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Fetian T, Grover A, Arndt KM. Histone H2B ubiquitylation: Connections to transcription and effects on chromatin structure. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195018. [PMID: 38331024 PMCID: PMC11098702 DOI: 10.1016/j.bbagrm.2024.195018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024]
Abstract
Nucleosomes are major determinants of eukaryotic genome organization and regulation. Many studies, incorporating a diversity of experimental approaches, have been focused on identifying and discerning the contributions of histone post-translational modifications to DNA-centered processes. Among these, monoubiquitylation of H2B (H2Bub) on K120 in humans or K123 in budding yeast is a critical histone modification that has been implicated in a wide array of DNA transactions. H2B is co-transcriptionally ubiquitylated and deubiquitylated via the concerted action of an extensive network of proteins. In addition to altering the chemical and physical properties of the nucleosome, H2Bub is important for the proper control of gene expression and for the deposition of other histone modifications. In this review, we discuss the molecular mechanisms underlying the ubiquitylation cycle of H2B and how it connects to the regulation of transcription and chromatin structure.
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Affiliation(s)
- Tasniem Fetian
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Aakash Grover
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States of America.
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2
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Qin B, Lu G, Chen X, Zheng C, Lin H, Liu Q, Shang J, Feng G. H2B oncohistones cause homologous recombination defect and genomic instability through reducing H2B monoubiquitination in Schizosaccharomyces pombe. J Biol Chem 2024; 300:107345. [PMID: 38718864 PMCID: PMC11167522 DOI: 10.1016/j.jbc.2024.107345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 06/02/2024] Open
Abstract
Canonical oncohistones are histone H3 mutations in the N-terminal tail associated with tumors and affect gene expression by altering H3 post-translational modifications (PTMs) and the epigenetic landscape. Noncanonical oncohistone mutations occur in both tails and globular domains of all four core histones and alter gene expression by perturbing chromatin remodeling. However, the effects and mechanisms of noncanonical oncohistones remain largely unknown. Here we characterized 16 noncanonical H2B oncohistones in the fission yeast Schizosaccharomyces pombe. We found that seven of them exhibited temperature sensitivities and 11 exhibited genotoxic sensitivities. A detailed study of two of these onco-mutants H2BG52D and H2BP102L revealed that they were defective in homologous recombination (HR) repair with compromised histone eviction and Rad51 recruitment. Interestingly, their genotoxic sensitivities and HR defects were rescued by the inactivation of the H2BK119 deubiquitination function of Ubp8 in the Spt-Ada-Gcn5-Acetyltransferase (SAGA) complex. The levels of H2BK119 monoubiquitination (H2Bub) in the H2BG52D and H2BP102L mutants are reduced in global genome and at local DNA break sites presumably due to enhanced recruitment of Ubp8 onto nucleosomes and are recovered upon loss of H2B deubiquitination function of the SAGA complex. Moreover, H2BG52D and H2BP102L heterozygotes exhibit genotoxic sensitivities and reduced H2Bub in cis. We therefore conclude that H2BG52D and H2BP102L oncohistones affect HR repair and genome stability via the reduction of H2Bub and propose that other noncanonical oncohistones may also affect histone PTMs to cause diseases.
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Affiliation(s)
- Bingxin Qin
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guangchun Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xuejin Chen
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Chenhua Zheng
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Huanteng Lin
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Qi Liu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jinjie Shang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Gang Feng
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, China; School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
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Lin CT, Ting RT, Ou YH, Shao TL, Lee MC. Protein degradation of Lsd1 is mediated by Bre1 yet opposed by Lsd1-interacting lncRNAs during fly follicle development. iScience 2024; 27:109683. [PMID: 38655201 PMCID: PMC11035368 DOI: 10.1016/j.isci.2024.109683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/13/2024] [Accepted: 04/04/2024] [Indexed: 04/26/2024] Open
Abstract
Tissue development, homeostasis, and repair all require efficient progenitor expansion. Lysine-specific demethylase 1 (Lsd1) maintains plastic epigenetic states to promote progenitor proliferation while overexpressed Lsd1 protein causes oncogenic gene expression in cancer cells. However, the precise regulation of Lsd1 protein expression at the molecular level to drive progenitor differentiation remains unclear. Here, using Drosophila melanogaster oogenesis as our experimental system, we discovered molecular machineries that modify Lsd1 protein stability in vivo. Through genetic and biochemical analyses, an E3 ubiquitin ligase, Bre1, was identified as required for follicle progenitor differentiation, likely by mediating Lsd1 protein degradation. Interestingly, specific Lsd1-interacting long non-coding RNAs (LINRs) were found to antagonize Bre1-mediated Lsd1 protein degradation. The intricate interplay discovered among the Lsd1 complex, LINRs and Bre1 provides insight into how Lsd1 protein stability is fine-tuned to underlie progenitor differentiation in vivo.
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Affiliation(s)
- Chun Ting Lin
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Info & Research Bldg, Rm 904, #155, Sec. 2, Li-Nong St, Taipei City 112, Taiwan
| | - Ruei-Teng Ting
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Info & Research Bldg, Rm 904, #155, Sec. 2, Li-Nong St, Taipei City 112, Taiwan
| | - Yang-Hsuan Ou
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Info & Research Bldg, Rm 904, #155, Sec. 2, Li-Nong St, Taipei City 112, Taiwan
| | - Tzu-Ling Shao
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Info & Research Bldg, Rm 904, #155, Sec. 2, Li-Nong St, Taipei City 112, Taiwan
| | - Ming-Chia Lee
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Info & Research Bldg, Rm 904, #155, Sec. 2, Li-Nong St, Taipei City 112, Taiwan
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4
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Francette AM, Arndt KM. Multiple direct and indirect roles of Paf1C in elongation, splicing, and histone post-translational modifications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591159. [PMID: 38712269 PMCID: PMC11071476 DOI: 10.1101/2024.04.25.591159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Paf1C is a highly conserved protein complex with critical functions during eukaryotic transcription. Previous studies have shown that Paf1C is multi-functional, controlling specific aspects of transcription, ranging from RNAPII processivity to histone modifications. However, it is unclear how specific Paf1C subunits directly impact transcription and coupled processes. We have compared conditional depletion to steady-state deletion for each Paf1C subunit to determine the direct and indirect contributions to gene expression in Saccharomyces cerevisiae. Using nascent transcript sequencing, RNAPII profiling, and modeling of transcription elongation dynamics, we have demonstrated direct effects of Paf1C subunits on RNAPII processivity and elongation rate and indirect effects on transcript splicing and repression of antisense transcripts. Further, our results suggest that the direct transcriptional effects of Paf1C cannot be readily assigned to any particular histone modification. This work comprehensively analyzes both the immediate and extended roles of each Paf1C subunit in transcription elongation and transcript regulation.
