1
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Le HQ, Hill MA, Kollak I, Keck M, Schroeder V, Wirth J, Skronska‐Wasek W, Schruf E, Strobel B, Stahl H, Herrmann FE, Campos AR, Li J, Quast K, Knebel D, Viollet C, Thomas MJ, Lamb D, Garnett JP. An EZH2-dependent transcriptional complex promotes aberrant epithelial remodelling after injury. EMBO Rep 2021; 22:e52785. [PMID: 34224201 PMCID: PMC8339687 DOI: 10.15252/embr.202152785] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/05/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022] Open
Abstract
Unveiling the molecular mechanisms of tissue remodelling following injury is imperative to elucidate its regenerative capacity and aberrant repair in disease. Using different omics approaches, we identified enhancer of zester homolog 2 (EZH2) as a key regulator of fibrosis in injured lung epithelium. Epithelial injury drives an enrichment of nuclear transforming growth factor-β-activated kinase 1 (TAK1) that mediates EZH2 phosphorylation to facilitate its liberation from polycomb repressive complex 2 (PRC2). This process results in the establishment of a transcriptional complex of EZH2, RNA-polymerase II (POL2) and nuclear actin, which orchestrates aberrant epithelial repair programmes. The liberation of EZH2 from PRC2 is accompanied by an EZH2-EZH1 switch to preserve H3K27me3 deposition at non-target genes. Loss of epithelial TAK1, EZH2 or blocking nuclear actin influx attenuates the fibrotic cascade and restores respiratory homeostasis. Accordingly, EZH2 inhibition significantly improves outcomes in a pulmonary fibrosis mouse model. Our results reveal an important non-canonical function of EZH2, paving the way for new therapeutic interventions in fibrotic lung diseases.
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Affiliation(s)
- Huy Q Le
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Matthew A Hill
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
- University of BathBathUK
| | - Ines Kollak
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Martina Keck
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Victoria Schroeder
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Johannes Wirth
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Wioletta Skronska‐Wasek
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Eva Schruf
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Benjamin Strobel
- Drug Discovery SciencesBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Heiko Stahl
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Franziska E Herrmann
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | | | - Jun Li
- Immunology and Respiratory Disease Research DepartmentBoehringer Ingelheim Pharmaceuticals, IncRidgefieldCTUSA
| | - Karsten Quast
- Global Computational Biology and Digital SciencesBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Dagmar Knebel
- Global Computational Biology and Digital SciencesBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Coralie Viollet
- Global Computational Biology and Digital SciencesBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - Matthew J Thomas
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
- University of BathBathUK
| | - David Lamb
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
| | - James P Garnett
- Lung Repair & Regeneration DepartmentBoehringer Ingelheim Pharma GmbH & Co. KGBiberachGermany
- Translational and Clinical Research InstituteNewcastle UniversityNewcastleUK
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2
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Venkat Ramani MK, Yang W, Irani S, Zhang Y. Simplicity is the Ultimate Sophistication-Crosstalk of Post-translational Modifications on the RNA Polymerase II. J Mol Biol 2021; 433:166912. [PMID: 33676925 PMCID: PMC8184622 DOI: 10.1016/j.jmb.2021.166912] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 12/19/2022]
Abstract
The highly conserved C-terminal domain (CTD) of the largest subunit of RNA polymerase II comprises a consensus heptad (Y1S2P3T4S5P6S7) repeated multiple times. Despite the simplicity of its sequence, the essential CTD domain orchestrates eukaryotic transcription and co-transcriptional processes, including transcription initiation, elongation, and termination, and mRNA processing. These distinct facets of the transcription cycle rely on specific post-translational modifications (PTM) of the CTD, in which five out of the seven residues in the heptad repeat are subject to phosphorylation. A hypothesis termed the "CTD code" has been proposed in which these PTMs and their combinations generate a sophisticated landscape for spatiotemporal recruitment of transcription regulators to Pol II. In this review, we summarize the recent experimental evidence understanding the biological role of the CTD, implicating a context-dependent theme that significantly enhances the ability of accurate transcription by RNA polymerase II. Furthermore, feedback communication between the CTD and histone modifications coordinates chromatin states with RNA polymerase II-mediated transcription, ensuring the effective and accurate conversion of information into cellular responses.
