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Abrhámová K, Groušlová M, Valentová A, Hao X, Liu B, Převorovský M, Gahura O, Půta F, Sunnerhagen P, Folk P. Truncating the spliceosomal 'rope protein' Prp45 results in Htz1 dependent phenotypes. RNA Biol 2024; 21:1-17. [PMID: 38711165 PMCID: PMC11085953 DOI: 10.1080/15476286.2024.2348896] [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] [Accepted: 04/24/2024] [Indexed: 05/08/2024] Open
Abstract
Spliceosome assembly contributes an important but incompletely understood aspect of splicing regulation. Prp45 is a yeast splicing factor which runs as an extended fold through the spliceosome, and which may be important for bringing its components together. We performed a whole genome analysis of the genetic interaction network of the truncated allele of PRP45 (prp45(1-169)) using synthetic genetic array technology and found chromatin remodellers and modifiers as an enriched category. In agreement with related studies, H2A.Z-encoding HTZ1, and the components of SWR1, INO80, and SAGA complexes represented prominent interactors, with htz1 conferring the strongest growth defect. Because the truncation of Prp45 disproportionately affected low copy number transcripts of intron-containing genes, we prepared strains carrying intronless versions of SRB2, VPS75, or HRB1, the most affected cases with transcription-related function. Intron removal from SRB2, but not from the other genes, partly repaired some but not all the growth phenotypes identified in the genetic screen. The interaction of prp45(1-169) and htz1Δ was detectable even in cells with SRB2 intron deleted (srb2Δi). The less truncated variant, prp45(1-330), had a synthetic growth defect with htz1Δ at 16°C, which also persisted in the srb2Δi background. Moreover, htz1Δ enhanced prp45(1-330) dependent pre-mRNA hyper-accumulation of both high and low efficiency splicers, genes ECM33 and COF1, respectively. We conclude that while the expression defects of low expression intron-containing genes contribute to the genetic interactome of prp45(1-169), the genetic interactions between prp45 and htz1 alleles demonstrate the sensitivity of spliceosome assembly, delayed in prp45(1-169), to the chromatin environment.
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Affiliation(s)
- Kateřina Abrhámová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Martina Groušlová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Anna Valentová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Xinxin Hao
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - František Půta
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Petr Folk
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
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2
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Separovich RJ, Wilkins MR. Ready, SET, Go: Post-translational regulation of the histone lysine methylation network in budding yeast. J Biol Chem 2021; 297:100939. [PMID: 34224729 PMCID: PMC8329514 DOI: 10.1016/j.jbc.2021.100939] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/25/2021] [Accepted: 07/01/2021] [Indexed: 11/21/2022] Open
Abstract
Histone lysine methylation is a key epigenetic modification that regulates eukaryotic transcription. Here, we comprehensively review the function and regulation of the histone methylation network in the budding yeast and model eukaryote, Saccharomyces cerevisiae. First, we outline the lysine methylation sites that are found on histone proteins in yeast (H3K4me1/2/3, H3K36me1/2/3, H3K79me1/2/3, and H4K5/8/12me1) and discuss their biological and cellular roles. Next, we detail the reduced but evolutionarily conserved suite of methyltransferase (Set1p, Set2p, Dot1p, and Set5p) and demethylase (Jhd1p, Jhd2p, Rph1p, and Gis1p) enzymes that are known to control histone lysine methylation in budding yeast cells. Specifically, we illustrate the domain architecture of the methylation enzymes and highlight the structural features that are required for their respective functions and molecular interactions. Finally, we discuss the prevalence of post-translational modifications on yeast histone methylation enzymes and how phosphorylation, acetylation, and ubiquitination in particular are emerging as key regulators of enzyme function. We note that it will be possible to completely connect the histone methylation network to the cell's signaling system, given that all methylation sites and cognate enzymes are known, most phosphosites on the enzymes are known, and the mapping of kinases to phosphosites is tractable owing to the modest set of protein kinases in yeast. Moving forward, we expect that the rich variety of post-translational modifications that decorates the histone methylation machinery will explain many of the unresolved questions surrounding the function and dynamics of this intricate epigenetic network.