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Affiliation(s)
- Alex M. Francette
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Karen M. Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
- Lead contact
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5
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Lyu Y, Yang Y, Talwar V, Lu H, Chen C, Salman S, Wicks EE, Huang TYT, Drehmer D, Wang Y, Zuo Q, Datan E, Jackson W, Dordai D, Wang R, Semenza GL. Hypoxia-inducible factor 1 recruits FACT and RNF20/40 to mediate histone ubiquitination and transcriptional activation of target genes. Cell Rep 2024; 43:113972. [PMID: 38517892 DOI: 10.1016/j.celrep.2024.113972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 02/01/2024] [Accepted: 03/01/2024] [Indexed: 03/24/2024] Open
Abstract
Hypoxia-inducible factor 1 (HIF-1) is a transcriptional activator that mediates cellular adaptation to decreased oxygen availability. HIF-1 recruits chromatin-modifying enzymes leading to changes in histone acetylation, citrullination, and methylation at target genes. Here, we demonstrate that hypoxia-inducible gene expression in estrogen receptor (ER)-positive MCF7 and ER-negative SUM159 human breast cancer cells requires the histone H2A/H2B chaperone facilitates chromatin transcription (FACT) and the H2B ubiquitin ligase RING finger protein 20/40 (RNF20/40). Knockdown of FACT or RNF20/40 expression leads to decreased transcription initiation and elongation at HIF-1 target genes. Mechanistically, FACT and RNF20/40 are recruited to hypoxia response elements (HREs) by HIF-1 and stabilize binding of HIF-1 (and each other) at HREs. Hypoxia induces the monoubiquitination of histone H2B at lysine 120 at HIF-1 target genes in an HIF-1-dependent manner. Together, these findings delineate a cooperative molecular mechanism by which FACT and RNF20/40 stabilize multiprotein complex formation at HREs and mediate histone ubiquitination to facilitate HIF-1 transcriptional activity.
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Affiliation(s)
- Yajing Lyu
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yongkang Yang
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA
| | - Varen Talwar
- Johns Hopkins University, Baltimore, MD 21218, USA
| | - Haiquan Lu
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA
| | - Chelsey Chen
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shaima Salman
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Elizabeth E Wicks
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tina Yi-Ting Huang
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daiana Drehmer
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yufeng Wang
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Qiaozhu Zuo
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Emmanuel Datan
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Walter Jackson
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dominic Dordai
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ru Wang
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gregg L Semenza
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA.
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Wang P, Fan N, Yang W, Cao P, Liu G, Zhao Q, Guo P, Li X, Lin X, Jiang N, Nashun B. Transcriptional regulation of FACT involves Coordination of chromatin accessibility and CTCF binding. J Biol Chem 2024; 300:105538. [PMID: 38072046 PMCID: PMC10808957 DOI: 10.1016/j.jbc.2023.105538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 11/14/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Histone chaperone FACT (facilitates chromatin transcription) is well known to promote chromatin recovery during transcription. However, the mechanism how FACT regulates genome-wide chromatin accessibility and transcription factor binding has not been fully elucidated. Through loss-of-function studies, we show here that FACT component Ssrp1 is required for DNA replication and DNA damage repair and is also essential for progression of cell phase transition and cell proliferation in mouse embryonic fibroblast cells. On the molecular level, absence of the Ssrp1 leads to increased chromatin accessibility, enhanced CTCF binding, and a remarkable change in dynamic range of gene expression. Our study thus unequivocally uncovers a unique mechanism by which FACT complex regulates transcription by coordinating genome-wide chromatin accessibility and CTCF binding.
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Affiliation(s)
- Peijun Wang
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China; School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Na Fan
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Wanting Yang
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China
| | - Pengbo Cao
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China
| | - Guojun Liu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Qi Zhao
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Pengfei Guo
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Xihe Li
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animals, Hohhot, China
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Ning Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
| | - Buhe Nashun
- Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, Inner Mongolia University, Hohhot, China; State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China.
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7
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Das SK, Huynh MT, Gao J, Sengupta B, Yadav SP, Lee TH. Methods to investigate nucleosome structure and dynamics with single-molecule FRET. Methods 2023; 215:17-27. [PMID: 37236433 PMCID: PMC10330475 DOI: 10.1016/j.ymeth.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/13/2023] [Accepted: 05/21/2023] [Indexed: 05/28/2023] Open
Abstract
The nucleosome is the fundamental building block of chromatin. Changes taking place at the nucleosome level are the molecular basis of chromatin transactions with various enzymes and factors. These changes are directly and indirectly regulated by chromatin modifications such as DNA methylation and histone post-translational modifications including acetylation, methylation, and ubiquitylation. Nucleosomal changes are often stochastic, unsynchronized, and heterogeneous, making it very difficult to monitor with traditional ensemble averaging methods. Diverse single-molecule fluorescence approaches have been employed to investigate the structure and structural changes of the nucleosome in the context of its interactions with various enzymes such as RNA Polymerase II, histone chaperones, transcription factors, and chromatin remodelers. We utilize diverse single-molecule fluorescence methods to study the nucleosomal changes accompanying these processes, elucidate the kinetics of these processes, and eventually learn the implications of various chromatin modifications in directly regulating these processes. The methods include two- and three-color single-molecule fluorescence resonance energy transfer (FRET), single-molecule fluorescence correlation spectroscopy, and fluorescence (co-)localization. Here we report the details of the two- and three-color single-molecule FRET methods we currently use. This report will help researchers design their single-molecule FRET approaches to investigating chromatin regulation at the nucleosome level.
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Affiliation(s)
- Subhra K Das
- Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA
| | - Mai T Huynh
- Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA
| | - Jia Gao
- Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA
| | - Bhaswati Sengupta
- Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA
| | - Satya P Yadav
- Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA
| | - Tae-Hee Lee
- Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA.
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8
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Fetian T, McShane BM, Horan NL, Shodja DN, True JD, Mosley AL, Arndt KM. Paf1 complex subunit Rtf1 stimulates H2B ubiquitylation by interacting with the highly conserved N-terminal helix of Rad6. Proc Natl Acad Sci U S A 2023; 120:e2220041120. [PMID: 37216505 PMCID: PMC10235976 DOI: 10.1073/pnas.2220041120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/05/2023] [Indexed: 05/24/2023] Open
Abstract
Histone modifications coupled to transcription elongation play important roles in regulating the accuracy and efficiency of gene expression. The monoubiquitylation of a conserved lysine in H2B (K123 in Saccharomyces cerevisiae; K120 in humans) occurs cotranscriptionally and is required for initiating a histone modification cascade on active genes. H2BK123 ubiquitylation (H2BK123ub) requires the RNA polymerase II (RNAPII)-associated Paf1 transcription elongation complex (Paf1C). Through its histone modification domain (HMD), the Rtf1 subunit of Paf1C directly interacts with the ubiquitin conjugase Rad6, leading to the stimulation of H2BK123ub in vivo and in vitro. To understand the molecular mechanisms that target Rad6 to its histone substrate, we identified the site of interaction for the HMD on Rad6. Using in vitro cross-linking followed by mass spectrometry, we localized the primary contact surface for the HMD to the highly conserved N-terminal helix of Rad6. Using a combination of genetic, biochemical, and in vivo protein cross-linking experiments, we characterized separation-of-function mutations in S. cerevisiae RAD6 that greatly impair the Rad6-HMD interaction and H2BK123 ubiquitylation but not other Rad6 functions. By employing RNA-sequencing as a sensitive approach for comparing mutant phenotypes, we show that mutating either side of the proposed Rad6-HMD interface yields strikingly similar transcriptome profiles that extensively overlap with those of a mutant that lacks the site of ubiquitylation in H2B. Our results fit a model in which a specific interface between a transcription elongation factor and a ubiquitin conjugase guides substrate selection toward a highly conserved chromatin target during active gene expression.
