cells. Interactions occur at promoter-proximal regions and frequently coincide with pausing of RNA Polymerase II (POL-II). Surprisingly, while PRC2-associated nascent transcripts are highly expressed, ablating PRC2 further upregulates expression via loss of pausing and enhanced transcription elongation. Thus, PRC2-nascent RNA complexes operate as rheostats to fine-tune transcription by regulating transitions between pausing and elongation, explaining why PRC2-RNA complexes frequently occur within active genes. Nascent RNA also targets PRC2 in cis and downregulates neighboring genes. We propose a unifying model in which RNA specifically recruits PRC2 to repress genes through POL-II pausing and, more classically, H3K27-trimethylation.
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Affiliation(s)
- Michael Rosenberg
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Roy Blum
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Barry Kesner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Eric Aeby
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jean-Michel Garant
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Attila Szanto
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA.
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27
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Abstract
Some long non-coding RNA (lncRNA) genes encode a functional RNA product, whereas others act as DNA elements or via the act of transcription . We describe here a ribozyme-based approach to deplete an endogenous lncRNA in mouse embryonic stem cells, with minimal disruption of its gene. This enables the role of the lncRNA product to be tested.
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Affiliation(s)
- Alex C Tuck
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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28
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Jutzi D, Campagne S, Schmidt R, Reber S, Mechtersheimer J, Gypas F, Schweingruber C, Colombo M, von Schroetter C, Loughlin FE, Devoy A, Hedlund E, Zavolan M, Allain FHT, Ruepp MD. Aberrant interaction of FUS with the U1 snRNA provides a molecular mechanism of FUS induced amyotrophic lateral sclerosis. Nat Commun 2020; 11:6341. [PMID: 33311468 PMCID: PMC7733473 DOI: 10.1038/s41467-020-20191-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022] Open
Abstract
Mutations in the RNA-binding protein Fused in Sarcoma (FUS) cause early-onset amyotrophic lateral sclerosis (ALS). However, a detailed understanding of central RNA targets of FUS and their implications for disease remain elusive. Here, we use a unique blend of crosslinking and immunoprecipitation (CLIP) and NMR spectroscopy to identify and characterise physiological and pathological RNA targets of FUS. We find that U1 snRNA is the primary RNA target of FUS via its interaction with stem-loop 3 and provide atomic details of this RNA-mediated mode of interaction with the U1 snRNP. Furthermore, we show that ALS-associated FUS aberrantly contacts U1 snRNA at the Sm site with its zinc finger and traps snRNP biogenesis intermediates in human and murine motor neurons. Altogether, we present molecular insights into a FUS toxic gain-of-function involving direct and aberrant RNA-binding and strengthen the link between two motor neuron diseases, ALS and spinal muscular atrophy (SMA).
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Affiliation(s)
- Daniel Jutzi
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Sébastien Campagne
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Ralf Schmidt
- Computational and Systems Biology, Biozentrum, University of Basel, CH-4056, Basel, Switzerland
| | - Stefan Reber
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Jonas Mechtersheimer
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Foivos Gypas
- Computational and Systems Biology, Biozentrum, University of Basel, CH-4056, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, CH-4058, Basel, Switzerland
| | | | - Martino Colombo
- Celgene Institute of Translational Research (CITRE), 41092, Seville, Spain
| | - Christine von Schroetter
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Fionna E Loughlin
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, CH-8093, Zürich, Switzerland
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Anny Devoy
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK
| | - Eva Hedlund
- Department of Neuroscience, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, CH-4056, Basel, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, CH-8093, Zürich, Switzerland.
| | - Marc-David Ruepp
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, UK.
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Glousker G, Briod A, Quadroni M, Lingner J. Human shelterin protein POT1 prevents severe telomere instability induced by homology-directed DNA repair. EMBO J 2020; 39:e104500. [PMID: 33073402 PMCID: PMC7705456 DOI: 10.15252/embj.2020104500] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 01/05/2023] Open
Abstract
The evolutionarily conserved POT1 protein binds single-stranded G-rich telomeric DNA and has been implicated in contributing to telomeric DNA maintenance and the suppression of DNA damage checkpoint signaling. Here, we explore human POT1 function through genetics and proteomics, discovering that a complete absence of POT1 leads to severe telomere maintenance defects that had not been anticipated from previous depletion studies in human cells. Conditional deletion of POT1 in HEK293E cells gives rise to rapid telomere elongation and length heterogeneity, branched telomeric DNA structures, telomeric R-loops, and telomere fragility. We determine the telomeric proteome upon POT1-loss, implementing an improved telomeric chromatin isolation protocol. We identify a large set of proteins involved in nucleic acid metabolism that engage with telomeres upon POT1-loss. Inactivation of the homology-directed repair machinery suppresses POT1-loss-mediated telomeric DNA defects. Our results unravel as major function of human POT1 the suppression of telomere instability induced by homology-directed repair.
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Affiliation(s)
- Galina Glousker
- School of Life SciencesSwiss Institute for Experimental Cancer Research (ISREC)Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Anna‐Sophia Briod
- School of Life SciencesSwiss Institute for Experimental Cancer Research (ISREC)Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | | | - Joachim Lingner
- School of Life SciencesSwiss Institute for Experimental Cancer Research (ISREC)Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
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30
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RNA nucleation by MSL2 induces selective X chromosome compartmentalization. Nature 2020; 589:137-142. [PMID: 33208948 DOI: 10.1038/s41586-020-2935-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/04/2020] [Indexed: 12/22/2022]
Abstract
Confinement of the X chromosome to a territory for dosage compensation is a prime example of how subnuclear compartmentalization is used to regulate transcription at the megabase scale. In Drosophila melanogaster, two sex-specific non-coding RNAs (roX1 and roX2) are transcribed from the X chromosome. They associate with the male-specific lethal (MSL) complex1, which acetylates histone H4 lysine 16 and thereby induces an approximately twofold increase in expression of male X-linked genes2,3. Current models suggest that X-over-autosome specificity is achieved by the recognition of cis-regulatory DNA high-affinity sites (HAS) by the MSL2 subunit4,5. However, HAS motifs are also found on autosomes, indicating that additional factors must stabilize the association of the MSL complex with the X chromosome. Here we show that the low-complexity C-terminal domain (CTD) of MSL2 renders its recruitment to the X chromosome sensitive to roX non-coding RNAs. roX non-coding RNAs and the MSL2 CTD form a stably condensed state, and functional analyses in Drosophila and mammalian cells show that their interactions are crucial for dosage compensation in vivo. Replacing the CTD of mammalian MSL2 with that from Drosophila and expressing roX in cis is sufficient to nucleate ectopic dosage compensation in mammalian cells. Thus, the condensing nature of roX-MSL2CTD is the primary determinant for specific compartmentalization of the X chromosome in Drosophila.