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Affiliation(s)
- Ryan J Separovich
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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3
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Lai F, Cheng Y, Zou J, Wang H, Zhu W, Wang X, Cheng H, Zhou R. Identification of Histone Modifications Reveals a Role of H2b Monoubiquitination in Transcriptional Regulation of dmrt1 in Monopterus albus. Int J Biol Sci 2021; 17:2009-2020. [PMID: 34131402 PMCID: PMC8193266 DOI: 10.7150/ijbs.59347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/23/2021] [Indexed: 01/14/2023] Open
Abstract
Gonadal trans-differentiation from ovary to testis occurs in a same individual, suggesting a role of epigenetic regulation. However, histone modifications concerning the sex reversal process remain elusive. We analyzed histone modifications using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Chromatin immunoprecipitation followed by sequencing (ChIP-seq) technology was used to test chromatin immunoprecipitation of gonads. Western blot analysis was performed to analyze protein expression. Immunofluorescence analysis was conducted to localize proteins in gonadal tissues. Here, we report a developmental atlas of histone modifications in the gonadal differentiation, including acetylation, methylation, and ubiquitination. We provided a detail distribution map of these modification sites including novel histone modifications along histones H2a, H2b, H3, and H4, and revealed their relationship with types of gonadal differentiation. We then determined a testis-enriched histone modification site, H2b monoubiquitination at K120, and its association with spermatogenesis. ChIP-seq demonstrated that the modification was highly enriched in the male sex-determining gene dmrt1 (doublesex and mab-3 related transcription factor 1), in particular, in its exon regions, suggesting its role in transcriptional regulation of dmrt1 in testis. Together, these data not only provide a new resource for epigenetic study in gonadal development, but also define an association of histone modifications with gonadal differentiation from ovary to testis.
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Affiliation(s)
- Fengling Lai
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yibin Cheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Juan Zou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Haoyu Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wang Zhu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xin Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hanhua Cheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Rongjia Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
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4
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Rambout X, Maquat LE. The nuclear cap-binding complex as choreographer of gene transcription and pre-mRNA processing. Genes Dev 2021; 34:1113-1127. [PMID: 32873578 PMCID: PMC7462061 DOI: 10.1101/gad.339986.120] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this review, Rambout and Maquat discuss known roles of the nuclear cap-binding complex (CBC) during the transcription of genes that encode proteins, stitching together past studies from diverse groups to describe the continuum of CBC-mediated checks and balances in eukaryotic cells. The largely nuclear cap-binding complex (CBC) binds to the 5′ caps of RNA polymerase II (RNAPII)-synthesized transcripts and serves as a dynamic interaction platform for a myriad of RNA processing factors that regulate gene expression. While influence of the CBC can extend into the cytoplasm, here we review the roles of the CBC in the nucleus, with a focus on protein-coding genes. We discuss differences between CBC function in yeast and mammals, covering the steps of transcription initiation, release of RNAPII from pausing, transcription elongation, cotranscriptional pre-mRNA splicing, transcription termination, and consequences of spurious transcription. We describe parameters known to control the binding of generic or gene-specific cofactors that regulate CBC activities depending on the process(es) targeted, illustrating how the CBC is an ever-changing choreographer of gene expression.
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Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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5
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Tellier M, Maudlin I, Murphy S. Transcription and splicing: A two-way street. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1593. [PMID: 32128990 DOI: 10.1002/wrna.1593] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/18/2019] [Accepted: 02/12/2020] [Indexed: 12/11/2022]
Abstract
RNA synthesis by RNA polymerase II and RNA processing are closely coupled during the transcription cycle of protein-coding genes. This coupling affords opportunities for quality control and regulation of gene expression and the effects can go in both directions. For example, polymerase speed can affect splice site selection and splicing can increase transcription and affect the chromatin landscape. Here we review the many ways that transcription and splicing influence one another, including how splicing "talks back" to transcription. We will also place the connections between transcription and splicing in the context of other RNA processing events that define the exons that will make up the final mRNA. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Isabella Maudlin
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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6
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Leung CS, Douglass SM, Morselli M, Obusan MB, Pavlyukov MS, Pellegrini M, Johnson TL. H3K36 Methylation and the Chromodomain Protein Eaf3 Are Required for Proper Cotranscriptional Spliceosome Assembly. Cell Rep 2020; 27:3760-3769.e4. [PMID: 31242410 PMCID: PMC6904931 DOI: 10.1016/j.celrep.2019.05.100] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/08/2019] [Accepted: 05/27/2019] [Indexed: 12/14/2022] Open
Abstract
In the eukaryotic cell, spliceosomes assemble onto pre-mRNA cotranscriptionally. Spliceosome assembly takes place in the context of the chromatin environment, suggesting that the state of the chromatin may affect splicing. The molecular details and mechanisms through which chromatin affects splicing, however, are still unclear. Here, we show a role for the histone methyltransferase Set2 and its histone modification, H3K36 methylation, in pre-mRNA splicing through high-throughput sequencing. Moreover, the effect of H3K36 methylation on pre-mRNA splicing is mediated through the chromodomain protein Eaf3. We find that Eaf3 is recruited to intron-containing genes and that Eaf3 interacts with the splicing factor Prp45. Eaf3 acts with Prp45 and Prp19 after formation of the precatalytic B complex around the time of splicing activation, thus revealing the step in splicing that is regulated by H3K36 methylation. These studies support a model whereby H3K36 facilitates recruitment of an "adapter protein" to support efficient, constitutive splicing.