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Affiliation(s)
| | - Wanjie Yang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, United States
| | - Seema Irani
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, United States
| | - Yan Zhang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, United States; The Institute for Cellular and Molecular Biology. University of Texas at Austin, Austin, TX 78712, United States.
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3
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Lyons DE, McMahon S, Ott M. A combinatorial view of old and new RNA polymerase II modifications. Transcription 2020; 11:66-82. [PMID: 32401151 DOI: 10.1080/21541264.2020.1762468] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The production of mRNA is a dynamic process that is highly regulated by reversible post-translational modifications of the C-terminal domain (CTD) of RNA polymerase II. The CTD is a highly repetitive domain consisting mostly of the consensus heptad sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Phosphorylation of serine residues within this repeat sequence is well studied, but modifications of all residues have been described. Here, we focus on integrating newly identified and lesser-studied CTD post-translational modifications into the existing framework. We also review the growing body of work demonstrating crosstalk between different CTD modifications and the functional consequences of such crosstalk on the dynamics of transcriptional regulation.
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Affiliation(s)
- Danielle E Lyons
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
| | - Sarah McMahon
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco , San Francisco, CA, USA
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco , San Francisco, CA, USA
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4
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Cornett EM, Ferry L, Defossez PA, Rothbart SB. Lysine Methylation Regulators Moonlighting outside the Epigenome. Mol Cell 2020; 75:1092-1101. [PMID: 31539507 DOI: 10.1016/j.molcel.2019.08.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/14/2019] [Accepted: 08/27/2019] [Indexed: 01/21/2023]
Abstract
Landmark discoveries made nearly two decades ago identified known transcriptional regulators as histone lysine methyltransferases. Since then, the field of lysine methylation signaling has been dominated by studies of how this small chemical posttranslational modification regulates gene expression and other chromatin-based processes. However, recent advances in mass-spectrometry-based proteomics have revealed that histones are just a subset of the thousands of eukaryotic proteins marked by lysine methylation. As the writers, erasers, and readers of histone lysine methylation are emerging as a promising therapeutic target class for cancer and other diseases, a key challenge for the field is to define the full spectrum of activities for these proteins. Here we summarize recent discoveries implicating non-histone lysine methylation as a major regulator of diverse cellular processes. We further discuss recent technological innovations that are enabling the expanded study of lysine methylation signaling. Collectively, these findings are shaping our understanding of the fundamental mechanisms of non-histone protein regulation through this dynamic and multi-functional posttranslational modification.
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Affiliation(s)
- Evan M Cornett
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - Laure Ferry
- Université de Paris, Epigenetics and Cell Fate, CNRS, 75013 Paris, France
| | | | - Scott B Rothbart
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
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5
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Burkholder NT, Sipe SN, Escobar EE, Venkatramani M, Irani S, Yang W, Wu H, Matthews WM, Brodbelt JS, Zhang Y. Mapping RNAPII CTD Phosphorylation Reveals That the Identity and Modification of Seventh Heptad Residues Direct Tyr1 Phosphorylation. ACS Chem Biol 2019; 14:2264-2275. [PMID: 31553563 DOI: 10.1021/acschembio.9b00610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The C-terminal domain (CTD) of the largest subunit in eukaryotic RNA polymerase II has a repetitive heptad sequence of Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 which is responsible for recruiting transcriptional regulatory factors. The seventh heptad residues in mammals are less conserved and subject to various post-translational modifications, but the consequences of such variations are not well understood. In this study, we use ultraviolet photodissociation mass spectrometry, kinetic assays, and structural analyses to dissect how different residues or modifications at the seventh heptad position alter Tyr1 phosphorylation. We found that negatively charged residues in this position promote phosphorylation of adjacent Tyr1 sites, whereas positively charged residues discriminate against it. Modifications that alter the charges on seventh heptad residues such as arginine citrullination negate such distinctions. Such specificity can be explained by conserved, positively charged pockets near the active sites of ABL1 and its homologues. Our results reveal a novel mechanism for variations or modifications in the seventh heptad position directing subsequent phosphorylation of other CTD sites, which can contribute to the formation of various modification combinations that likely impact transcriptional regulation.