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Affiliation(s)
- Tasniem Fetian
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA15260
| | - Brendan M. McShane
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA15260
| | - Nicole L. Horan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA15260
| | - Donya N. Shodja
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA15260
| | - Jason D. True
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN46202
| | - Amber L. Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN46202
| | - Karen M. Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA15260
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Huynh MT, Sengupta B, Krajewski WA, Lee TH. Effects of Histone H2B Ubiquitylations and H3K79me 3 on Transcription Elongation. ACS Chem Biol 2023; 18:537-548. [PMID: 36857155 PMCID: PMC10023449 DOI: 10.1021/acschembio.2c00887] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Post-translational modifications of histone proteins often mediate gene regulation by altering the global and local stability of the nucleosome, the basic gene-packing unit of eukaryotes. We employed semisynthetic approaches to introduce histone H2B ubiquitylations at K34 (H2BK34ub) and K120 (H2BK120ub) and H3K79 trimethylation (H3K79me3). With these modified histones, we investigated their effects on the kinetics of transcription elongation by RNA polymerase II (Pol II) using single-molecule FRET. Pol II pauses at several locations within the nucleosome for a few seconds to minutes, which governs the overall transcription efficiency. We found that H2B ubiquitylations suppress pauses and shorten the pause durations near the nucleosome entry while H3K79me3 shortens the pause durations and increases the rate of RNA elongation near the center of the nucleosome. We also found that H2BK34ub facilitates partial rewrapping of the nucleosome upon Pol II passage. These observations suggest that H2B ubiquitylations promote transcription elongation and help maintain the chromatin structure by inducing and stabilizing nucleosome intermediates and that H3K79me3 facilitates Pol II progression possibly by destabilizing the local structure of the nucleosome. Our results provide the mechanisms of how these modifications coupled by a network of regulatory proteins facilitate transcription in two different regions of the nucleosome and help maintain the chromatin structure during active transcription.
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Affiliation(s)
- Mai T. Huynh
- Department of Chemistry, The Pennsylvania State University, State College, PA 16801, USA
| | - Bhaswati Sengupta
- Department of Chemistry, The Pennsylvania State University, State College, PA 16801, USA
| | - Wladyslaw A. Krajewski
- N. K. Koltsov Institute of Developmental Biology of Russian Academy of Sciences, Vavilova str. 26, Moscow, 119334, Russia
| | - Tae-Hee Lee
- Department of Chemistry, The Pennsylvania State University, State College, PA 16801, USA
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Zhang Y, Zhang Q, Zhang Y, Han J. The Role of Histone Modification in DNA Replication-Coupled Nucleosome Assembly and Cancer. Int J Mol Sci 2023; 24:ijms24054939. [PMID: 36902370 PMCID: PMC10003558 DOI: 10.3390/ijms24054939] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/28/2023] [Accepted: 01/29/2023] [Indexed: 03/08/2023] Open
Abstract
Histone modification regulates replication-coupled nucleosome assembly, DNA damage repair, and gene transcription. Changes or mutations in factors involved in nucleosome assembly are closely related to the development and pathogenesis of cancer and other human diseases and are essential for maintaining genomic stability and epigenetic information transmission. In this review, we discuss the role of different types of histone posttranslational modifications in DNA replication-coupled nucleosome assembly and disease. In recent years, histone modification has been found to affect the deposition of newly synthesized histones and the repair of DNA damage, further affecting the assembly process of DNA replication-coupled nucleosomes. We summarize the role of histone modification in the nucleosome assembly process. At the same time, we review the mechanism of histone modification in cancer development and briefly describe the application of histone modification small molecule inhibitors in cancer therapy.
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Huynh MT, Sengupta B, Krajewski WA, Lee TH. The Effects of Histone H2B ubiquitylations and H3K79me 3 on Transcription Elongation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522859. [PMID: 36712011 PMCID: PMC9881898 DOI: 10.1101/2023.01.05.522859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Post-translational modifications of histone proteins often mediate gene regulation by altering the global and local stability of the nucleosome, the basic gene-packing unit of eukaryotes. We employed semi-synthetic approaches to introduce histone H2B ubiquitylations at K34 (H2BK34ub) and K120 (H2BK120ub) and H3 K79 trimethylation (H3K79me3). With these modified histones, we investigated their effects on the kinetics of transcription elongation by RNA Polymerase II (Pol II) using single-molecule FRET. Pol II pauses at several locations within the nucleosome for a few seconds to minutes, which governs the overall transcription efficiency. We found that H2B ubiquitylations suppress pauses and shorten the pause durations near the nucleosome entry while H3K79me3 shortens the pause durations and increases the rate of RNA elongation near the center of the nucleosome. We also found that H2BK34ub facilitates partial rewrapping of the nucleosome upon Pol II passage. These observations suggest that H2B ubiquitylations promote transcription elongation and help maintain the chromatin structure by inducing and stabilizing nucleosome intermediates and that H3K79me3 facilitates Pol II progression possibly by destabilizing the local structure of the nucleosome. Our results provide the mechanisms of how these modifications coupled by a network of regulatory proteins facilitate transcription in two different regions of the nucleosome and help maintain the chromatin structure during active transcription.
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12
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Fanourgakis S, Synacheri AC, Lavigne MD, Konstantopoulos D, Fousteri M. Histone H2Bub dynamics in the 5' region of active genes are tightly linked to the UV-induced transcriptional response. Comput Struct Biotechnol J 2022; 21:614-629. [PMID: 36659919 PMCID: PMC9823127 DOI: 10.1016/j.csbj.2022.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/22/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
The timing and location of writing and erasing of histone modifications determine gene expression programs and are tightly controlled processes. One such modification is the monoubiquitination of histone H2B (H2Bub), whose precise level during transcription elongation is dynamically regulated by the synergistic action of RNF20/40 ubiquitin-ligase and the de-ubiquitinase (DUB) of the ATXN7L3-containing DUB modules. Here, we characterize the dynamics of H2Bub in transcription and explore its role in perspective with the recently updated model of UV damage-induced transcription reorganization. Employing integrative analysis of genome-wide high-throughput approaches, transcription inhibitors and ATXN7L3-DUB knockdown cells, we find that H2Bub levels and patterns depend on intron-exon architecture both in steady state and upon UV. Importantly, our analysis reveals a widespread redistribution of this histone mark, rather than a uniform loss as previously suggested, which closely mirrors the post-UV dynamics of elongating RNA Polymerase II (RNAPII) at transcribed loci. The observed effects are due to a direct inter-dependence on RNAPII local concentration and speed, and we show that deficient ATXN7L3-mediated DUB activity leads to increased elongation rates in both non-irradiated and irradiated conditions. Our data and the implementation of a high-resolution computational framework reveal that the H2Bub pattern follows that of RNAPII, both in the ATXNL3 knockdown and in response to UV guaranteeing faithful elongation speed, especially in the context of the transcription-driven DNA damage response.