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Affiliation(s)
- Calvin S Leung
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Stephen M Douglass
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marco Morselli
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Matthew B Obusan
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marat S Pavlyukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russian Federation
| | - Matteo Pellegrini
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Tracy L Johnson
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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7
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Neugebauer KM. Nascent RNA and the Coordination of Splicing with Transcription. Cold Spring Harb Perspect Biol 2019; 11:11/8/a032227. [PMID: 31371351 DOI: 10.1101/cshperspect.a032227] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
At each active protein-encoding gene, nascent RNA is tethered to the DNA axis by elongating RNA polymerase II (Pol II) and is continuously altered by splicing and other processing events during its synthesis. This review discusses the development of three major methods that enable us to track the conversion of precursor messenger RNA (pre-mRNA) to messenger RNA (mRNA) products in vivo: live-cell imaging, metabolic labeling of RNA, and RNA-seq of purified nascent RNA. These approaches are complementary, addressing distinct issues of transcription rates and intron lifetimes alongside spatial information regarding the gene position of Pol II at which spliceosomes act. The findings will be placed in the context of active transcription units, each of which-because of the presence of nascent RNA, Pol II, and features of the chromatin environment-will recruit a potentially gene-specific constellation of RNA binding proteins and processing machineries.
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Affiliation(s)
- Karla M Neugebauer
- Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
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8
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Histone 2B monoubiquitination complex integrates transcript elongation with RNA processing at circadian clock and flowering regulators. Proc Natl Acad Sci U S A 2019; 116:8060-8069. [PMID: 30923114 DOI: 10.1073/pnas.1806541116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
HISTONE MONOUBIQUITINATION1 (HUB1) and its paralog HUB2 act in a conserved heterotetrameric complex in the chromatin-mediated transcriptional modulation of developmental programs, such as flowering time, dormancy, and the circadian clock. The KHD1 and SPEN3 proteins were identified as interactors of the HUB1 and HUB2 proteins with in vitro RNA-binding activity. Mutants in SPEN3 and KHD1 had reduced rosette and leaf areas. Strikingly, in spen3 mutants, the flowering time was slightly, but significantly, delayed, as opposed to the early flowering time in the hub1-4 mutant. The mutant phenotypes in biomass and flowering time suggested a deregulation of their respective regulatory genes CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) and FLOWERING LOCUS C (FLC) that are known targets of the HUB1-mediated histone H2B monoubiquitination (H2Bub). Indeed, in the spen3-1 and hub1-4 mutants, the circadian clock period was shortened as observed by luciferase reporter assays, the levels of the CCA1α and CCA1β splice forms were altered, and the CCA1 expression and H2Bub levels were reduced. In the spen3-1 mutant, the delay in flowering time was correlated with an enhanced FLC expression, possibly due to an increased distal versus proximal ratio of its antisense COOLAIR transcript. Together with transcriptomic and double-mutant analyses, our data revealed that the HUB1 interaction with SPEN3 links H2Bub during transcript elongation with pre-mRNA processing at CCA1 Furthermore, the presence of an intact HUB1 at the FLC is required for SPEN3 function in the formation of the FLC-derived antisense COOLAIR transcripts.
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9
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Fournier LA, Kumar A, Stirling PC. Chromatin as a Platform for Modulating the Replication Stress Response. Genes (Basel) 2018; 9:genes9120622. [PMID: 30544989 PMCID: PMC6316668 DOI: 10.3390/genes9120622] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/03/2018] [Accepted: 12/04/2018] [Indexed: 02/06/2023] Open
Abstract
Eukaryotic DNA replication occurs in the context of chromatin. Recent years have seen major advances in our understanding of histone supply, histone recycling and nascent histone incorporation during replication. Furthermore, much is now known about the roles of histone remodellers and post-translational modifications in replication. It has also become clear that nucleosome dynamics during replication play critical roles in genome maintenance and that chromatin modifiers are important for preventing DNA replication stress. An understanding of how cells deploy specific nucleosome modifiers, chaperones and remodellers directly at sites of replication fork stalling has been building more slowly. Here we will specifically discuss recent advances in understanding how chromatin composition contribute to replication fork stability and restart.
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Affiliation(s)
| | - Arun Kumar
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
| | - Peter C Stirling
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 1L3, Canada.