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31
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Aeby E, Lee HG, Lee YW, Kriz A, Del Rosario BC, Oh HJ, Boukhali M, Haas W, Lee JT. Decapping enzyme 1A breaks X-chromosome symmetry by controlling Tsix elongation and RNA turnover. Nat Cell Biol 2020; 22:1116-1129. [PMID: 32807903 PMCID: PMC12082808 DOI: 10.1038/s41556-020-0558-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/09/2020] [Indexed: 12/27/2022]
Abstract
How allelic asymmetry is generated remains a major unsolved problem in epigenetics. Here we model the problem using X-chromosome inactivation by developing "BioRBP", an enzymatic RNA-proteomic method that enables probing of low-abundance interactions and an allelic RNA-depletion and -tagging system. We identify messenger RNA-decapping enzyme 1A (DCP1A) as a key regulator of Tsix, a noncoding RNA implicated in allelic choice through X-chromosome pairing. DCP1A controls Tsix half-life and transcription elongation. Depleting DCP1A causes accumulation of X-X pairs and perturbs the transition to monoallelic Tsix expression required for Xist upregulation. While ablating DCP1A causes hyperpairing, forcing Tsix degradation resolves pairing and enables Xist upregulation. We link pairing to allelic partitioning of CCCTC-binding factor (CTCF) and show that tethering DCP1A to one Tsix allele is sufficient to drive monoallelic Xist expression. Thus, DCP1A flips a bistable switch for the mutually exclusive determination of active and inactive Xs.
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Affiliation(s)
- Eric Aeby
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Hun-Goo Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Yong-Woo Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Andrea Kriz
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Brian C Del Rosario
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Hyun Jung Oh
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Myriam Boukhali
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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32
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Jain Goyal M, Zhao X, Bozhinova M, Andrade-López K, de Heus C, Schulze-Dramac S, Müller-McNicoll M, Klumperman J, Béthune J. A paralog-specific role of COPI vesicles in the neuronal differentiation of mouse pluripotent cells. Life Sci Alliance 2020; 3:3/9/e202000714. [PMID: 32665377 PMCID: PMC7368096 DOI: 10.26508/lsa.202000714] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 12/03/2022] Open
Abstract
The paralogous COPI coat subunit γ1-COP plays a unique role in promoting neurite outgrowth during the neuronal differentiation of mouse pluripotent cells. Coat protein complex I (COPI)–coated vesicles mediate membrane trafficking between Golgi cisternae as well as retrieval of proteins from the Golgi to the endoplasmic reticulum. There are several flavors of the COPI coat defined by paralogous subunits of the protein complex coatomer. However, whether paralogous COPI proteins have specific functions is currently unknown. Here, we show that the paralogous coatomer subunits γ1-COP and γ2-COP are differentially expressed during the neuronal differentiation of mouse pluripotent cells. Moreover, through a combination of genome editing experiments, we demonstrate that whereas γ-COP paralogs are largely functionally redundant, γ1-COP specifically promotes neurite outgrowth. Our work stresses a role of the COPI pathway in neuronal polarization and provides evidence for distinct functions for coatomer paralogous subunits in this process.
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Affiliation(s)
- Manu Jain Goyal
- Junior Research Group, Cluster of Excellence CellNetworks, Heidelberg, Germany.,Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Xiyan Zhao
- Junior Research Group, Cluster of Excellence CellNetworks, Heidelberg, Germany.,Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Mariya Bozhinova
- Junior Research Group, Cluster of Excellence CellNetworks, Heidelberg, Germany.,Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Karla Andrade-López
- Junior Research Group, Cluster of Excellence CellNetworks, Heidelberg, Germany.,Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Cecilia de Heus
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Sandra Schulze-Dramac
- RNA Regulation Group, Cluster of Excellence "Macromolecular Complexes," Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Michaela Müller-McNicoll
- RNA Regulation Group, Cluster of Excellence "Macromolecular Complexes," Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Julien Béthune
- Junior Research Group, Cluster of Excellence CellNetworks, Heidelberg, Germany .,Heidelberg University Biochemistry Center, Heidelberg, Germany
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33
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Li X, Pritykin Y, Concepcion CP, Lu Y, La Rocca G, Zhang M, King B, Cook PJ, Au YW, Popow O, Paulo JA, Otis HG, Mastroleo C, Ogrodowski P, Schreiner R, Haigis KM, Betel D, Leslie CS, Ventura A. High-Resolution In Vivo Identification of miRNA Targets by Halo-Enhanced Ago2 Pull-Down. Mol Cell 2020; 79:167-179.e11. [PMID: 32497496 DOI: 10.1016/j.molcel.2020.05.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 03/18/2020] [Accepted: 05/06/2020] [Indexed: 12/19/2022]
Abstract
The identification of microRNA (miRNA) targets by Ago2 crosslinking-immunoprecipitation (CLIP) methods has provided major insights into the biology of this important class of non-coding RNAs. However, these methods are technically challenging and not easily applicable to an in vivo setting. To overcome these limitations and facilitate the investigation of miRNA functions in vivo, we have developed a method based on a genetically engineered mouse harboring a conditional Halo-Ago2 allele expressed from the endogenous Ago2 locus. By using a resin conjugated to the HaloTag ligand, Ago2-miRNA-mRNA complexes can be purified from cells and tissues expressing the endogenous Halo-Ago2 allele. We demonstrate the reproducibility and sensitivity of this method in mouse embryonic stem cells, developing embryos, adult tissues, and autochthonous mouse models of human brain and lung cancers. This method and the datasets we have generated will facilitate the characterization of miRNA-mRNA networks in vivo under physiological and pathological conditions.