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6
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Gregersen LH, Mitter R, Ugalde AP, Nojima T, Proudfoot NJ, Agami R, Stewart A, Svejstrup JQ. SCAF4 and SCAF8, mRNA Anti-Terminator Proteins. Cell 2019; 177:1797-1813.e18. [PMID: 31104839 PMCID: PMC6579486 DOI: 10.1016/j.cell.2019.04.038] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 02/04/2019] [Accepted: 04/17/2019] [Indexed: 12/30/2022]
Abstract
Accurate regulation of mRNA termination is required for correct gene expression. Here, we describe a role for SCAF4 and SCAF8 as anti-terminators, suppressing the use of early, alternative polyadenylation (polyA) sites. The SCAF4/8 proteins bind the hyper-phosphorylated RNAPII C-terminal repeat domain (CTD) phosphorylated on both Ser2 and Ser5 and are detected at early, alternative polyA sites. Concomitant knockout of human SCAF4 and SCAF8 results in altered polyA selection and subsequent early termination, leading to expression of truncated mRNAs and proteins lacking functional domains and is cell lethal. While SCAF4 and SCAF8 work redundantly to suppress early mRNA termination, they also have independent, non-essential functions. SCAF8 is an RNAPII elongation factor, whereas SCAF4 is required for correct termination at canonical, distal transcription termination sites in the presence of SCAF8. Together, SCAF4 and SCAF8 coordinate the transition between elongation and termination, ensuring correct polyA site selection and RNAPII transcriptional termination in human cells.
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Affiliation(s)
- Lea H Gregersen
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Alejandro P Ugalde
- The Netherlands Cancer Institute (NKI-AVL), Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Nicholas J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Reuven Agami
- The Netherlands Cancer Institute (NKI-AVL), Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Aengus Stewart
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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7
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Ali I, Ruiz DG, Ni Z, Johnson JR, Zhang H, Li PC, Khalid MM, Conrad RJ, Guo X, Min J, Greenblatt J, Jacobson M, Krogan NJ, Ott M. Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins. Mol Cell 2019; 74:1164-1174.e4. [PMID: 31054975 DOI: 10.1016/j.molcel.2019.04.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/26/2019] [Accepted: 03/30/2019] [Indexed: 01/01/2023]
Abstract
Post-translational modifications of the RNA polymerase II C-terminal domain (CTD) coordinate the transcription cycle. Crosstalk between different modifications is poorly understood. Here, we show how acetylation of lysine residues at position 7 of characteristic heptad repeats (K7ac)-only found in higher eukaryotes-regulates phosphorylation of serines at position 5 (S5p), a conserved mark of polymerases initiating transcription. We identified the regulator of pre-mRNA-domain-containing (RPRD) proteins as reader proteins of K7ac. K7ac enhanced CTD peptide binding to the CTD-interacting domain (CID) of RPRD1A and RPRD1B proteins in isothermal calorimetry and molecular modeling experiments. Deacetylase inhibitors increased K7ac- and decreased S5-phosphorylated polymerases, consistent with acetylation-dependent S5 dephosphorylation by an RPRD-associated S5 phosphatase. Consistent with this model, RPRD1B knockdown increased S5p but enhanced K7ac, indicating that RPRD proteins recruit K7 deacetylases, including HDAC1. We also report autoregulatory crosstalk between K7ac and S5p via RPRD proteins and their interactions with acetyl- and phospho-eraser proteins.