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10
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Oliete-Calvo P, Serrano-Quílez J, Nuño-Cabanes C, Pérez-Martínez ME, Soares LM, Dichtl B, Buratowski S, Pérez-Ortín JE, Rodríguez-Navarro S. A role for Mog1 in H2Bub1 and H3K4me3 regulation affecting RNAPII transcription and mRNA export. EMBO Rep 2018; 19:embr.201845992. [PMID: 30249596 DOI: 10.15252/embr.201845992] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 08/28/2018] [Accepted: 08/31/2018] [Indexed: 12/11/2022] Open
Abstract
Monoubiquitination of histone H2B (to H2Bub1) is required for downstream events including histone H3 methylation, transcription, and mRNA export. The mechanisms and players regulating these events have not yet been completely delineated. Here, we show that the conserved Ran-binding protein Mog1 is required to sustain normal levels of H2Bub1 and H3K4me3 in Saccharomyces cerevisiae Mog1 is needed for gene body recruitment of Rad6, Bre1, and Rtf1 that are involved in H2B ubiquitination and genetically interacts with these factors. We provide evidence that the absence of MOG1 impacts on cellular processes such as transcription, DNA replication, and mRNA export, which are linked to H2Bub1. Importantly, the mRNA export defect in mog1Δ strains is exacerbated by the absence of factors that decrease H2Bub1 levels. Consistent with a role in sustaining H2Bub and H3K4me3 levels, Mog1 co-precipitates with components that participate in these modifications such as Bre1, Rtf1, and the COMPASS-associated factors Shg1 and Sdc1. These results reveal a novel role for Mog1 in H2B ubiquitination, transcription, and mRNA biogenesis.
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Affiliation(s)
- Paula Oliete-Calvo
- Gene expression and mRNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Joan Serrano-Quílez
- Gene expression and mRNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Gene expression and mRNA Metabolism Laboratory, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Carme Nuño-Cabanes
- Gene expression and mRNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Gene expression and mRNA Metabolism Laboratory, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - María E Pérez-Martínez
- Departamento de Bioquímica y Biología Molecular and E.R.I. Biotecmed, Facultad de Biología, Universitat de València, Burjassot, Spain
| | - Luis M Soares
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Bernhard Dichtl
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Centre for Cellular and Molecular Biology, Deakin University, Geelong, Vic., Australia
| | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular and E.R.I. Biotecmed, Facultad de Biología, Universitat de València, Burjassot, Spain
| | - Susana Rodríguez-Navarro
- Gene expression and mRNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain .,Gene expression and mRNA Metabolism Laboratory, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
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11
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Dargemont C, Babour A. Novel functions for chromatin dynamics in mRNA biogenesis beyond transcription. Nucleus 2017; 8:482-488. [PMID: 28816581 DOI: 10.1080/19491034.2017.1342916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The first step of gene expression results in the production of mRNA ribonucleoparticles (mRNPs) that are exported to the cytoplasm via the NPC for translation into the cytoplasm. During this process, the mRNA molecule synthesized by RNA polymerase II (Pol II) undergoes extensive maturation, folding and packaging events that are intimately coupled to its synthesis. All these events take place in a chromatin context and it is therefore not surprising that a growing number of studies recently reported specific contributions of chromatin dynamics to various steps of mRNP biogenesis. In this extra view, we replace our recent findings highlighting the contribution of the yeast chromatin remodeling complex ISW1 to nuclear mRNA quality control in the context of the recent literature.
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Affiliation(s)
- Catherine Dargemont
- a Université Paris Diderot, Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212 , Hôpital St. Louis 1, Paris , France
| | - Anna Babour
- a Université Paris Diderot, Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212 , Hôpital St. Louis 1, Paris , France
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12
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Herzel L, Ottoz DSM, Alpert T, Neugebauer KM. Splicing and transcription touch base: co-transcriptional spliceosome assembly and function. Nat Rev Mol Cell Biol 2017; 18:637-650. [PMID: 28792005 DOI: 10.1038/nrm.2017.63] [Citation(s) in RCA: 225] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Several macromolecular machines collaborate to produce eukaryotic messenger RNA. RNA polymerase II (Pol II) translocates along genes that are up to millions of base pairs in length and generates a flexible RNA copy of the DNA template. This nascent RNA harbours introns that are removed by the spliceosome, which is a megadalton ribonucleoprotein complex that positions the distant ends of the intron into its catalytic centre. Emerging evidence that the catalytic spliceosome is physically close to Pol II in vivo implies that transcription and splicing occur on similar timescales and that the transcription and splicing machineries may be spatially constrained. In this Review, we discuss aspects of spliceosome assembly, transcription elongation and other co-transcriptional events that allow the temporal coordination of co-transcriptional splicing.