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Affiliation(s)
- Xiaoyi Li
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yuri Pritykin
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Carla P Concepcion
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yuheng Lu
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Gaspare La Rocca
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Minsi Zhang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Bryan King
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Peter J Cook
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Yu Wah Au
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Internal Medicine (Nephrology), Leiden University Medical Center, Zuid-Holland, 2333 ZA, the Netherlands
| | - Olesja Popow
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hannah G Otis
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY 10065, USA
| | - Chiara Mastroleo
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Paul Ogrodowski
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ryan Schreiner
- Margaret Dyson Vision Research Institute, Department of Ophthalmology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Kevin M Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Doron Betel
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA; Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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34
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Bracher L, Ferro I, Pulido-Quetglas C, Ruepp MD, Johnson R, Polacek N. Human vtRNA1-1 Levels Modulate Signaling Pathways and Regulate Apoptosis in Human Cancer Cells. Biomolecules 2020; 10:biom10040614. [PMID: 32316166 PMCID: PMC7226377 DOI: 10.3390/biom10040614] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/06/2020] [Accepted: 04/14/2020] [Indexed: 12/17/2022] Open
Abstract
Regulatory non-protein coding RNAs perform a remarkable variety of complex biological functions. Previously, we demonstrated a role of the human non-coding vault RNA1-1 (vtRNA1-1) in inhibiting intrinsic and extrinsic apoptosis in several cancer cell lines. Yet on the molecular level, the function of the vtRNA1-1 is still not fully clear. Here, we created HeLa knock-out cell lines revealing that prolonged starvation triggers elevated levels of apoptosis in the absence of vtRNA1-1 but not in vtRNA1-3 knock-out cells. Next-generation deep sequencing of the mRNome identified the PI3K/Akt pathway and the ERK1/2 MAPK cascade, two prominent signaling axes, to be misregulated in the absence of vtRNA1-1 during starvation-mediated cell death conditions. Expression of vtRNA1-1 mutants identified a short stretch of 24 nucleotides of the vtRNA1-1 central domain as being essential for successful maintenance of apoptosis resistance. This study describes a cell signaling-dependent contribution of the human vtRNA1-1 to starvation-induced programmed cell death.
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Affiliation(s)
- Lisamaria Bracher
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland; (L.B.); (I.F.); (M.-D.R.)
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland;
| | - Iolanda Ferro
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland; (L.B.); (I.F.); (M.-D.R.)
| | - Carlos Pulido-Quetglas
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland;
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland;
- Department of BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland; (L.B.); (I.F.); (M.-D.R.)
- United Kingdom Dementia Research Institute, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, London SE5 9NU, UK
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland;
- Department of BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Norbert Polacek
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland; (L.B.); (I.F.); (M.-D.R.)
- Correspondence:
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35
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Tan L, Hu Y, Li Y, Yang L, Cai X, Liu W, He J, Wu Y, Liu T, Wang N, Yang Y, Adelstein RS, Wang A. Investigation of the molecular biology underlying the pronounced high gene targeting frequency at the Myh9 gene locus in mouse embryonic stem cells. PLoS One 2020; 15:e0230126. [PMID: 32226034 PMCID: PMC7105122 DOI: 10.1371/journal.pone.0230126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 02/23/2020] [Indexed: 11/21/2022] Open
Abstract
The generation of genetically modified mouse models derived from gene targeting (GT) in mouse embryonic stem (ES) cells (mESCs) has greatly advanced both basic and clinical research. Our previous finding that gene targeting at the Myh9 exon2 site in mESCs has a pronounced high homologous recombination (HR) efficiency (>90%) has facilitated the generation of a series of nonmuscle myosin II (NM II) related mouse models. Furthermore, the Myh9 gene locus has been well demonstrated to be a new safe harbor for site-specific insertion of other exogenous genes. In the current study, we intend to investigate the molecular biology underlying for this high HR efficiency from other aspects. Our results confirmed some previously characterized properties and revealed some unreported observations: 1) The comparison and analysis of the targeting events occurring at the Myh9 and several widely used loci for targeting transgenesis, including ColA1, HPRT, ROSA26, and the sequences utilized for generating these targeting constructs, indicated that a total length about 6 kb with approximate 50% GC-content of the 5’ and 3’ homologous arms, may facilitate a better performance in terms of GT efficiency. 2) Despite increasing the length of the homologous arms, shifting the targeting site from the Myh9 exon2, to intron2, or exon3 led to a gradually reduced GT frequency (91.7, 71.8 and 50.0%, respectively). This finding provides the first evidence that the HR frequency may also be associated with the targeting site even in the same locus. Meanwhile, the decreased trend of the GT efficiency at these targeting sites was consistent with the reduced percentage of simple sequence repeat (SSR) and short interspersed nuclear elements (SINEs) in the sequences for generating the targeting constructs, suggesting the potential effects of these DNA elements on GT efficiency; 3) Our series of targeting experiments and analyses with truncated 5’ and 3’ arms at the Myh9 exon2 site demonstrated that GT efficiency positively correlates with the total length of the homologous arms (R = 0.7256, p<0.01), confirmed that a 2:1 ratio of the length, a 50% GC-content and the higher amount of SINEs for the 5’ and 3’ arms may benefit for appreciable GT frequency. Though more investigations are required, the Myh9 gene locus appears to be an ideal location for identifying HR-related cis and trans factors, which in turn provide mechanistic insights and also facilitate the practical application of gene editing.