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Affiliation(s)
- Ibraheem Ali
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Zuyao Ni
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | | | - Heng Zhang
- Structural Genomics Consortium, University of Toronto, ON, Canada
| | - Pao-Chen Li
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Mir M Khalid
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ryan J Conrad
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Xinghua Guo
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, ON, Canada
| | | | - Matthew Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA; California Institute for Quantitative Biosciences (QBC), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences (QBC), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Melanie Ott
- J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
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8
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Burriss KH, Mosley AL. Methods review: Mass spectrometry analysis of RNAPII complexes. Methods 2019; 159-160:105-114. [PMID: 30902665 DOI: 10.1016/j.ymeth.2019.03.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/04/2019] [Accepted: 03/17/2019] [Indexed: 12/20/2022] Open
Abstract
RNA Polymerase II (RNAPII) is responsible for transcribing multiple RNA species throughout eukaryotes. A variety of protein-protein interactions occur throughout the transcription cycle for coordinated regulation of transcription initiation, elongation, and/or termination. Taking a proteomics approach to study RNAPII transcription thereby offers a comprehensive view of both RNAPII biology and the variety of proteins that regulate the process itself. This review will focus on how mass spectrometry (MS) methods have expanded understanding of RNAPII and its transcription-regulatory interaction partners. The application of affinity purification mass spectrometry has led to the discovery of a number of novel groups of proteins that regulate an array of RNAPII biology ranging from nuclear import to regulation of phosphorylation state. Additionally, a number of methods have been developed using mass spectrometry to measure protein subunit stoichiometry within and across protein complexes and to perform various types of architectural analysis using structural proteomics approaches. The key methods that we will focus on related to RNAPII mass spectrometry analyses include: affinity purification mass spectrometry, protein post-translational modification analysis, crosslinking mass spectrometry, and native mass spectrometry.
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Affiliation(s)
- Katlyn Hughes Burriss
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46402, United States
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46402, United States; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46402, United States.
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9
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Sharma P, Lioutas A, Fernandez-Fuentes N, Quilez J, Carbonell-Caballero J, Wright RHG, Di Vona C, Le Dily F, Schüller R, Eick D, Oliva B, Beato M. Arginine Citrullination at the C-Terminal Domain Controls RNA Polymerase II Transcription. Mol Cell 2018; 73:84-96.e7. [PMID: 30472187 DOI: 10.1016/j.molcel.2018.10.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/31/2018] [Accepted: 10/09/2018] [Indexed: 12/21/2022]
Abstract
The post-translational modification of key residues at the C-terminal domain of RNA polymerase II (RNAP2-CTD) coordinates transcription, splicing, and RNA processing by modulating its capacity to act as a landing platform for a variety of protein complexes. Here, we identify a new modification at the CTD, the deimination of arginine and its conversion to citrulline by peptidyl arginine deiminase 2 (PADI2), an enzyme that has been associated with several diseases, including cancer. We show that, among PADI family members, only PADI2 citrullinates R1810 (Cit1810) at repeat 31 of the CTD. Depletion of PADI2 or loss of R1810 results in accumulation of RNAP2 at transcription start sites, reduced gene expression, and inhibition of cell proliferation. Cit1810 is needed for interaction with the P-TEFb (positive transcription elongation factor b) kinase complex and for its recruitment to chromatin. In this way, CTD-Cit1810 favors RNAP2 pause release and efficient transcription in breast cancer cells.