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Affiliation(s)
- Lydia Herzel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Diana S M Ottoz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Tara Alpert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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13
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The Chromatin Remodeler ISW1 Is a Quality Control Factor that Surveys Nuclear mRNP Biogenesis. Cell 2017; 167:1201-1214.e15. [PMID: 27863241 DOI: 10.1016/j.cell.2016.10.048] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/12/2016] [Accepted: 10/27/2016] [Indexed: 02/07/2023]
Abstract
Chromatin dynamics play an essential role in regulating DNA transaction processes, but it is unclear whether transcription-associated chromatin modifications control the mRNA ribonucleoparticles (mRNPs) pipeline from synthesis to nuclear exit. Here, we identify the yeast ISW1 chromatin remodeling complex as an unanticipated mRNP nuclear export surveillance factor that retains export-incompetent transcripts near their transcription site. This tethering activity of ISW1 requires chromatin binding and is independent of nucleosome sliding activity or changes in RNA polymerase II processivity. Combination of in vivo UV-crosslinking and genome-wide RNA immunoprecipitation assays show that Isw1 and its cofactors interact directly with premature mRNPs. Our results highlight that the concerted action of Isw1 and the nuclear exosome ensures accurate surveillance mechanism that proofreads the efficiency of mRNA biogenesis.
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14
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Alpert T, Herzel L, Neugebauer KM. Perfect timing: splicing and transcription rates in living cells. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27873472 DOI: 10.1002/wrna.1401] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/12/2016] [Accepted: 09/26/2016] [Indexed: 12/27/2022]
Abstract
An important step toward understanding gene regulation is the elucidation of the time necessary for the completion of individual steps. Measurement of reaction rates can reveal potential nodes for regulation. For example, measurements of in vivo transcription elongation rates reveal regulation by DNA sequence, gene architecture, and chromatin. Pre-mRNA splicing is regulated by transcription elongation rates and vice versa, yet the rates of RNA processing reactions remain largely elusive. Since the 1980s, numerous model systems and approaches have been used to determine the precise timing of splicing in vivo. Because splicing can be co-transcriptional, the position of Pol II when splicing is detected has been used as a proxy for time by some investigators. In addition to these 'distance-based' measurements, 'time-based' measurements have been possible through live cell imaging, metabolic labeling of RNA, and gene induction. Yet splicing rates can be convolved by the time it takes for transcription, spliceosome assembly and spliceosome disassembly. The variety of assays and systems used has, perhaps not surprisingly, led to reports of widely differing splicing rates in vivo. Recently, single molecule RNA-seq has indicated that splicing occurs more quickly than previously deduced. Here we comprehensively review these findings and discuss evidence that splicing and transcription rates are closely coordinated, facilitating the efficiency of gene expression. On the other hand, introduction of splicing delays through as yet unknown mechanisms provide opportunity for regulation. More work is needed to understand how cells optimize the rates of gene expression for a range of biological conditions. WIREs RNA 2017, 8:e1401. doi: 10.1002/wrna.1401 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Tara Alpert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Lydia Herzel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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15
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Niño CA, Guet D, Gay A, Brutus S, Jourquin F, Mendiratta S, Salamero J, Géli V, Dargemont C. Posttranslational marks control architectural and functional plasticity of the nuclear pore complex basket. J Cell Biol 2016; 212:167-80. [PMID: 26783300 PMCID: PMC4738382 DOI: 10.1083/jcb.201506130] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Ubiquitin modifications of the nuclear pore complex (NPC) control the architectural plasticity of the nuclear basket, contributing to its tethering to the core NPC, with consequences on the cellular response to DNA damage and telomere recombination. The nuclear pore complex (NPC) serves as both the unique gate between the nucleus and the cytoplasm and a major platform that coordinates nucleocytoplasmic exchanges, gene expression, and genome integrity. To understand how the NPC integrates these functional constraints, we dissected here the posttranslational modifications of the nuclear basket protein Nup60 and analyzed how they intervene to control the plasticity of the NPC. Combined approaches highlight the role of monoubiquitylation in regulating the association dynamics of Nup60 and its partner, Nup2, with the NPC through an interaction with Nup84, a component of the Y complex. Although major nuclear transport routes are not regulated by Nup60 modifications, monoubiquitylation of Nup60 is stimulated upon genotoxic stress and regulates the DNA-damage response and telomere repair. Together, these data reveal an original mechanism contributing to the plasticity of the NPC at a molecular-organization and functional level.