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Affiliation(s)
- Lei Tan
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Yi Hu
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Yalan Li
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Lingchen Yang
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Xiong Cai
- Institute of Innovation and Applied Research in Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Wei Liu
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Jiayi He
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Yingxin Wu
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Tanbin Liu
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
| | - Naidong Wang
- Laboratory of Functional Proteomics (LFP), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, HUNAU, Changsha, Hunan, China
| | - Yi Yang
- Laboratory of Functional Proteomics (LFP), The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, HUNAU, Changsha, Hunan, China
| | - Robert S. Adelstein
- Laboratory of Molecular Cardiology (LMC), NHLBI/NIH, Bethesda, MD, United States of America
| | - Aibing Wang
- Laboratory of Animal Disease Prevention & Control and Animal Model, The Key Laboratory of Animal Vaccine & Protein Engineering, College of Veterinary Medicine, Hunan Agricultural University (HUNAU), Changsha, Hunan, China
- Laboratory of Molecular Cardiology (LMC), NHLBI/NIH, Bethesda, MD, United States of America
- * E-mail:
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36
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Tuck AC, Rankova A, Arpat AB, Liechti LA, Hess D, Iesmantavicius V, Castelo-Szekely V, Gatfield D, Bühler M. Mammalian RNA Decay Pathways Are Highly Specialized and Widely Linked to Translation. Mol Cell 2020; 77:1222-1236.e13. [PMID: 32048998 PMCID: PMC7083229 DOI: 10.1016/j.molcel.2020.01.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/11/2019] [Accepted: 01/07/2020] [Indexed: 12/24/2022]
Abstract
RNA decay is crucial for mRNA turnover and surveillance and misregulated in many diseases. This complex system is challenging to study, particularly in mammals, where it remains unclear whether decay pathways perform specialized versus redundant roles. Cytoplasmic pathways and links to translation are particularly enigmatic. By directly profiling decay factor targets and normal versus aberrant translation in mouse embryonic stem cells (mESCs), we uncovered extensive decay pathway specialization and crosstalk with translation. XRN1 (5'-3') mediates cytoplasmic bulk mRNA turnover whereas SKIV2L (3'-5') is universally recruited by ribosomes, tackling aberrant translation and sometimes modulating mRNA abundance. Further exploring translation surveillance revealed AVEN and FOCAD as SKIV2L interactors. AVEN prevents ribosome stalls at structured regions, which otherwise require SKIV2L for clearance. This pathway is crucial for histone translation, upstream open reading frame (uORF) regulation, and counteracting ribosome arrest on small ORFs. In summary, we uncovered key targets, components, and functions of mammalian RNA decay pathways and extensive coupling to translation.
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Affiliation(s)
- Alex Charles Tuck
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Aneliya Rankova
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Alaaddin Bulak Arpat
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Luz Angelica Liechti
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Vytautas Iesmantavicius
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | | | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 10, 4003 Basel, Switzerland.
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37
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ChromID identifies the protein interactome at chromatin marks. Nat Biotechnol 2020; 38:728-736. [PMID: 32123383 PMCID: PMC7289633 DOI: 10.1038/s41587-020-0434-2] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/23/2020] [Indexed: 01/05/2023]
Abstract
Chromatin modifications regulate genome function by recruiting protein factors to the genome. However, the protein composition at distinct chromatin modifications remains to be fully characterized. Here, we use natural protein domains as modular building blocks to develop engineered chromatin readers (eCRs) selective for DNA methylation and histone tri-methylation at H3K4, H3K9 a H3K27 residues. We first demonstrate their utility as selective chromatin binders in living cells by stably expressing eCRs in mouse embryonic stem cells and measuring their subnuclear localisation, genomic distribution and histone modification–binding preference. By fusing eCRs to the biotin ligase BASU, we establish ChromID, a method for identifying the chromatin-dependent protein interactome based on proximity biotinylation, and apply it to distinct chromatin modifications in mouse stem cells. Using a synthetic dual-modification reader, we also uncover the protein composition at bivalent promoters marked by H3K4me3 and H3K27me3. These results highlight the ability of ChromID to obtain a detailed view of protein interaction networks on chromatin.
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38
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Welte T, Tuck AC, Papasaikas P, Carl SH, Flemr M, Knuckles P, Rankova A, Bühler M, Großhans H. The RNA hairpin binder TRIM71 modulates alternative splicing by repressing MBNL1. Genes Dev 2019; 33:1221-1235. [PMID: 31371437 PMCID: PMC6719626 DOI: 10.1101/gad.328492.119] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/19/2019] [Indexed: 01/19/2023]
Abstract
In this study, Welte et al. investigated the dual roles of mammalian TRIM71, a phylogenetically conserved regulator of development, in the control of stem cell fate. They demonstrate that TRIM71 shapes the transcriptome of mESCs predominantly through its RNA-binding activity and identify a set of primary targets consistently regulated in various human and mouse cell lines, including MBNL1/Muscleblind. TRIM71/LIN-41, a phylogenetically conserved regulator of development, controls stem cell fates. Mammalian TRIM71 exhibits both RNA-binding and protein ubiquitylation activities, but the functional contribution of either activity and relevant primary targets remain poorly understood. Here, we demonstrate that TRIM71 shapes the transcriptome of mouse embryonic stem cells (mESCs) predominantly through its RNA-binding activity. We reveal that TRIM71 binds targets through 3′ untranslated region (UTR) hairpin motifs and that it acts predominantly by target degradation. TRIM71 mutations implicated in etiogenesis of human congenital hydrocephalus impair target silencing. We identify a set of primary targets consistently regulated in various human and mouse cell lines, including MBNL1 (Muscleblind-like protein 1). MBNL1 promotes cell differentiation through regulation of alternative splicing, and we demonstrate that TRIM71 promotes embryonic splicing patterns through MBNL1 repression. Hence, repression of MBNL1-dependent alternative splicing may contribute to TRIM71's function in regulating stem cell fates.
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Affiliation(s)
- Thomas Welte
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Alex C Tuck
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Panagiotis Papasaikas
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.,These authors contributed equally to this work
| | - Sarah H Carl
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.,These authors contributed equally to this work
| | - Matyas Flemr
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Philip Knuckles
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Aneliya Rankova
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, 4056 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, 4056 Basel, Switzerland
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, 4056 Basel, Switzerland
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39
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Regulation of Microtubule Nucleation in Mouse Bone Marrow-Derived Mast Cells by Protein Tyrosine Phosphatase SHP-1. Cells 2019; 8:cells8040345. [PMID: 30979083 PMCID: PMC6523986 DOI: 10.3390/cells8040345] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/30/2019] [Accepted: 04/10/2019] [Indexed: 12/20/2022] Open
Abstract
The antigen-mediated activation of mast cells initiates signaling events leading to their degranulation, to the release of inflammatory mediators, and to the synthesis of cytokines and chemokines. Although rapid and transient microtubule reorganization during activation has been described, the molecular mechanisms that control their rearrangement are largely unknown. Microtubule nucleation is mediated by γ-tubulin complexes. In this study, we report on the regulation of microtubule nucleation in bone marrow-derived mast cells (BMMCs) by Src homology 2 (SH2) domain-containing protein tyrosine phosphatase 1 (SHP-1; Ptpn6). Reciprocal immunoprecipitation experiments and pull-down assays revealed that SHP-1 is present in complexes containing γ-tubulin complex proteins and protein tyrosine kinase Syk. Microtubule regrowth experiments in cells with deleted SHP-1 showed a stimulation of microtubule nucleation, and phenotypic rescue experiments confirmed that SHP-1 represents a negative regulator of microtubule nucleation in BMMCs. Moreover, the inhibition of the SHP-1 activity by inhibitors TPI-1 and NSC87877 also augmented microtubule nucleation. The regulation was due to changes in γ-tubulin accumulation. Further experiments with antigen-activated cells showed that the deletion of SHP-1 stimulated the generation of microtubule protrusions, the activity of Syk kinase, and degranulation. Our data suggest a novel mechanism for the suppression of microtubule formation in the later stages of mast cell activation.