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13
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Chen JJ, Stermer D, Tanny JC. Decoding histone ubiquitylation. Front Cell Dev Biol 2022; 10:968398. [PMID: 36105353 PMCID: PMC9464978 DOI: 10.3389/fcell.2022.968398] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Histone ubiquitylation is a critical part of both active and repressed transcriptional states, and lies at the heart of DNA damage repair signaling. The histone residues targeted for ubiquitylation are often highly conserved through evolution, and extensive functional studies of the enzymes that catalyze the ubiquitylation and de-ubiquitylation of histones have revealed key roles linked to cell growth and division, development, and disease in model systems ranging from yeast to human cells. Nonetheless, the downstream consequences of these modifications have only recently begun to be appreciated on a molecular level. Here we review the structure and function of proteins that act as effectors or “readers” of histone ubiquitylation. We highlight lessons learned about how ubiquitin recognition lends specificity and function to intermolecular interactions in the context of transcription and DNA repair, as well as what this might mean for how we think about histone modifications more broadly.
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14
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Zhou D, Wu Z, Park JG, Fiches GN, Li TW, Ma Q, Huang H, Biswas A, Martinez-Sobrido L, Santoso NG, Zhu J. FACT subunit SUPT16H associates with BRD4 and contributes to silencing of interferon signaling. Nucleic Acids Res 2022; 50:8700-8718. [PMID: 35904816 PMCID: PMC9410884 DOI: 10.1093/nar/gkac645] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 06/26/2022] [Accepted: 07/20/2022] [Indexed: 11/14/2022] Open
Abstract
FACT (FAcilitates Chromatin Transcription) is a heterodimeric protein complex composed of SUPT16H and SSRP1, and a histone chaperone participating in chromatin remodeling during gene transcription. FACT complex is profoundly regulated, and contributes to both gene activation and suppression. Here we reported that SUPT16H, a subunit of FACT, is acetylated in both epithelial and natural killer (NK) cells. The histone acetyltransferase TIP60 contributes to the acetylation of SUPT16H middle domain (MD) at lysine 674 (K674). Such acetylation of SUPT16H is recognized by bromodomain protein BRD4, which promotes protein stability of SUPT16H in both epithelial and NK cells. We further demonstrated that SUPT16H-BRD4 associates with histone modification enzymes (HDAC1, EZH2), and further regulates their activation status and/or promoter association as well as affects the relevant histone marks (H3ac, H3K9me3 and H3K27me3). BRD4 is known to profoundly regulate interferon (IFN) signaling, while such function of SUPT16H has never been explored. Surprisingly, our results revealed that SUPT16H genetic knockdown via RNAi or pharmacological inhibition by using its inhibitor, curaxin 137 (CBL0137), results in the induction of IFNs and interferon-stimulated genes (ISGs). Through this mechanism, depletion or inhibition of SUPT16H is shown to efficiently inhibit infection of multiple viruses, including Zika, influenza, and SARS-CoV-2. Furthermore, we demonstrated that depletion or inhibition of SUPT16H also causes the remarkable activation of IFN signaling in NK cells, which promotes the NK-mediated killing of virus-infected cells in a co-culture system using human primary NK cells. Overall, our studies unraveled the previously un-appreciated role of FACT complex in coordinating with BRD4 and regulating IFN signaling in both epithelial and NK cells, and also proposed the novel application of the FACT inhibitor CBL0137 to treat viral infections.
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Affiliation(s)
- Dawei Zhou
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Zhenyu Wu
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Department of Biomedical Informatics, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Jun-Gyu Park
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Guillaume N Fiches
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Tai-Wei Li
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Qin Ma
- Department of Biomedical Informatics, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Huachao Huang
- Department of Medicine, Columbia University Medical Center, NY, NY 10032, USA
| | - Ayan Biswas
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | | | - Netty G Santoso
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Jian Zhu
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
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15
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Schoelz JM, Riddle NC. Functions of HP1 proteins in transcriptional regulation. Epigenetics Chromatin 2022; 15:14. [PMID: 35526078 PMCID: PMC9078007 DOI: 10.1186/s13072-022-00453-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/18/2022] [Indexed: 01/24/2023] Open
Abstract
In eukaryotes, DNA is packaged into chromatin, which presents significant barriers to transcription. Non-histone chromatin proteins such as the Heterochromatin Protein 1 (HP1) proteins are critical regulators of transcription, contributing to gene regulation through a variety of molecular mechanisms. HP1 proteins are highly conserved, and many eukaryotic genomes contain multiple HP1 genes. Given the presence of multiple HP1 family members within a genome, HP1 proteins can have unique as well as shared functions. Here, we review the mechanisms by which HP1 proteins contribute to the regulation of transcription. Focusing on the Drosophila melanogaster HP1 proteins, we examine the role of these proteins in regulating the transcription of genes, transposable elements, and piRNA clusters. In D. melanogaster, as in other species, HP1 proteins can act as transcriptional repressors and activators. The available data reveal that the precise impact of HP1 proteins on gene expression is highly context dependent, on the specific HP1 protein involved, on its protein partners present, and on the specific chromatin context the interaction occurs in. As a group, HP1 proteins utilize a variety of mechanisms to contribute to transcriptional regulation, including both transcriptional (i.e. chromatin-based) and post-transcriptional (i.e. RNA-based) processes. Despite extensive studies of this important protein family, open questions regarding their functions in gene regulation remain, specifically regarding the role of hetero- versus homodimerization and post-translational modifications of HP1 proteins.