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Affiliation(s)
- Priyanka Sharma
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Antonios Lioutas
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Narcis Fernandez-Fuentes
- IBERS, Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth SY23 3EB, UK
| | - Javier Quilez
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - José Carbonell-Caballero
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Roni H G Wright
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Chiara Di Vona
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - François Le Dily
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Roland Schüller
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany
| | - Baldomero Oliva
- Universitat Pompeu Fabra (UPF), Barcelona, Spain; Structural Bioinformatics Laboratory (GRIB-IMIM), Department of Experimental and Health Sciences, Barcelona 08003, Spain
| | - Miguel Beato
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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10
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Ferrai C, Torlai Triglia E, Risner-Janiczek JR, Rito T, Rackham OJ, de Santiago I, Kukalev A, Nicodemi M, Akalin A, Li M, Ungless MA, Pombo A. RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation. Mol Syst Biol 2017; 13:946. [PMID: 29038337 PMCID: PMC5658700 DOI: 10.15252/msb.20177754] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Polycomb repression in mouse embryonic stem cells (ESCs) is tightly associated with promoter co‐occupancy of RNA polymerase II (RNAPII) which is thought to prime genes for activation during early development. However, it is unknown whether RNAPII poising is a general feature of Polycomb repression, or is lost during differentiation. Here, we map the genome‐wide occupancy of RNAPII and Polycomb from pluripotent ESCs to non‐dividing functional dopaminergic neurons. We find that poised RNAPII complexes are ubiquitously present at Polycomb‐repressed genes at all stages of neuronal differentiation. We observe both loss and acquisition of RNAPII and Polycomb at specific groups of genes reflecting their silencing or activation. Strikingly, RNAPII remains poised at transcription factor genes which are silenced in neurons through Polycomb repression, and have major roles in specifying other, non‐neuronal lineages. We conclude that RNAPII poising is intrinsically associated with Polycomb repression throughout differentiation. Our work suggests that the tight interplay between RNAPII poising and Polycomb repression not only instructs promoter state transitions, but also may enable promoter plasticity in differentiated cells.
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Affiliation(s)
- Carmelo Ferrai
- Epigenetic Regulation and Chromatin Architecture, Max Delbrück Center for Molecular Medicine, Berlin, Germany .,Genome Function, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Elena Torlai Triglia
- Epigenetic Regulation and Chromatin Architecture, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Jessica R Risner-Janiczek
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK.,Stem Cell Neurogenesis, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK.,Neurophysiology Group, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK
| | - Tiago Rito
- Epigenetic Regulation and Chromatin Architecture, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Inês de Santiago
- Genome Function, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Alexander Kukalev
- Epigenetic Regulation and Chromatin Architecture, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Altuna Akalin
- Scientific Bioinformatics Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Meng Li
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK.,Stem Cell Neurogenesis, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK
| | - Mark A Ungless
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK .,Neurophysiology Group, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK
| | - Ana Pombo
- Epigenetic Regulation and Chromatin Architecture, Max Delbrück Center for Molecular Medicine, Berlin, Germany .,Genome Function, MRC London Institute of Medical Sciences (previously MRC Clinical Sciences Centre), London, UK.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK.,Institute for Biology, Humboldt-Universität zu Berlin, Berlin Germany
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11
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Blank MF, Chen S, Poetz F, Schnölzer M, Voit R, Grummt I. SIRT7-dependent deacetylation of CDK9 activates RNA polymerase II transcription. Nucleic Acids Res 2017; 45:2675-2686. [PMID: 28426094 PMCID: PMC5389538 DOI: 10.1093/nar/gkx053] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/20/2017] [Indexed: 01/08/2023] Open
Abstract
SIRT7 is an NAD+-dependent protein deacetylase that regulates cell growth and proliferation. Previous studies have shown that SIRT7 is required for RNA polymerase I (Pol I) transcription and pre-rRNA processing. Here, we took a proteomic approach to identify novel molecular targets and characterize the role of SIRT7 in non-nucleolar processes. We show that SIRT7 interacts with numerous proteins involved in transcriptional regulation and RNA metabolism, the majority of interactions requiring ongoing transcription. In addition to its role in Pol I transcription, we found that SIRT7 also regulates transcription of snoRNAs and mRNAs. Mechanistically, SIRT7 promotes the release of P-TEFb from the inactive 7SK snRNP complex and deacetylates CDK9, a subunit of the elongation factor P-TEFb, which activates transcription by phosphorylating serine 2 within the C-terminal domain (CTD) of Pol II. SIRT7 counteracts GCN5-directed acetylation of lysine 48 within the catalytic domain of CDK9, deacetylation promoting CTD phosphorylation and transcription elongation.