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40
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Villegas F, Lehalle D, Mayer D, Rittirsch M, Stadler MB, Zinner M, Olivieri D, Vabres P, Duplomb-Jego L, De Bont ESJM, Duffourd Y, Duijkers F, Avila M, Geneviève D, Houcinat N, Jouan T, Kuentz P, Lichtenbelt KD, Thauvin-Robinet C, St-Onge J, Thevenon J, van Gassen KLI, van Haelst M, van Koningsbruggen S, Hess D, Smallwood SA, Rivière JB, Faivre L, Betschinger J. Lysosomal Signaling Licenses Embryonic Stem Cell Differentiation via Inactivation of Tfe3. Cell Stem Cell 2018; 24:257-270.e8. [PMID: 30595499 DOI: 10.1016/j.stem.2018.11.021] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 09/21/2018] [Accepted: 11/20/2018] [Indexed: 12/31/2022]
Abstract
Self-renewal and differentiation of pluripotent murine embryonic stem cells (ESCs) is regulated by extrinsic signaling pathways. It is less clear whether cellular metabolism instructs developmental progression. In an unbiased genome-wide CRISPR/Cas9 screen, we identified components of a conserved amino-acid-sensing pathway as critical drivers of ESC differentiation. Functional analysis revealed that lysosome activity, the Ragulator protein complex, and the tumor-suppressor protein Folliculin enable the Rag GTPases C and D to bind and seclude the bHLH transcription factor Tfe3 in the cytoplasm. In contrast, ectopic nuclear Tfe3 represses specific developmental and metabolic transcriptional programs that are associated with peri-implantation development. We show differentiation-specific and non-canonical regulation of Rag GTPase in ESCs and, importantly, identify point mutations in a Tfe3 domain required for cytoplasmic inactivation as potentially causal for a human developmental disorder. Our work reveals an instructive and biomedically relevant role of metabolic signaling in licensing embryonic cell fate transitions.
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Affiliation(s)
- Florian Villegas
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4003 Basel, Switzerland
| | - Daphné Lehalle
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon et Université de Bourgogne, 21079 Dijon, France; Equipe GAD, INSERM LNC UMR 1231, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - Daniela Mayer
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4003 Basel, Switzerland
| | - Melanie Rittirsch
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Marietta Zinner
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4003 Basel, Switzerland
| | - Daniel Olivieri
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Pierre Vabres
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon et Université de Bourgogne, 21079 Dijon, France; Equipe GAD, INSERM LNC UMR 1231, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France; Département de Dermatologie, CHU Dijon, Dijon, France
| | - Laurence Duplomb-Jego
- Equipe GAD, INSERM LNC UMR 1231, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - Eveline S J M De Bont
- Department of Pediatric Oncology/Hematology, Beatrix Children's Hospital, University Medical Centre Groningen, Groningen, the Netherlands
| | - Yannis Duffourd
- Equipe GAD, INSERM LNC UMR 1231, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - Floor Duijkers
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Magali Avila
- Equipe GAD, INSERM LNC UMR 1231, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - David Geneviève
- Department of Clinical Genetics, University Medical Centre Montpellier, Montpellier, France
| | - Nada Houcinat
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon et Université de Bourgogne, 21079 Dijon, France; Equipe GAD, INSERM LNC UMR 1231, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - Thibaud Jouan
- Equipe GAD, INSERM LNC UMR 1231, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - Paul Kuentz
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon et Université de Bourgogne, 21079 Dijon, France; Equipe GAD, INSERM LNC UMR 1231, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - Klaske D Lichtenbelt
- Department of Genetics, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands
| | - Christel Thauvin-Robinet
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon et Université de Bourgogne, 21079 Dijon, France; Equipe GAD, INSERM LNC UMR 1231, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - Judith St-Onge
- Equipe GAD, INSERM LNC UMR 1231, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France; Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Julien Thevenon
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon et Université de Bourgogne, 21079 Dijon, France; Equipe GAD, INSERM LNC UMR 1231, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht (UMCU), Utrecht, the Netherlands
| | - Mieke van Haelst
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | | | - Jean-Baptiste Rivière
- Equipe GAD, INSERM LNC UMR 1231, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France; Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada; Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC H3A 1B1, Canada
| | - Laurence Faivre
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon et Université de Bourgogne, 21079 Dijon, France; Equipe GAD, INSERM LNC UMR 1231, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - Joerg Betschinger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
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41
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Facultative dosage compensation of developmental genes on autosomes in Drosophila and mouse embryonic stem cells. Nat Commun 2018; 9:3626. [PMID: 30194291 PMCID: PMC6128902 DOI: 10.1038/s41467-018-05642-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/04/2018] [Indexed: 12/25/2022] Open
Abstract
Haploinsufficiency and aneuploidy are two phenomena, where gene dosage alterations cause severe defects ultimately resulting in developmental failures and disease. One remarkable exception is the X chromosome, where copy number differences between sexes are buffered by dosage compensation systems. In Drosophila, the Male-Specific Lethal complex (MSLc) mediates upregulation of the single male X chromosome. The evolutionary origin and conservation of this process orchestrated by MSL2, the only male-specific protein within the fly MSLc, have remained unclear. Here, we report that MSL2, in addition to regulating the X chromosome, targets autosomal genes involved in patterning and morphogenesis. Precise regulation of these genes by MSL2 is required for proper development. This set of dosage-sensitive genes maintains such regulation during evolution, as MSL2 binds and similarly regulates mouse orthologues via Histone H4 lysine 16 acetylation. We propose that this gene-by-gene dosage compensation mechanism was co-opted during evolution for chromosome-wide regulation of the Drosophila male X. In Drosophila the Male-Specific Lethal complex (MSLc) mediates upregulation of the single male X chromosome. Here the authors provide evidence that MSL2 also targets autosomal genes required for proper development and that MSL2 binds and similarly regulates mouse orthologues.