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Affiliation(s)
- John M Schoelz
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nicole C Riddle
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
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16
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Cohen A, Pataki E, Kupiec M, Weisman R. TOR complex 2 contributes to regulation of gene expression via inhibiting Gcn5 recruitment to subtelomeric and DNA replication stress genes. PLoS Genet 2022; 18:e1010061. [PMID: 35157728 PMCID: PMC8880919 DOI: 10.1371/journal.pgen.1010061] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/25/2022] [Accepted: 01/28/2022] [Indexed: 11/18/2022] Open
Abstract
The fission yeast TOR complex 2 (TORC2) is required for gene silencing at subtelomeric regions and for the induction of gene transcription in response to DNA replication stress. Thus, TORC2 affects transcription regulation both negatively and positively. Whether these two TORC2-dependent functions share a common molecular mechanism is currently unknown. Here, we show that Gad8 physically interacts with proteins that regulate transcription, including subunits of the Spt-Ada-Gcn5-acetyltransferase (SAGA) complex and the BET bromodomain protein Bdf2. We demonstrate that in the absence of TORC2, Gcn5, the histone acetyltransferase subunit of SAGA, accumulates at subtelomeric genes and at non-induced promoters of DNA replication genes. Remarkably, the loss of Gcn5 in TORC2 mutant cells restores gene silencing as well as transcriptional induction in response to DNA replication stress. Loss of Bdf2 alleviates excess of Gcn5 binding in TORC2 mutant cells and also rescues the aberrant regulation of transcription in these cells. Furthermore, the loss of either SAGA or Bdf2 suppresses the sensitivity of TORC2 mutant cells to a variety of stresses, including DNA replication, DNA damage, temperature and nutrient stresses. We suggest a role of TORC2 in transcriptional regulation that is critical for gene silencing and gene induction in response to stress and involves the binding of Gcn5 to the chromatin. A fundamental characteristic of signaling pathways is their role in the regulation of gene expression. Target of rapamycin (TOR), an atypical protein kinase, is a component of two highly conserved TOR complexes: TORC1 and TORC2. These complexes affect nuclear functions through their activity in the cytoplasm as well as directly, through nuclear TOR pools. We previously showed that in fission yeast, TORC2 and its downstream substrate Gad8 associate with the chromatin fraction. We have also demonstrated that TORC2-Gad8 is required for gene silencing and transcriptional induction in response to stresses. Here, we demonstrate that Gad8 physically associates with proteins of the transcriptional machinery. We found that the loss of two positive transcriptional regulators, the SAGA complex and the bromodomain protein Bdf2, restored gene silencing as well as stress-induced transcriptional induction in TORC2 mutant cells. Our data suggests that TORC2-Gad8 contributes to gene regulation through a mechanism involving the inhibition of the accumulation of Gcn5 at the chromatin. These findings suggest a novel and possibly conserved functional relationship between TORC2, Gcn5 and Bdf2. These proteins and protein complexes are key targets in cancer therapies, thus, deciphering their functional relationship may be valuable for combination therapy in personalized medicine.
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Affiliation(s)
- Adiel Cohen
- Department of Natural and Life Sciences, The Open University of Israel, Ra’anana, Israel
| | - Emese Pataki
- Department of Natural and Life Sciences, The Open University of Israel, Ra’anana, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine & Cancer Research, Tel Aviv University, Tel Aviv, Israel
| | - Ronit Weisman
- Department of Natural and Life Sciences, The Open University of Israel, Ra’anana, Israel
- * E-mail:
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17
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The histone chaperone FACT facilitates heterochromatin spreading by regulating histone turnover and H3K9 methylation states. Cell Rep 2021; 37:109944. [PMID: 34731638 PMCID: PMC8608617 DOI: 10.1016/j.celrep.2021.109944] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/14/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
Heterochromatin formation requires three distinct steps: nucleation, self-propagation (spreading) along the chromosome, and faithful maintenance after each replication cycle. Impeding any of those steps induces heterochromatin defects and improper gene expression. The essential histone chaperone FACT (facilitates chromatin transcription) has been implicated in heterochromatin silencing, but the mechanisms by which FACT engages in this process remain opaque. Here, we pinpoint its function to the heterochromatin spreading process in fission yeast. FACT impairment reduces nucleation-distal H3K9me3 and HP1/Swi6 accumulation at subtelomeres and derepresses genes in the vicinity of heterochromatin boundaries. FACT promotes spreading by repressing heterochromatic histone turnover, which is crucial for the H3K9me2 to me3 transition that enables spreading. FACT mutant spreading defects are suppressed by removal of the H3K9 methylation antagonist Epe1. Together, our study identifies FACT as a histone chaperone that promotes heterochromatin spreading and lends support to the model that regulated histone turnover controls the propagation of repressive methylation marks. Heterochromatin establishment requires distinct nucleation and spreading steps. Murawska et al. show that the conserved and essential histone chaperone FACT facilitates the heterochromatin spreading process by maintaining low heterochromatic histone turnover, which enables a productive H3K9 trimethylation step by the methyltransferase Clr4 in fission yeast.
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18
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Subtelomeric Chromatin in the Fission Yeast S. pombe. Microorganisms 2021; 9:microorganisms9091977. [PMID: 34576871 PMCID: PMC8466458 DOI: 10.3390/microorganisms9091977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/06/2021] [Accepted: 09/14/2021] [Indexed: 01/15/2023] Open
Abstract
Telomeres play important roles in safeguarding the genome. The specialized repressive chromatin that assembles at telomeres and subtelomeric domains is key to this protective role. However, in many organisms, the repetitive nature of telomeric and subtelomeric sequences has hindered research efforts. The fission yeast S. pombe has provided an important model system for dissection of chromatin biology due to the relative ease of genetic manipulation and strong conservation of important regulatory proteins with higher eukaryotes. Telomeres and the telomere-binding shelterin complex are highly conserved with mammals, as is the assembly of constitutive heterochromatin at subtelomeres. In this review, we seek to summarize recent work detailing the assembly of distinct chromatin structures within subtelomeric domains in fission yeast. These include the heterochromatic SH subtelomeric domains, the telomere-associated sequences (TAS), and ST chromatin domains that assemble highly condensed chromatin clusters called knobs. Specifically, we review new insights into the sequence of subtelomeric domains, the distinct types of chromatin that assemble on these sequences and how histone H3 K36 modifications influence these chromatin structures. We address the interplay between the subdomains of chromatin structure and how subtelomeric chromatin is influenced by both the telomere-bound shelterin complexes and by euchromatic chromatin regulators internal to the subtelomeric domain. Finally, we demonstrate that telomere clustering, which is mediated via the condensed ST chromatin knob domains, does not depend on knob assembly within these domains but on Set2, which mediates H3K36 methylation.
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19
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Shirra MK, Kocik RA, Ellison MA, Arndt KM. Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2021; 11:6360461. [PMID: 34499735 PMCID: PMC8527469 DOI: 10.1093/g3journal/jkab298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/17/2021] [Indexed: 11/13/2022]
Abstract
Maintenance of chromatin structure under the disruptive force of transcription requires cooperation among numerous regulatory factors. Histone post-translational modifications can regulate nucleosome stability and influence the disassembly and reassembly of nucleosomes during transcription elongation. The Paf1 transcription elongation complex, Paf1C, is required for several transcription-coupled histone modifications, including the mono-ubiquitylation of H2B. In Saccharomyces cerevisiae, amino acid substitutions in the Rtf1 subunit of Paf1C greatly diminish H2B ubiquitylation and cause transcription to initiate at a cryptic promoter within the coding region of the FLO8 gene, an indicator of chromatin disruption. In a genetic screen to identify factors that functionally interact with Paf1C, we identified mutations in HDA3, a gene encoding a subunit of the Hda1C histone deacetylase (HDAC), as suppressors of an rtf1 mutation. Absence of Hda1C also suppresses the cryptic initiation phenotype of other mutants defective in H2B ubiquitylation. The genetic interactions between Hda1C and the H2B ubiquitylation pathway appear specific: loss of Hda1C does not suppress the cryptic initiation phenotypes of other chromatin mutants and absence of other HDACs does not suppress the absence of H2B ubiquitylation. Providing further support for an appropriate balance of histone acetylation in regulating cryptic initiation, absence of the Sas3 histone acetyltransferase elevates cryptic initiation in rtf1 mutants. Our data suggest that the H2B ubiquitylation pathway and Hda1C coordinately regulate chromatin structure during transcription elongation and point to a potential role for a HDAC in supporting chromatin accessibility.