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Affiliation(s)
- Carlos A Niño
- University Paris Diderot, Sorbonne Paris Cité, Pathologie et Virologie Moléculaire, Institut National de la Santé et de la Recherche Medicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Equipe labellisée Ligue contre le cancer, Hôpital St. Louis, 75475 Paris, France
| | - David Guet
- University Paris Diderot, Sorbonne Paris Cité, Pathologie et Virologie Moléculaire, Institut National de la Santé et de la Recherche Medicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Equipe labellisée Ligue contre le cancer, Hôpital St. Louis, 75475 Paris, France
| | - Alexandre Gay
- University Paris Diderot, Sorbonne Paris Cité, Pathologie et Virologie Moléculaire, Institut National de la Santé et de la Recherche Medicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Equipe labellisée Ligue contre le cancer, Hôpital St. Louis, 75475 Paris, France
| | - Sergine Brutus
- University Paris Diderot, Sorbonne Paris Cité, Pathologie et Virologie Moléculaire, Institut National de la Santé et de la Recherche Medicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Equipe labellisée Ligue contre le cancer, Hôpital St. Louis, 75475 Paris, France
| | - Frédéric Jourquin
- Aix-Marseille University, CNRS UMR 7258, INSERM UMR1068, Institut Paoli-Calmettes, Cancer Research Center of Marseille, Equipe labellisée Ligue contre le cancer, 13273 Marseille, France
| | - Shweta Mendiratta
- University Paris Diderot, Sorbonne Paris Cité, Pathologie et Virologie Moléculaire, Institut National de la Santé et de la Recherche Medicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Equipe labellisée Ligue contre le cancer, Hôpital St. Louis, 75475 Paris, France
| | - Jean Salamero
- Institut Curie, PSL Research University, CNRS UMR 144, Pierre-and-Marie-Curie Université, Team-Space time imaging of endomembranes and organelles dynamics and PICT-IBiSA Imaging Core Facility, 75005 Paris, France
| | - Vincent Géli
- Aix-Marseille University, CNRS UMR 7258, INSERM UMR1068, Institut Paoli-Calmettes, Cancer Research Center of Marseille, Equipe labellisée Ligue contre le cancer, 13273 Marseille, France
| | - Catherine Dargemont
- University Paris Diderot, Sorbonne Paris Cité, Pathologie et Virologie Moléculaire, Institut National de la Santé et de la Recherche Medicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Equipe labellisée Ligue contre le cancer, Hôpital St. Louis, 75475 Paris, France
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16
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Sorenson MR, Jha DK, Ucles SA, Flood DM, Strahl BD, Stevens SW, Kress TL. Histone H3K36 methylation regulates pre-mRNA splicing in Saccharomyces cerevisiae. RNA Biol 2016; 13:412-26. [PMID: 26821844 DOI: 10.1080/15476286.2016.1144009] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Co-transcriptional splicing takes place in the context of a highly dynamic chromatin architecture, yet the role of chromatin restructuring in coordinating transcription with RNA splicing has not been fully resolved. To further define the contribution of histone modifications to pre-mRNA splicing in Saccharomyces cerevisiae, we probed a library of histone point mutants using a reporter to monitor pre-mRNA splicing. We found that mutation of H3 lysine 36 (H3K36) - a residue methylated by Set2 during transcription elongation - exhibited phenotypes similar to those of pre-mRNA splicing mutants. We identified genetic interactions between genes encoding RNA splicing factors and genes encoding the H3K36 methyltransferase Set2 and the demethylase Jhd1 as well as point mutations of H3K36 that block methylation. Consistent with the genetic interactions, deletion of SET2, mutations modifying the catalytic activity of Set2 or H3K36 point mutations significantly altered expression of our reporter and reduced splicing of endogenous introns. These effects were dependent on the association of Set2 with RNA polymerase II and H3K36 dimethylation. Additionally, we found that deletion of SET2 reduces the association of the U2 and U5 snRNPs with chromatin. Thus, our study provides the first evidence that H3K36 methylation plays a role in co-transcriptional RNA splicing in yeast.
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Affiliation(s)
- Matthew R Sorenson
- a Graduate Program in Microbiology, The University of Texas at Austin , Austin , Texas , USA
| | - Deepak K Jha
- b Department of Biochemistry and Biophysics , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina , USA
| | - Stefanie A Ucles
- c Department of Biology , The College of New Jersey , Ewing , NJ , USA
| | - Danielle M Flood
- c Department of Biology , The College of New Jersey , Ewing , NJ , USA
| | - Brian D Strahl
- b Department of Biochemistry and Biophysics , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina , USA.,d Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill , Chapel Hill , North Carolina , USA
| | - Scott W Stevens
- e Department of Molecular Biosciences , University of Texas at Austin , Austin , Texas , USA.,f Institute for Cellular and Molecular Biology, University of Texas at Austin , Austin , Texas , USA
| | - Tracy L Kress
- c Department of Biology , The College of New Jersey , Ewing , NJ , USA
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17
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Valero ML, Sendra R, Pamblanco M. Tandem affinity purification of histones, coupled to mass spectrometry, identifies associated proteins and new sites of post-translational modification in Saccharomyces cerevisiae. J Proteomics 2016; 136:183-92. [PMID: 26778144 DOI: 10.1016/j.jprot.2016.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 12/17/2015] [Accepted: 01/04/2016] [Indexed: 02/06/2023]
Abstract
Histones and their post-translational modifications contribute to regulating fundamental biological processes in all eukaryotic cells. We have applied a conventional tandem affinity purification strategy to histones H3 and H4 of the yeast Saccharomyces cerevisiae. Mass spectrometry analysis of the co-purified proteins revealed multiple associated proteins, including core histones, which indicates that tagged histones may be incorporated to the nucleosome particle. Among the many other co-isolated proteins there are histone chaperones, elements of chromatin remodeling, of nucleosome assembly/disassembly, and of histone modification complexes. The histone chaperone Rtt106p, two members of chromatin assembly FACT complex and Psh1p, an ubiquitin ligase, were the most abundant proteins obtained with both H3-TAP and H4-TAP, regardless of the cell extraction medium stringency. Our mass spectrometry analyses have also revealed numerous novel post-translational modifications, including 30 new chemical modifications in histones, mainly by ubiquitination. We have discovered not only new sites of ubiquitination but that, besides lysine, also serine and threonine residues are targets of ubiquitination on yeast histones. Our results show the standard tandem affinity purification procedure is suitable for application to yeast histones, in order to isolate and characterize histone-binding proteins and post-translational modifications, avoiding the bias caused by histone purification from a chromatin-enriched fraction.