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Affiliation(s)
- Maximilian F Blank
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Sifan Chen
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Fabian Poetz
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Renate Voit
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Ingrid Grummt
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
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12
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Gibbs EB, Lu F, Portz B, Fisher MJ, Medellin BP, Laremore TN, Zhang YJ, Gilmour DS, Showalter SA. Phosphorylation induces sequence-specific conformational switches in the RNA polymerase II C-terminal domain. Nat Commun 2017; 8:15233. [PMID: 28497798 PMCID: PMC5437310 DOI: 10.1038/ncomms15233] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 03/09/2017] [Indexed: 01/25/2023] Open
Abstract
The carboxy-terminal domain (CTD) of the RNA polymerase II (Pol II) large subunit cycles through phosphorylation states that correlate with progression through the transcription cycle and regulate nascent mRNA processing. Structural analyses of yeast and mammalian CTD are hampered by their repetitive sequences. Here we identify a region of the Drosophila melanogaster CTD that is essential for Pol II function in vivo and capitalize on natural sequence variations within it to facilitate structural analysis. Mass spectrometry and NMR spectroscopy reveal that hyper-Ser5 phosphorylation transforms the local structure of this region via proline isomerization. The sequence context of this switch tunes the activity of the phosphatase Ssu72, leading to the preferential de-phosphorylation of specific heptads. Together, context-dependent conformational switches and biased dephosphorylation suggest a mechanism for the selective recruitment of cis-proline-specific regulatory factors and region-specific modulation of the CTD code that may augment gene regulation in developmentally complex organisms.
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Affiliation(s)
- Eric B Gibbs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Feiyue Lu
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Bede Portz
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Michael J Fisher
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Brenda P Medellin
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA.,Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Tatiana N Laremore
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Yan Jessie Zhang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA.,Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - David S Gilmour
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Scott A Showalter
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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13
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The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain. Nat Rev Mol Cell Biol 2017; 18:263-273. [PMID: 28248323 DOI: 10.1038/nrm.2017.10] [Citation(s) in RCA: 300] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The carboxy-terminal domain (CTD) extends from the largest subunit of RNA polymerase II (Pol II) as a long, repetitive and largely unstructured polypeptide chain. Throughout the transcription process, the CTD is dynamically modified by post-translational modifications, many of which facilitate or hinder the recruitment of key regulatory factors of Pol II that collectively constitute the 'CTD code'. Recent studies have revealed how the physicochemical properties of the CTD promote phase separation in the presence of other low-complexity domains. Here, we discuss the intricacies of the CTD code and how the newly characterized physicochemical properties of the CTD expand the function of the CTD beyond the code.
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14
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Abstract
Transcription and splicing are fundamental steps in gene expression. These processes have been studied intensively over the past four decades, and very recent findings are challenging some of the formerly established ideas. In particular, splicing was shown to occur much faster than previously thought, with the first spliced products observed as soon as splice junctions emerge from RNA polymerase II (Pol II). Splicing was also found coupled to a specific phosphorylation pattern of Pol II carboxyl-terminal domain (CTD), suggesting a new layer of complexity in the CTD code. Moreover, phosphorylation of the CTD may be scarcer than expected, and other post-translational modifications of the CTD are emerging with unanticipated roles in gene expression regulation.