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Affiliation(s)
- Margaret K Shirra
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Rachel A Kocik
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Mitchell A Ellison
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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20
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Jeronimo C, Angel A, Nguyen VQ, Kim JM, Poitras C, Lambert E, Collin P, Mellor J, Wu C, Robert F. FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner. Mol Cell 2021; 81:3542-3559.e11. [PMID: 34380014 DOI: 10.1016/j.molcel.2021.07.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 05/25/2021] [Accepted: 07/12/2021] [Indexed: 12/29/2022]
Abstract
The histone chaperone FACT occupies transcribed regions where it plays prominent roles in maintaining chromatin integrity and preserving epigenetic information. How it is targeted to transcribed regions, however, remains unclear. Proposed models include docking on the RNA polymerase II (RNAPII) C-terminal domain (CTD), recruitment by elongation factors, recognition of modified histone tails, and binding partially disassembled nucleosomes. Here, we systematically test these and other scenarios in Saccharomyces cerevisiae and find that FACT binds transcribed chromatin, not RNAPII. Through a combination of high-resolution genome-wide mapping, single-molecule tracking, and mathematical modeling, we propose that FACT recognizes the +1 nucleosome, as it is partially unwrapped by the engaging RNAPII, and spreads to downstream nucleosomes aided by the chromatin remodeler Chd1. Our work clarifies how FACT interacts with genes, suggests a processive mechanism for FACT function, and provides a framework to further dissect the molecular mechanisms of transcription-coupled histone chaperoning.
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Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Andrew Angel
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Vu Q Nguyen
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jee Min Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Christian Poitras
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Elie Lambert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Pierre Collin
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boulevard Édouard-Montpetit, Montréal, QC H3T 1J4, Canada.
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21
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Measurement of histone replacement dynamics with genetically encoded exchange timers in yeast. Nat Biotechnol 2021; 39:1434-1443. [PMID: 34239087 DOI: 10.1038/s41587-021-00959-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 05/17/2021] [Indexed: 12/15/2022]
Abstract
Histone exchange between histones carrying position-specific marks and histones bearing general marks is important for gene regulation, but understanding of histone exchange remains incomplete. To overcome the poor time resolution of conventional pulse-chase histone labeling, we present a genetically encoded histone exchange timer sensitive to the duration that two tagged histone subunits co-reside at an individual genomic locus. We apply these sensors to map genome-wide patterns of histone exchange in yeast using single samples. Comparing H3 exchange in cycling and G1-arrested cells suggests that replication-independent H3 exchange occurs at several hundred nucleosomes (<1% of all nucleosomes) per minute, with a maximal rate at histone promoters. We observed substantial differences between the two nucleosome core subcomplexes: H2A-H2B subcomplexes undergo rapid transcription-dependent replacement within coding regions, whereas H3-H4 replacement occurs predominantly within promoter nucleosomes, in association with gene activation or repression. Our timers allow the in vivo study of histone exchange dynamics with minute time scale resolution.
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22
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Leng H, Liu S, Lei Y, Tang Y, Gu S, Hu J, Chen S, Feng J, Li Q. FACT interacts with Set3 HDAC and fine-tunes GAL1 transcription in response to environmental stimulation. Nucleic Acids Res 2021; 49:5502-5519. [PMID: 33963860 PMCID: PMC8191775 DOI: 10.1093/nar/gkab312] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 01/22/2023] Open
Abstract
The histone chaperone facilitates chromatin transactions (FACT) functions in various DNA transactions. How FACT performs these multiple functions remains largely unknown. Here, we found, for the first time, that the N-terminal domain of its Spt16 subunit interacts with the Set3 histone deacetylase complex (Set3C) and that FACT and Set3C function in the same pathway to regulate gene expression in some settings. We observed that Spt16-G132D mutant proteins show defects in binding to Set3C but not other reported FACT interactors. At the permissive temperature, induction of the GAL1 and GAL10 genes is reduced in both spt16-G132D and set3Δ cells, whereas transient upregulation of GAL10 noncoding RNA (ncRNA), which is transcribed from the 3′ end of the GAL10 gene, is elevated. Mutations that inhibit GAL10 ncRNA transcription reverse the GAL1 and GAL10 induction defects in spt16-G132D and set3Δ mutant cells. Mechanistically, set3Δ and FACT (spt16-G132D) mutants show reduced histone acetylation and increased nucleosome occupancy at the GAL1 promoter under inducing conditions and inhibition of GAL10 ncRNA transcription also partially reverses these chromatin changes. These results indicate that FACT interacts with Set3C, which in turn prevents uncontrolled GAL10 ncRNA expression and fine-tunes the expression of GAL genes upon a change in carbon source.
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Affiliation(s)
- He Leng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shaofeng Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yang Lei
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yuantao Tang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shijia Gu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Genome Editing Research Center, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jianxun Feng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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23
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Pinto D, Pagé V, Fisher RP, Tanny JC. New connections between ubiquitylation and methylation in the co-transcriptional histone modification network. Curr Genet 2021; 67:695-705. [PMID: 34089069 DOI: 10.1007/s00294-021-01196-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/27/2021] [Accepted: 05/29/2021] [Indexed: 01/01/2023]
Abstract
Co-transcriptional histone modifications are a ubiquitous feature of RNA polymerase II (RNAPII) transcription, with profound but incompletely understood effects on gene expression. Unlike the covalent marks found at promoters, which are thought to be instructive for transcriptional activation, these modifications occur in gene bodies as a result of transcription, which has made elucidation of their functions challenging. Here we review recent insights into the regulation and roles of two such modifications: monoubiquitylation of histone H2B at lysine 120 (H2Bub1) and methylation of histone H3 at lysine 36 (H3K36me). Both H2Bub1 and H3K36me are enriched in the coding regions of transcribed genes, with highly overlapping distributions, but they were thought to work largely independently. We highlight our recent demonstration that, as was previously shown for H3K36me, H2Bub1 signals to the histone deacetylase (HDAC) complex Rpd3S/Clr6-CII, and that Rpd3S/Clr6-CII and H2Bub1 function in the same pathway to repress aberrant antisense transcription initiating within gene coding regions. Moreover, both of these histone modification pathways are influenced by protein phosphorylation catalyzed by the cyclin-dependent kinases (CDKs) that regulate RNAPII elongation, chiefly Cdk9. Therefore, H2Bub1 and H3K36me are more tightly linked than previously thought, sharing both upstream regulatory inputs and downstream effectors. Moreover, these newfound connections suggest extensive, bidirectional signaling between RNAPII elongation complexes and chromatin-modifying enzymes, which helps to determine transcriptional outputs and should be a focus for future investigation.
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Affiliation(s)
- Daniel Pinto
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Vivane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada.