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42
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Ren C, Xu K, Segal DJ, Zhang Z. Strategies for the Enrichment and Selection of Genetically Modified Cells. Trends Biotechnol 2018; 37:56-71. [PMID: 30135027 DOI: 10.1016/j.tibtech.2018.07.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 02/06/2023]
Abstract
Programmable artificial nucleases have transitioned over the past decade from ZFNs and TALENs to CRISPR/Cas systems, which have been ubiquitously used with great success to modify genomes. The efficiencies of knockout and knockin vary widely among distinct cell types and genomic loci and depend on the nuclease delivery and cleavage efficiencies. Moreover, genetically modified cells are almost phenotypically indistinguishable from normal counterparts, making screening and isolating positive cells rather challenging and time-consuming. To address this issue, we review several strategies for the enrichment and selection of genetically modified cells, including transfection-positive selection, nuclease-positive selection, genome-targeted positive selection, and knockin-positive selection, to provide a reference for future genome research and gene therapy studies.
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Affiliation(s)
- Chonghua Ren
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China; College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China; Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA; These authors contributed equally to this article
| | - Kun Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China; These authors contributed equally to this article
| | - David Jay Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Zhiying Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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43
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Tuck AC, Natarajan KN, Rice GM, Borawski J, Mohn F, Rankova A, Flemr M, Wenger A, Nutiu R, Teichmann S, Bühler M. Distinctive features of lincRNA gene expression suggest widespread RNA-independent functions. Life Sci Alliance 2018; 1:e201800124. [PMID: 30456373 PMCID: PMC6238598 DOI: 10.26508/lsa.201800124] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 07/13/2018] [Accepted: 07/13/2018] [Indexed: 02/06/2023] Open
Abstract
Eukaryotic genomes produce RNAs lacking protein-coding potential, with enigmatic roles. We integrated three approaches to study large intervening noncoding RNA (lincRNA) gene functions. First, we profiled mouse embryonic stem cells and neural precursor cells at single-cell resolution, revealing lincRNAs expressed in specific cell types, cell subpopulations, or cell cycle stages. Second, we assembled a transcriptome-wide atlas of nuclear lincRNA degradation by identifying targets of the exosome cofactor Mtr4. Third, we developed a reversible depletion system to separate the role of a lincRNA gene from that of its RNA. Our approach distinguished lincRNA loci functioning in trans from those modulating local gene expression. Some genes express stable and/or abundant lincRNAs in single cells, but many prematurely terminate transcription and produce lincRNAs rapidly degraded by the nuclear exosome. This suggests that besides RNA-dependent functions, lincRNA loci act as DNA elements or through transcription. Our integrative approach helps distinguish these mechanisms.
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Affiliation(s)
- Alex C Tuck
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Kedar Nath Natarajan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Danish Institute of Advanced Study and Functional Genomics and Metabolism Unit, University of Southern Denmark, Denmark
| | - Greggory M Rice
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jason Borawski
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Fabio Mohn
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Aneliya Rankova
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Matyas Flemr
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Alice Wenger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Razvan Nutiu
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Sarah Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
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44
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Gu T, Lin X, Cullen SM, Luo M, Jeong M, Estecio M, Shen J, Hardikar S, Sun D, Su J, Rux D, Guzman A, Lee M, Qi LS, Chen JJ, Kyba M, Huang Y, Chen T, Li W, Goodell MA. DNMT3A and TET1 cooperate to regulate promoter epigenetic landscapes in mouse embryonic stem cells. Genome Biol 2018; 19:88. [PMID: 30001199 PMCID: PMC6042404 DOI: 10.1186/s13059-018-1464-7] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 06/15/2018] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND DNA methylation is a heritable epigenetic mark, enabling stable but reversible gene repression. In mammalian cells, DNA methyltransferases (DNMTs) are responsible for modifying cytosine to 5-methylcytosine (5mC), which can be further oxidized by the TET dioxygenases to ultimately cause DNA demethylation. However, the genome-wide cooperation and functions of these two families of proteins, especially at large under-methylated regions, called canyons, remain largely unknown. RESULTS Here we demonstrate that DNMT3A and TET1 function in a complementary and competitive manner in mouse embryonic stem cells to mediate proper epigenetic landscapes and gene expression. The longer isoform of DNMT3A, DNMT3A1, exhibits significant enrichment at distal promoters and canyon edges, but is excluded from proximal promoters and canyons where TET1 shows prominent binding. Deletion of Tet1 increases DNMT3A1 binding capacity at and around genes with wild-type TET1 binding. However, deletion of Dnmt3a has a minor effect on TET1 binding on chromatin, indicating that TET1 may limit DNA methylation partially by protecting its targets from DNMT3A and establishing boundaries for DNA methylation. Local CpG density may determine their complementary binding patterns and therefore that the methylation landscape is encoded in the DNA sequence. Furthermore, DNMT3A and TET1 impact histone modifications which in turn regulate gene expression. In particular, they regulate Polycomb Repressive Complex 2 (PRC2)-mediated H3K27me3 enrichment to constrain gene expression from bivalent promoters. CONCLUSIONS We conclude that DNMT3A and TET1 regulate the epigenome and gene expression at specific targets via their functional interplay.