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Affiliation(s)
- Noélia Custódio
- a Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa , Lisboa , Portugal
| | - Maria Carmo-Fonseca
- a Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa , Lisboa , Portugal
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15
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The pol II CTD: new twists in the tail. Nat Struct Mol Biol 2016; 23:771-7. [DOI: 10.1038/nsmb.3285] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 08/03/2016] [Indexed: 12/13/2022]
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16
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Abstract
In this issue of Molecular Cell, Schüller et al. (2016) and Suh et al. (2016) describe genetic and mass spectrometry methodologies for mapping phosphorylation sites on the tandem repeats of the RNA polymerase II CTD. The results suggest that the CTD Code may be simpler than expected.
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Affiliation(s)
- Jeffry L Corden
- Department of Molecular Biology and Genetics, Johns Hopkins Medical School, Baltimore, MD 21205, USA.
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17
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Hintermair C, Voß K, Forné I, Heidemann M, Flatley A, Kremmer E, Imhof A, Eick D. Specific threonine-4 phosphorylation and function of RNA polymerase II CTD during M phase progression. Sci Rep 2016; 6:27401. [PMID: 27264542 PMCID: PMC4893663 DOI: 10.1038/srep27401] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/18/2016] [Indexed: 11/08/2022] Open
Abstract
Dynamic phosphorylation of Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 heptad-repeats in the C-terminal domain (CTD) of the large subunit coordinates progression of RNA polymerase (Pol) II through the transcription cycle. Here, we describe an M phase-specific form of Pol II phosphorylated at Thr4, but not at Tyr1, Ser2, Ser5, and Ser7 residues. Thr4 phosphorylated Pol II binds to centrosomes and midbody and interacts with the Thr4-specific Polo-like kinase 1. Binding of Pol II to centrosomes does not require the CTD but may involve subunits of the non-canonical R2TP-Prefoldin-like complex, which bind to and co-localize with Pol II at centrosomes. CTD Thr4 mutants, but not Ser2 and Ser5 mutants, display severe mitosis and cytokinesis defects characterized by multipolar spindles and polyploid cells. We conclude that proper M phase progression of cells requires binding of Pol II to centrosomes to facilitate regulation of mitosis and cytokinesis in a CTD Thr4-P dependent manner.
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Affiliation(s)
- Corinna Hintermair
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science (CIPSM), Marchioninistrasse 25, 81377 Munich, Germany
| | - Kirsten Voß
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science (CIPSM), Marchioninistrasse 25, 81377 Munich, Germany
| | - Ignasi Forné
- Biomedical Center Munich, Center of Integrated Protein Science (CIPSM), ZFP, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Martin Heidemann
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science (CIPSM), Marchioninistrasse 25, 81377 Munich, Germany
| | - Andrew Flatley
- Institute of Molecular Immunology, Helmholtz Center Munich, Marchioninistrasse 25, 81377 Munich, Germany
| | - Elisabeth Kremmer
- Institute of Molecular Immunology, Helmholtz Center Munich, Marchioninistrasse 25, 81377 Munich, Germany
| | - Axel Imhof
- Biomedical Center Munich, Center of Integrated Protein Science (CIPSM), ZFP, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science (CIPSM), Marchioninistrasse 25, 81377 Munich, Germany
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18
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Jeronimo C, Collin P, Robert F. The RNA Polymerase II CTD: The Increasing Complexity of a Low-Complexity Protein Domain. J Mol Biol 2016; 428:2607-2622. [DOI: 10.1016/j.jmb.2016.02.006] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 01/27/2016] [Accepted: 02/02/2016] [Indexed: 01/18/2023]
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19
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Abstract
The RNAPII-CTD functions as a binding platform for coordinating the recruitment of transcription associated factors. Altering CTD function results in gene expression defects, although mounting evidence suggests that these effects likely vary among species and loci. Here we highlight emerging evidence of species- and loci-specific functions for the RNAPII-CTD.
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Affiliation(s)
- Maria J Aristizabal
- a Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia , Vancouver , British Columbia , Canada
| | - Michael S Kobor
- a Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia , Vancouver , British Columbia , Canada
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