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Viktorovskaya O, Chuang J, Jain D, Reim NI, López-Rivera F, Murawska M, Spatt D, Churchman LS, Park PJ, Winston F. Essential histone chaperones collaborate to regulate transcription and chromatin integrity. Genes Dev 2021; 35:698-712. [PMID: 33888559 PMCID: PMC8091981 DOI: 10.1101/gad.348431.121] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/30/2021] [Indexed: 12/15/2022]
Abstract
Histone chaperones are critical for controlling chromatin integrity during transcription, DNA replication, and DNA repair. Three conserved and essential chaperones, Spt6, Spn1/Iws1, and FACT, associate with elongating RNA polymerase II and interact with each other physically and/or functionally; however, there is little understanding of their individual functions or their relationships with each other. In this study, we selected for suppressors of a temperature-sensitive spt6 mutation that disrupts the Spt6-Spn1 physical interaction and that also causes both transcription and chromatin defects. This selection identified novel mutations in FACT. Surprisingly, suppression by FACT did not restore the Spt6-Spn1 interaction, based on coimmunoprecipitation, ChIP, and mass spectrometry experiments. Furthermore, suppression by FACT bypassed the complete loss of Spn1. Interestingly, the FACT suppressor mutations cluster along the FACT-nucleosome interface, suggesting that they alter FACT-nucleosome interactions. In agreement with this observation, we showed that the spt6 mutation that disrupts the Spt6-Spn1 interaction caused an elevated level of FACT association with chromatin, while the FACT suppressors reduced the level of FACT-chromatin association, thereby restoring a normal Spt6-FACT balance on chromatin. Taken together, these studies reveal previously unknown regulation between histone chaperones that is critical for their essential in vivo functions.
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Affiliation(s)
- Olga Viktorovskaya
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - James Chuang
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dhawal Jain
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Natalia I Reim
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Francheska López-Rivera
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Magdalena Murawska
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dan Spatt
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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25
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Zhou D, Park JG, Wu Z, Huang H, Fiches GN, Biswas A, Li TW, Ma Q, Martinez-Sobrido L, Santoso N, Zhu J. FACT subunit SUPT16H associates with BRD4 and contributes to silencing of antiviral interferon signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.21.440833. [PMID: 33907746 PMCID: PMC8077571 DOI: 10.1101/2021.04.21.440833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
FACT ( FA cilitates C hromatin T ranscription) is a heterodimeric protein complex composed of SUPT16H and SSRP1, and a histone chaperone participating in chromatin remodeling during gene transcription. FACT complex is profoundly regulated, and contributes to both gene activation and suppression. Here we reported that SUPT16H, a subunit of FACT, is acetylated at lysine 674 (K674) of middle domain (MD), which involves TIP60 histone acetyltransferase. Such acetylation of SUPT16H is recognized by bromodomain protein BRD4, which promotes protein stability of SUPT16H. We further demonstrated that SUPT16H-BRD4 associates with histone modification enzymes (EZH2, HDAC1) and affects histone marks (H3K9me3, H3K27me3 and H3ac). BRD4 is known to profoundly regulate interferon (IFN) signaling, while such function of SUPT16H has never been explored. Surprisingly, our results revealed that SUPT16H genetic knockdown via RNAi or pharmacological inhibition by using its inhibitor, curaxin 137 (CBL0137), results in the induction of IFNs and interferon-stimulated genes (ISGs). Through this mechanism, CBL0137 is shown to efficiently inhibit infection of multiple viruses, including Zika, influenza, and SARS-CoV-2. Furthermore, we demonstrated that CBL0137 also causes the remarkable activation of IFN signaling in natural killer (NK) cells, which promotes the NK-mediated killing of virus-infected cells in a co-culture system using human primary NK cells. Overall, our studies unraveled the previously un-appreciated role of FACT complex in regulating IFN signaling in both epithelial and NK cells, and also proposed the novel application of CBL0137 to treat viral infections.
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Affiliation(s)
- Dawei Zhou
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Jun-Gyu Park
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Zhenyu Wu
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
- Department of Biomedical Informatics, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Huachao Huang
- Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Guillaume N. Fiches
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Ayan Biswas
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Tai-Wei Li
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Qin Ma
- Department of Biomedical Informatics, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | | | - Netty Santoso
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Jian Zhu
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
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26
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Proteasomal Regulation of Mammalian SPT16 in Controlling Transcription. Mol Cell Biol 2021; 41:MCB.00452-20. [PMID: 33526453 DOI: 10.1128/mcb.00452-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/22/2021] [Indexed: 02/07/2023] Open
Abstract
FACT (facilitates chromatin transcription), an essential and evolutionarily conserved heterodimer from yeast to humans, controls transcription and is found to be upregulated in various cancers. However, the basis for such upregulation is not clearly understood. Our recent results deciphering a new ubiquitin-proteasome system regulation of the FACT subunit SPT16 in orchestrating transcription in yeast hint at the involvement of the proteasome in controlling FACT in humans, with a link to cancer. To test this, we carried out experiments in human embryonic kidney (HEK293) cells, which revealed that human SPT16 undergoes ubiquitylation and that its abundance is increased following inhibition of the proteolytic activity of the proteasome, thus implying proteasomal regulation of human SPT16. Furthermore, we find that the increased abundance/expression of SPT16 in HEK293 cells alters the transcription of genes, including ones associated with cancer, and that the proteasomal degradation of SPT16 is impaired in kidney cancer (Caki-2) cells to upregulate SPT16. Like human SPT16, murine SPT16 in C2C12 cells also undergoes ubiquitylation and proteasomal degradation to regulate transcription. Collectively, our results reveal a proteasomal regulation of mammalian SPT16, with physiological relevance in controlling transcription, and implicate such proteasomal control in the upregulation of SPT16 in cancer.
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27
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Wang P, Yang W, Zhao S, Nashun B. Regulation of chromatin structure and function: insights into the histone chaperone FACT. Cell Cycle 2021; 20:465-479. [PMID: 33590780 DOI: 10.1080/15384101.2021.1881726] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In eukaryotic cells, changes in chromatin accessibility are necessary for chromatin to maintain its highly dynamic nature at different times during the cell cycle. Histone chaperones interact with histones and regulate chromatin dynamics. Facilitates chromatin transcription (FACT) is an important histone chaperone that plays crucial roles during various cellular processes. Here, we analyze the structural characteristics of FACT, discuss how FACT regulates nucleosome/chromatin reorganization and summarize possible functions of FACT in transcription, replication, and DNA repair. The possible involvement of FACT in cell fate determination is also discussed.Abbreviations: FACT: facilitates chromatin transcription, Spt16: suppressor of Ty16, SSRP1: structure-specific recognition protein-1, NTD: N-terminal domain, DD: dimerization domain, MD: middle domain, CTD: C-terminus domain, IDD: internal intrinsically disordered domain, HMG: high mobility group, CID: C-terminal intrinsically disordered domain, Nhp6: non-histone chromosomal protein 6, RNAPII: RNA polymerase II, CK2: casein kinase 2, AID: acidic inner disorder, PIC: pre-initiation complex, IR: ionizing radiation, DDSB: DNA double-strand break, PARlation: poly ADP-ribosylation, BER: base-excision repair, UVSSA: UV-stimulated scaffold protein A, HR: homologous recombination, CAF-1: chromatin assembly factor 1, Asf1: anti-silencing factor 1, Rtt106: regulator of Ty1 transposition protein 106, H3K56ac: H3K56 acetylation, KD: knock down, SETD2: SET domain containing 2, H3K36me3: trimethylation of lysine36 in histone H3, H2Bub: H2B ubiquitination, iPSCs: induced pluripotent stem cells, ESC: embryonic stem cell, H3K4me3: trimethylation of lysine 4 on histone H3 protein subunit, CHD1: chromodomain protein.