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Affiliation(s)
- Tianpeng Gu
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xueqiu Lin
- Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Sean M Cullen
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Min Luo
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mira Jeong
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Marcos Estecio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Swanand Hardikar
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Deqiang Sun
- Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Jianzhong Su
- Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Danielle Rux
- Lillehei Heart Institute and Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Anna Guzman
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Minjung Lee
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Lei Stanley Qi
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Jia-Jia Chen
- Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Michael Kyba
- Lillehei Heart Institute and Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Wei Li
- Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
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45
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Baliou S, Adamaki M, Kyriakopoulos AM, Spandidos DA, Panayiotidis M, Christodoulou I, Zoumpourlis V. CRISPR therapeutic tools for complex genetic disorders and cancer (Review). Int J Oncol 2018; 53:443-468. [PMID: 29901119 PMCID: PMC6017271 DOI: 10.3892/ijo.2018.4434] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/18/2018] [Indexed: 12/13/2022] Open
Abstract
One of the fundamental discoveries in the field of biology is the ability to modulate the genome and to monitor the functional outputs derived from genomic alterations. In order to unravel new therapeutic options, scientists had initially focused on inducing genetic alterations in primary cells, in established cancer cell lines and mouse models using either RNA interference or cDNA overexpression or various programmable nucleases [zinc finger nucleases (ZNF), transcription activator-like effector nucleases (TALEN)]. Even though a huge volume of data was produced, its use was neither cheap nor accurate. Therefore, the clustered regularly interspaced short palindromic repeats (CRISPR) system was evidenced to be the next step in genome engineering tools. CRISPR-associated protein 9 (Cas9)-mediated genetic perturbation is simple, precise and highly efficient, empowering researchers to apply this method to immortalized cancerous cell lines, primary cells derived from mouse and human origins, xenografts, induced pluripotent stem cells, organoid cultures, as well as the generation of genetically engineered animal models. In this review, we assess the development of the CRISPR system and its therapeutic applications to a wide range of complex diseases (particularly distinct tumors), aiming at personalized therapy. Special emphasis is given to organoids and CRISPR screens in the design of innovative therapeutic approaches. Overall, the CRISPR system is regarded as an eminent genome engineering tool in therapeutics. We envision a new era in cancer biology during which the CRISPR-based genome engineering toolbox will serve as the fundamental conduit between the bench and the bedside; nonetheless, certain obstacles need to be addressed, such as the eradication of side-effects, maximization of efficiency, the assurance of delivery and the elimination of immunogenicity.
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Affiliation(s)
- Stella Baliou
- National Hellenic Research Foundation, 11635 Athens, Greece
| | - Maria Adamaki
- National Hellenic Research Foundation, 11635 Athens, Greece
| | | | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion 71003, Greece
| | - Mihalis Panayiotidis
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, NE1 8ST, UK
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46
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Activity-dependent neuroprotective protein recruits HP1 and CHD4 to control lineage-specifying genes. Nature 2018; 557:739-743. [PMID: 29795351 DOI: 10.1038/s41586-018-0153-8] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 04/13/2018] [Indexed: 01/18/2023]
Abstract
De novo mutations in ADNP, which encodes activity-dependent neuroprotective protein (ADNP), have recently been found to underlie Helsmoortel-Van der Aa syndrome, a complex neurological developmental disorder that also affects several other organ functions 1 . ADNP is a putative transcription factor that is essential for embryonic development 2 . However, its precise roles in transcriptional regulation and development are not understood. Here we show that ADNP interacts with the chromatin remodeller CHD4 and the chromatin architectural protein HP1 to form a stable complex, which we refer to as ChAHP. Besides mediating complex assembly, ADNP recognizes DNA motifs that specify binding of ChAHP to euchromatin. Genetic ablation of ChAHP components in mouse embryonic stem cells results in spontaneous differentiation concomitant with premature activation of lineage-specific genes and in a failure to differentiate towards the neuronal lineage. Molecularly, ChAHP-mediated repression is fundamentally different from canonical HP1-mediated silencing: HP1 proteins, in conjunction with histone H3 lysine 9 trimethylation (H3K9me3), are thought to assemble broad heterochromatin domains that are refractory to transcription. ChAHP-mediated repression, however, acts in a locally restricted manner by establishing inaccessible chromatin around its DNA-binding sites and does not depend on H3K9me3-modified nucleosomes. Together, our results reveal that ADNP, via the recruitment of HP1 and CHD4, regulates the expression of genes that are crucial for maintaining distinct cellular states and assures accurate cell fate decisions upon external cues. Such a general role of ChAHP in governing cell fate plasticity may explain why ADNP mutations affect several organs and body functions and contribute to cancer progression1,3,4. Notably, we found that the integrity of the ChAHP complex is disrupted by nonsense mutations identified in patients with Helsmoortel-Van der Aa syndrome, and this could be rescued by aminoglycosides that suppress translation termination 5 . Therefore, patients might benefit from therapeutic agents that are being developed to promote ribosomal read-through of premature stop codons6,7.
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47
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Knuckles P, Lence T, Haussmann IU, Jacob D, Kreim N, Carl SH, Masiello I, Hares T, Villaseñor R, Hess D, Andrade-Navarro MA, Biggiogera M, Helm M, Soller M, Bühler M, Roignant JY. Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m 6A machinery component Wtap/Fl(2)d. Genes Dev 2018. [PMID: 29535189 PMCID: PMC5900714 DOI: 10.1101/gad.309146.117] [Citation(s) in RCA: 439] [Impact Index Per Article: 62.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
In this study, Knuckles et al. identified Flacc/Zc3h13 as a novel interactor of m6A methyltransferase complex components in Drosophila and mice. They show that Flacc promotes the recruitment of the methyltransferase to mRNA by bridging Fl(2)d to the mRNA-binding factor Nito, providing novel insights into the conservation and regulation of the m6A machinery. N6-methyladenosine (m6A) is the most abundant mRNA modification in eukaryotes, playing crucial roles in multiple biological processes. m6A is catalyzed by the activity of methyltransferase-like 3 (Mettl3), which depends on additional proteins whose precise functions remain poorly understood. Here we identified Zc3h13 (zinc finger CCCH domain-containing protein 13)/Flacc [Fl(2)d-associated complex component] as a novel interactor of m6A methyltransferase complex components in Drosophila and mice. Like other components of this complex, Flacc controls m6A levels and is involved in sex determination in Drosophila. We demonstrate that Flacc promotes m6A deposition by bridging Fl(2)d to the mRNA-binding factor Nito. Altogether, our work advances the molecular understanding of conservation and regulation of the m6A machinery.