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Affiliation(s)
- M Luz Valero
- Secció de Proteòmica, Servei Central de Suport a la Investigació Experimental (SCSIE), Universitat de València, C/Dr. Moliner 50, 46100, Burjassot, València, Spain.
| | - Ramon Sendra
- Departament de Bioquímica i Biologia Molecular, Universitat de València, C/Dr. Moliner 50, 46100, Burjassot, València, Spain.
| | - Mercè Pamblanco
- Departament de Bioquímica i Biologia Molecular, Universitat de València, C/Dr. Moliner 50, 46100, Burjassot, València, Spain.
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18
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Patrick KL, Ryan CJ, Xu J, Lipp JJ, Nissen KE, Roguev A, Shales M, Krogan NJ, Guthrie C. Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast. PLoS Genet 2015; 11:e1005074. [PMID: 25825871 PMCID: PMC4380400 DOI: 10.1371/journal.pgen.1005074] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/16/2015] [Indexed: 12/19/2022] Open
Abstract
Although numerous regulatory connections between pre-mRNA splicing and chromatin have been demonstrated, the precise mechanisms by which chromatin factors influence spliceosome assembly and/or catalysis remain unclear. To probe the genetic network of pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe, we constructed an epistatic mini-array profile (E-MAP) and discovered many new connections between chromatin and splicing. Notably, the nucleosome remodeler SWI/SNF had strong genetic interactions with components of the U2 snRNP SF3 complex. Overexpression of SF3 components in ΔSWI/SNF cells led to inefficient splicing of many fission yeast introns, predominantly those with non-consensus splice sites. Deletion of SWI/SNF decreased recruitment of the splicing ATPase Prp2, suggesting that SWI/SNF promotes co-transcriptional spliceosome assembly prior to first step catalysis. Importantly, defects in SWI/SNF as well as SF3 overexpression each altered nucleosome occupancy along intron-containing genes, illustrating that the chromatin landscape both affects—and is affected by—co-transcriptional splicing. It has recently become apparent that most introns are removed from pre-mRNA while the transcript is still engaged with RNA polymerase II (RNAPII). To gain insight into possible roles for chromatin in co-transcriptional splicing, we generated a genome-wide genetic interaction map in fission yeast and uncovered numerous connections between splicing and chromatin. The SWI/SNF remodeling complex is typically thought to activate gene expression by relieving barriers to polymerase elongation imposed by nucleosomes. Here we show that this remodeler is important for an early step in splicing in which Prp2, an RNA-dependent ATPase, is recruited to the assembling spliceosome to promote catalytic activation. Interestingly, introns with sub-optimal splice sites are particularly dependent on SWI/SNF, suggesting the impact of nucleosome dynamics on the kinetics of spliceosome assembly and catalysis. By monitoring nucleosome occupancy, we show significant alterations in nucleosome density in particular splicing and chromatin mutants, which generally paralleled the levels of RNAPII. Taken together, our findings challenge the notion that nucleosomes simply act as barriers to elongation; rather, we suggest that polymerase pausing at nucleosomes can activate gene expression by allowing more time for co-transcriptional splicing.
