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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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He B, Bie Q, Zhao R, Yan Y, Dong G, Zhang B, Wang S, Xu W, Tian D, Hao Y, Zhang Y, Zhao M, Xiong H, Zhang B. Arachidonic acid released by PIK3CA mutant tumor cells triggers malignant transformation of colonic epithelium by inducing chromatin remodeling. Cell Rep Med 2024; 5:101510. [PMID: 38614093 PMCID: PMC11148513 DOI: 10.1016/j.xcrm.2024.101510] [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: 10/31/2023] [Revised: 02/07/2024] [Accepted: 03/20/2024] [Indexed: 04/15/2024]
Abstract
Key gene mutations are essential for colorectal cancer (CRC) development; however, how the mutated tumor cells impact the surrounding normal cells to promote tumor progression has not been well defined. Here, we report that PIK3CA mutant tumor cells transmit oncogenic signals and result in malignant transformation of intestinal epithelial cells (IECs) via paracrine exosomal arachidonic acid (AA)-induced H3K4 trimethylation. Mechanistically, PIK3CA mutations sustain SGK3-FBW7-mediated stability of the cPLA2 protein, leading to the synthetic increase in AA, which is transported through exosome and accumulated in IECs. Transferred AA directly binds Menin and strengthens the interactions of Menin and MLL1/2 methyltransferase. Finally, the combination of VTP50469, an inhibitor of the Menin-MLL interaction, and alpelisib synergistically represses PDX tumors harboring PIK3CA mutations. Together, these findings unveil the metabolic link between PIK3CA mutant tumor cells and the IECs, highlighting AA as the potential target for the treatment of patients with CRC harboring PIK3CA mutations.
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Affiliation(s)
- Baoyu He
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong 272000, China; School of Integrative Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, China
| | - Qingli Bie
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong 272000, China; School of Integrative Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, China
| | - Rou Zhao
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong 272000, China
| | - Yugang Yan
- School of Medical Engineering, Jining Medical University, Jining, Shandong 272067, China
| | - Guanjun Dong
- Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, Shandong 272067, China
| | - Baogui Zhang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong 272000, China
| | - Sen Wang
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong 272000, China
| | - Wenrong Xu
- Key Laboratory of Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212000, China
| | - Dongxing Tian
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong 272000, China
| | - Yujun Hao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Yanhua Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Mingsheng Zhao
- Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, Shandong 272067, China
| | - Huabao Xiong
- Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, Shandong 272067, China.
| | - Bin Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong 272000, China.
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3
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Liu R, Chen X, Zhao F, Jiang Y, Lu Z, Ji H, Feng Y, Li J, Zhang H, Zheng J, Zhang J, Zhao Y. The COMPASS Complex Regulates Fungal Development and Virulence through Histone Crosstalk in the Fungal Pathogen Cryptococcus neoformans. J Fungi (Basel) 2023; 9:672. [PMID: 37367608 DOI: 10.3390/jof9060672] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 06/28/2023] Open
Abstract
The Complex of Proteins Associated with Set1 (COMPASS) methylates lysine K4 on histone H3 (H3K4) and is conserved from yeast to humans. Its subunits and regulatory roles in the meningitis-causing fungal pathogen Cryptococcus neoformans remain unknown. Here we identified the core subunits of the COMPASS complex in C. neoformans and C. deneoformans and confirmed their conserved roles in H3K4 methylation. Through AlphaFold modeling, we found that Set1, Bre2, Swd1, and Swd3 form the catalytic core of the COMPASS complex and regulate the cryptococcal yeast-to-hypha transition, thermal tolerance, and virulence. The COMPASS complex-mediated histone H3K4 methylation requires H2B mono-ubiquitination by Rad6/Bre1 and the Paf1 complex in order to activate the expression of genes specific for the yeast-to-hypha transition in C. deneoformans. Taken together, our findings demonstrate that putative COMPASS subunits function as a unified complex, contributing to cryptococcal development and virulence.
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Affiliation(s)
- Ruoyan Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaoyu Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Fujie Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yixuan Jiang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhenguo Lu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Huining Ji
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuanyuan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junqiang Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Heng Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Youbao Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
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4
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Chan J, Kumar A, Kono H. RNAPII driven post-translational modifications of nucleosomal histones. Trends Genet 2022; 38:1076-1095. [PMID: 35618507 DOI: 10.1016/j.tig.2022.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 04/08/2022] [Accepted: 04/22/2022] [Indexed: 12/12/2022]
Abstract
The current understanding of how specific distributions of histone post-translational modifications (PTMs) are achieved throughout the chromatin remains incomplete. This review focuses on the role of RNA polymerase II (RNAPII) in establishing H2BK120/K123 ubiquitination and H3K4/K36 methylation distribution. The rate of RNAPII transcription is mainly a function of the RNAPII elongation and recruitment rates. Two major mechanisms link RNAPII's transcription rate to the distribution of PTMs. First, the phosphorylation patterns of Ser2P/Ser5P in the C-terminal domain of RNAPII change as a function of time, since the start of elongation, linking them to the elongation rate. Ser2P/Ser5P recruits specific histone PTM enzymes/activators to the nucleosome. Second, multiple rounds of binding and catalysis by the enzymes are required to establish higher methylations (H3K4/36me3). Thus, methylation states are determined by the transcription rate. In summary, the first mechanism determines the location of methylations in the gene, while the second mechanism determines the methylation state.