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Affiliation(s)
- Philip Knuckles
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, Basel 4002, Switzerland
| | - Tina Lence
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Irmgard U Haussmann
- School of Life Science, Faculty of Health and Life Sciences, Coventry University, Coventry CV1 5FB, United Kingdom.,School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Dominik Jacob
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Nastasja Kreim
- Bioinformatics Core Facility, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Sarah H Carl
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel 4058, Switzerland
| | - Irene Masiello
- Institute of Molecular Biology, 55128 Mainz, Germany.,Laboratory of Cell Biology and Neurobiology, Department of Animal Biology, University of Pavia, Pavia 27100, Italy
| | - Tina Hares
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Rodrigo Villaseñor
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, Basel 4002, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Miguel A Andrade-Navarro
- Institute of Molecular Biology, 55128 Mainz, Germany.,Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Marco Biggiogera
- Laboratory of Cell Biology and Neurobiology, Department of Animal Biology, University of Pavia, Pavia 27100, Italy
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Matthias Soller
- School of Life Science, Faculty of Health and Life Sciences, Coventry University, Coventry CV1 5FB, United Kingdom
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, Basel 4002, Switzerland
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48
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Manzo M, Ambrosi C, Baubec T. Genome-Wide Profiling of DNA Methyltransferases in Mammalian Cells. Methods Mol Biol 2018; 1766:157-174. [PMID: 29605852 PMCID: PMC7611273 DOI: 10.1007/978-1-4939-7768-0_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is currently the method of choice to determine binding sites of chromatin-associated factors in a genome-wide manner. Here, we describe a method to investigate the binding preferences of mammalian DNA methyltransferases (DNMT) based on ChIP-seq using biotin-tagging. Stringent ChIP of DNMT proteins based on the strong interaction between biotin and avidin circumvents limitations arising from low antibody specificity and ensures reproducible enrichment. DNMT-bound DNA fragments are ligated to sequencing adaptors, amplified and sequenced on a high-throughput sequencing instrument. Bioinformatic analysis gives valuable information about the binding preferences of DNMTs genome-wide and around promoter regions. This method is unconventional due to the use of genetically engineered cells; however, it allows specific and reliable determination of DNMT binding.
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Affiliation(s)
- Massimiliano Manzo
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland,Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich, 8057, Zurich, Switzerland
| | - Christina Ambrosi
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland,Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich, 8057, Zurich, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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49
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Reber S, Mechtersheimer J, Nasif S, Benitez JA, Colombo M, Domanski M, Jutzi D, Hedlund E, Ruepp MD. CRISPR-Trap: a clean approach for the generation of gene knockouts and gene replacements in human cells. Mol Biol Cell 2017; 29:75-83. [PMID: 29167381 PMCID: PMC5909934 DOI: 10.1091/mbc.e17-05-0288] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/27/2017] [Accepted: 11/16/2017] [Indexed: 01/08/2023] Open
Abstract
CRISPR/Cas9-based genome editing offers the possibility to knock out almost any gene of interest in an affordable and simple manner. The most common strategy is the introduction of a frameshift into the open reading frame (ORF) of the target gene which truncates the coding sequence (CDS) and targets the corresponding transcript for degradation by nonsense-mediated mRNA decay (NMD). However, we show that transcripts containing premature termination codons (PTCs) are not always degraded efficiently and can generate C-terminally truncated proteins which might have residual or dominant negative functions. Therefore, we recommend an alternative approach for knocking out genes, which combines CRISPR/Cas9 with gene traps (CRISPR-Trap) and is applicable to ∼50% of all spliced human protein-coding genes and a large subset of lncRNAs. CRISPR-Trap completely prevents the expression of the ORF and avoids expression of C-terminal truncated proteins. We demonstrate the feasibility of CRISPR-Trap by utilizing it to knock out several genes in different human cell lines. Finally, we also show that this approach can be used to efficiently generate gene replacements allowing for modulation of protein levels for otherwise lethal knockouts (KOs). Thus, CRISPR-Trap offers several advantages over conventional KO approaches and allows for generation of clean CRISPR/Cas9-based KOs.
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Affiliation(s)
- Stefan Reber
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Jonas Mechtersheimer
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Sofia Nasif
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | | | - Martino Colombo
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Michal Domanski
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
| | - Daniel Jutzi
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012 Bern, Switzerland
| | - Eva Hedlund
- Department of Neuroscience, Karolinska Institutet,171 77 Stockholm, Sweden
| | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, CH-3012 Bern, Switzerland
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50
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Takata N, Abbey D, Fiore L, Acosta S, Feng R, Gil HJ, Lavado A, Geng X, Interiano A, Neale G, Eiraku M, Sasai Y, Oliver G. An Eye Organoid Approach Identifies Six3 Suppression of R-spondin 2 as a Critical Step in Mouse Neuroretina Differentiation. Cell Rep 2017; 21:1534-1549. [PMID: 29117559 PMCID: PMC5728169 DOI: 10.1016/j.celrep.2017.10.041] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/20/2017] [Accepted: 10/11/2017] [Indexed: 02/01/2023] Open
Abstract
Recent advances in self-organizing, 3-dimensional tissue cultures of embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) provided an in vitro model that recapitulates many aspects of the in vivo developmental steps. Using Rax-GFP-expressing ESCs, newly generated Six3-/- iPSCs, and conditional null Six3delta/f;Rax-Cre ESCs, we identified Six3 repression of R-spondin 2 (Rspo2) as a required step during optic vesicle morphogenesis and neuroretina differentiation. We validated these results in vivo by showing that transient ectopic expression of Rspo2 in the anterior neural plate of transgenic mouse embryos was sufficient to inhibit neuroretina differentiation. Additionally, using a chimeric eye organoid assay, we determined that Six3 null cells exert a non-cell-autonomous repressive effect during optic vesicle formation and neuroretina differentiation. Our results further validate the organoid culture system as a reliable and fast alternative to identify and evaluate genes involved in eye morphogenesis and neuroretina differentiation in vivo.
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Affiliation(s)
- Nozomu Takata
- Center for Vascular and Developmental Biology, Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA
| | - Deepti Abbey
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Luciano Fiore
- Center for Vascular and Developmental Biology, Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA
| | - Sandra Acosta
- Center for Vascular and Developmental Biology, Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA
| | - Ruopeng Feng
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hyea Jin Gil
- Center for Vascular and Developmental Biology, Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA
| | - Alfonso Lavado
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xin Geng
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ashley Interiano
- Department of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Geoffrey Neale
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mototsugu Eiraku
- Laboratory for in vitro Histogenesis, RIKEN Center for Developmental Biology, Kobe, Hyogo 650-0047, Japan; Laboratory of Developmental Systems, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, Kyoto 606-8507, Japan
| | - Yoshiki Sasai
- Laboratory for Organogenesis and Neurogenesis, RIKEN Center for Developmental Biology, Kobe, Hyogo 650-0047, Japan
| | - Guillermo Oliver
- Center for Vascular and Developmental Biology, Feinberg Cardiovascular Research Institute, Northwestern University, Chicago, IL 60611, USA.
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