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Affiliation(s)
- Kristin L. Patrick
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
| | - Colm J. Ryan
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- California Institute for Quantitative Biosciences, QB3, San Francisco, California, United States of America
| | - Jiewei Xu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- California Institute for Quantitative Biosciences, QB3, San Francisco, California, United States of America
| | - Jesse J. Lipp
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
| | - Kelly E. Nissen
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
| | - Assen Roguev
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- California Institute for Quantitative Biosciences, QB3, San Francisco, California, United States of America
| | - Nevan J. Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
- California Institute for Quantitative Biosciences, QB3, San Francisco, California, United States of America
- J. David Gladstone Institutes, San Francisco, California, United States of America
| | - Christine Guthrie
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, United States of America
- * E-mail:
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19
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Bonizec M, Hérissant L, Pokrzywa W, Geng F, Wenzel S, Howard GC, Rodriguez P, Krause S, Tansey WP, Hoppe T, Dargemont C. The ubiquitin-selective chaperone Cdc48/p97 associates with Ubx3 to modulate monoubiquitylation of histone H2B. Nucleic Acids Res 2014; 42:10975-86. [PMID: 25183520 PMCID: PMC4176170 DOI: 10.1093/nar/gku786] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 08/18/2014] [Accepted: 08/18/2014] [Indexed: 11/14/2022] Open
Abstract
Cdc48/p97 is an evolutionary conserved ubiquitin-dependent chaperone involved in a broad array of cellular functions due to its ability to associate with multiple cofactors. Aside from its role in removing RNA polymerase II from chromatin after DNA damage, little is known about how this AAA-ATPase is involved in the transcriptional process. Here, we show that yeast Cdc48 is recruited to chromatin in a transcription-coupled manner and modulates gene expression. Cdc48, together with its cofactor Ubx3 controls monoubiquitylation of histone H2B, a conserved modification regulating nucleosome dynamics and chromatin organization. Mechanistically, Cdc48 facilitates the recruitment of Lge1, a cofactor of the H2B ubiquitin ligase Bre1. The function of Cdc48 in controlling H2B ubiquitylation appears conserved in human cells because disease-related mutations or chemical inhibition of p97 function affected the amount of ubiquitylated H2B in muscle cells. Together, these results suggest a prominent role of Cdc48/p97 in the coordination of chromatin remodeling with gene transcription to define cellular differentiation processes.
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Affiliation(s)
- Mélanie Bonizec
- Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, University of Paris Diderot, Hôpital St. Louis 1, Avenue Claude Vellefaux 75475 Paris Cedex 10, France
| | - Lucas Hérissant
- Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, University of Paris Diderot, Hôpital St. Louis 1, Avenue Claude Vellefaux 75475 Paris Cedex 10, France
| | - Wojciech Pokrzywa
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Fuqiang Geng
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN 37232, USA
| | - Sabine Wenzel
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN 37232, USA
| | - Gregory C Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN 37232, USA
| | - Paco Rodriguez
- Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, University of Paris Diderot, Hôpital St. Louis 1, Avenue Claude Vellefaux 75475 Paris Cedex 10, France
| | - Sabine Krause
- Laboratory for Molecular Myology, Friedrich Baur Institute, Department of Neurology, Ludwig Maximilians University, Munich, Germany
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN 37232, USA
| | - Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Catherine Dargemont
- Sorbonne Paris Cité, INSERM UMR944, CNRS UMR7212, Equipe labellisée Ligue contre le cancer, University of Paris Diderot, Hôpital St. Louis 1, Avenue Claude Vellefaux 75475 Paris Cedex 10, France
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20
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Fuchs G, Hollander D, Voichek Y, Ast G, Oren M. Cotranscriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate. Genome Res 2014; 24:1572-83. [PMID: 25049226 PMCID: PMC4199367 DOI: 10.1101/gr.176487.114] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Various histone modifications decorate nucleosomes within transcribed genes. Among these, monoubiquitylation of histone H2B (H2Bub1) and methylation of histone H3 on lysines 36 (H3K36me2/3) and 79 (H3K79me2/3) correlate positively with gene expression. By measuring the progression of the transcriptional machinery along genes within live cells, we now report that H2B monoubiquitylation occurs cotranscriptionally and accurately reflects the advance of RNA polymerase II (Pol II). In contrast, H3K36me3 and H3K79me2 are less dynamic and represent Pol II movement less faithfully. High-resolution ChIP-seq reveals that H2Bub1 levels are selectively reduced at exons and decrease in an exon-dependent stepwise manner toward the 3' end of genes. Exonic depletion of H2Bub1 in gene bodies is highly correlated with Pol II pausing at exons, suggesting elongation rate changes associated with intron-exon structure. In support of this notion, H2Bub1 levels were found to be significantly correlated with transcription elongation rates measured in various cell lines. Overall, our data shed light on the organization of H2Bub1 within transcribed genes and single out H2Bub1 as a reliable marker for ongoing transcription elongation.
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Affiliation(s)
- Gilad Fuchs
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dror Hollander
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv 69978, Israel
| | - Yoav Voichek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv 69978, Israel
| | - Moshe Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel;
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