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Affiliation(s)
- Peijun Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Wanting Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Shuxin Zhao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Buhe Nashun
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
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28
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Formosa T, Winston F. The role of FACT in managing chromatin: disruption, assembly, or repair? Nucleic Acids Res 2020; 48:11929-11941. [PMID: 33104782 PMCID: PMC7708052 DOI: 10.1093/nar/gkaa912] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/20/2022] Open
Abstract
FACT (FAcilitates Chromatin Transcription) has long been considered to be a transcription elongation factor whose ability to destabilize nucleosomes promotes RNAPII progression on chromatin templates. However, this is just one function of this histone chaperone, as FACT also functions in DNA replication. While broadly conserved among eukaryotes and essential for viability in many organisms, dependence on FACT varies widely, with some differentiated cells proliferating normally in its absence. It is therefore unclear what the core functions of FACT are, whether they differ in different circumstances, and what makes FACT essential in some situations but not others. Here, we review recent advances and propose a unifying model for FACT activity. By analogy to DNA repair, we propose that the ability of FACT to both destabilize and assemble nucleosomes allows it to monitor and restore nucleosome integrity as part of a system of chromatin repair, in which disruptions in the packaging of DNA are sensed and returned to their normal state. The requirement for FACT then depends on the level of chromatin disruption occurring in the cell, and the cell's ability to tolerate packaging defects. The role of FACT in transcription would then be just one facet of a broader system for maintaining chromatin integrity.
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Affiliation(s)
- Tim Formosa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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29
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Chen F, Zhang W, Xie D, Gao T, Dong Z, Lu X. Histone chaperone FACT represses retrotransposon MERVL and MERVL-derived cryptic promoters. Nucleic Acids Res 2020; 48:10211-10225. [PMID: 32894293 PMCID: PMC7544220 DOI: 10.1093/nar/gkaa732] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022] Open
Abstract
Endogenous retroviruses (ERVs) were usually silenced by various histone modifications on histone H3 variants and respective histone chaperones in embryonic stem cells (ESCs). However, it is still unknown whether chaperones of other histones could repress ERVs. Here, we show that H2A/H2B histone chaperone FACT plays a critical role in silencing ERVs and ERV-derived cryptic promoters in ESCs. Loss of FACT component Ssrp1 activated MERVL whereas the re-introduction of Ssrp1 rescued the phenotype. Additionally, Ssrp1 interacted with MERVL and suppressed cryptic transcription of MERVL-fused genes. Remarkably, Ssrp1 interacted with and recruited H2B deubiquitinase Usp7 to Ssrp1 target genes. Suppression of Usp7 caused similar phenotypes as loss of Ssrp1. Furthermore, Usp7 acted by deubiquitinating H2Bub and thereby repressed the expression of MERVL-fused genes. Taken together, our study uncovers a unique mechanism by which FACT complex silences ERVs and ERV-derived cryptic promoters in ESCs.
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Affiliation(s)
- Fuquan Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Weiyu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Dan Xie
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Tingting Gao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
| | - Zhiqiang Dong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Life Sciences, Nankai University, Tianjin 300307, People's Republic of China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300350, People's Republic of China
- College of Pharmacy, Nankai University, Tianjin 300350, People's Republic of China
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30
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Sansó M, Parua PK, Pinto D, Svensson JP, Pagé V, Bitton DA, MacKinnon S, Garcia P, Hidalgo E, Bähler J, Tanny JC, Fisher RP. Cdk9 and H2Bub1 signal to Clr6-CII/Rpd3S to suppress aberrant antisense transcription. Nucleic Acids Res 2020; 48:7154-7168. [PMID: 32496538 PMCID: PMC7367204 DOI: 10.1093/nar/gkaa474] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/26/2020] [Indexed: 12/13/2022] Open
Abstract
Mono-ubiquitylation of histone H2B (H2Bub1) and phosphorylation of elongation factor Spt5 by cyclin-dependent kinase 9 (Cdk9) occur during transcription by RNA polymerase II (RNAPII), and are mutually dependent in fission yeast. It remained unclear whether Cdk9 and H2Bub1 cooperate to regulate the expression of individual genes. Here, we show that Cdk9 inhibition or H2Bub1 loss induces intragenic antisense transcription of ∼10% of fission yeast genes, with each perturbation affecting largely distinct subsets; ablation of both pathways de-represses antisense transcription of over half the genome. H2Bub1 and phospho-Spt5 have similar genome-wide distributions; both modifications are enriched, and directly proportional to each other, in coding regions, and decrease abruptly around the cleavage and polyadenylation signal (CPS). Cdk9-dependence of antisense suppression at specific genes correlates with high H2Bub1 occupancy, and with promoter-proximal RNAPII pausing. Genetic interactions link Cdk9, H2Bub1 and the histone deacetylase Clr6-CII, while combined Cdk9 inhibition and H2Bub1 loss impair Clr6-CII recruitment to chromatin and lead to decreased occupancy and increased acetylation of histones within gene coding regions. These results uncover novel interactions between co-transcriptional histone modification pathways, which link regulation of RNAPII transcription elongation to suppression of aberrant initiation.
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Affiliation(s)
- Miriam Sansó
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Pabitra K Parua
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Pinto
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - J Peter Svensson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Viviane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Danny A Bitton
- Research Department of Genetics, Evolution & Environment, University College, London, UK
| | - Sarah MacKinnon
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Patricia Garcia
- Departament de Ciènces Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena Hidalgo
- Departament de Ciènces Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jürg Bähler
- Research Department of Genetics, Evolution & Environment, University College, London, UK
| | - Jason C Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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31
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Nuclear Envelope Proteins Modulating the Heterochromatin Formation and Functions in Fission Yeast. Cells 2020; 9:cells9081908. [PMID: 32824370 PMCID: PMC7464478 DOI: 10.3390/cells9081908] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 12/16/2022] Open
Abstract
The nuclear envelope (NE) consists of the inner and outer nuclear membranes (INM and ONM), and the nuclear pore complex (NPC), which penetrates the double membrane. ONM continues with the endoplasmic reticulum (ER). INM and NPC can interact with chromatin to regulate the genetic activities of the chromosome. Studies in the fission yeast Schizosaccharomyces pombe have contributed to understanding the molecular mechanisms underlying heterochromatin formation by the RNAi-mediated and histone deacetylase machineries. Recent studies have demonstrated that NE proteins modulate heterochromatin formation and functions through interactions with heterochromatic regions, including the pericentromeric and the sub-telomeric regions. In this review, we first introduce the molecular mechanisms underlying the heterochromatin formation and functions in fission yeast, and then summarize the NE proteins that play a role in anchoring heterochromatic regions and in modulating heterochromatin formation and functions, highlighting roles for a conserved INM protein, Lem2.
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