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Affiliation(s)
- Justin Chan
- Molecular Modelling and Simulation (MMS) Team, Institute for Quantum Life Science (iQLS), National Institutes for Quantum Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Amarjeet Kumar
- Molecular Modelling and Simulation (MMS) Team, Institute for Quantum Life Science (iQLS), National Institutes for Quantum Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modelling and Simulation (MMS) Team, Institute for Quantum Life Science (iQLS), National Institutes for Quantum Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan.
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5
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Erlendson AA, Freitag M. Not all Is SET for Methylation: Evolution of Eukaryotic Protein Methyltransferases. Methods Mol Biol 2022; 2529:3-40. [PMID: 35733008 DOI: 10.1007/978-1-0716-2481-4_1] [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] [Indexed: 06/15/2023]
Abstract
Dynamic posttranslational modifications to canonical histones that constitute the nucleosome (H2A, H2B, H3, and H4) control all aspects of enzymatic transactions with DNA. Histone methylation has been studied heavily for the past 20 years, and our mechanistic understanding of the control and function of individual methylation events on specific histone arginine and lysine residues has been greatly improved over the past decade, driven by excellent new tools and methods. Here, we will summarize what is known about the distribution and some of the functions of protein methyltransferases from all major eukaryotic supergroups. The main conclusion is that protein, and specifically histone, methylation is an ancient process. Many taxa in all supergroups have lost some subfamilies of both protein arginine methyltransferases (PRMT) and the heavily studied SET domain lysine methyltransferases (KMT). Over time, novel subfamilies, especially of SET domain proteins, arose. We use the interactions between H3K27 and H3K36 methylation as one example for the complex circuitry of histone modifications that make up the "histone code," and we discuss one recent example (Paramecium Ezl1) for how extant enzymes that may resemble more ancient SET domain KMTs are able to modify two lysine residues that have divergent functions in plants, fungi, and animals. Complexity of SET domain KMT function in the well-studied plant and animal lineages arose not only by gene duplication but also acquisition of novel DNA- and histone-binding domains in certain subfamilies.
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Affiliation(s)
- Allyson A Erlendson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA.
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6
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Trainor BM, Ciccaglione K, Czymek M, Law MJ. Distinct requirements for the COMPASS core subunits Set1, Swd1, and Swd3 during meiosis in the budding yeast Saccharomyces cerevisiae. G3 GENES|GENOMES|GENETICS 2021; 11:6342418. [PMID: 34849786 PMCID: PMC8527496 DOI: 10.1093/g3journal/jkab283] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/02/2021] [Indexed: 11/21/2022]
Abstract
Meiosis-specific chromatin structures, guided by histone modifications, are critical mediators of a meiotic transient transcription program and progression through prophase I. Histone H3K4 can be methylated up to three times by the Set1-containing COMPASS complex and each methylation mark corresponds to a different chromatin conformation. The level of H3K4 modification is directed by the activity of additional COMPASS components. In this study, we characterized the role of the COMPASS subunits during meiosis in Saccharomyces cerevisiae. In vegetative cells, previous studies revealed a role for subunits Swd2, Sdc1, and Bre2 for H3K4me2 while Spp1 supported trimethylation. However, we found that Bre2 and Sdc1 are required for H3K4me3 as yeast prepare to enter meiosis while Spp1 is not. Interestingly, we identified distinct meiotic functions for the core COMPASS complex members that required for all H3K4me, Set1, Swd1, and Swd3. While Set1 and Swd1 are required for progression through early meiosis, Swd3 is critical for late meiosis and spore morphogenesis. Furthermore, the meiotic requirement for Set1 is independent of H3K4 methylation, suggesting the presence of nonhistone substrates. Finally, checkpoint suppression analyses indicate that Set1 and Swd1 are required for both homologous recombination and chromosome segregation. These data suggest that COMPASS has important new roles for meiosis that are independent of its well-characterized functions during mitotic divisions.
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Affiliation(s)
- Brandon M Trainor
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University-School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Kerri Ciccaglione
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University-School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Miranda Czymek
- Biochemistry and Molecular Biology Program, School of Natural Sciences and Mathematics, Stockton University, Galloway, NJ 08205, USA
| | - Michael J Law
- Biochemistry and Molecular Biology Program, School of Natural Sciences and Mathematics, Stockton University, Galloway, NJ 08205, USA
- Biology Program, School of Natural Sciences and Mathematics, Stockton University, Galloway, NJ 08205, USA
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7
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Separovich RJ, Wilkins MR. Ready, SET, Go: Post-translational regulation of the histone lysine methylation network in budding yeast. J Biol Chem 2021; 297:100939. [PMID: 34224729 PMCID: PMC8329514 DOI: 10.1016/j.jbc.2021.100939] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/25/2021] [Accepted: 07/01/2021] [Indexed: 11/21/2022] Open
Abstract
Histone lysine methylation is a key epigenetic modification that regulates eukaryotic transcription. Here, we comprehensively review the function and regulation of the histone methylation network in the budding yeast and model eukaryote, Saccharomyces cerevisiae. First, we outline the lysine methylation sites that are found on histone proteins in yeast (H3K4me1/2/3, H3K36me1/2/3, H3K79me1/2/3, and H4K5/8/12me1) and discuss their biological and cellular roles. Next, we detail the reduced but evolutionarily conserved suite of methyltransferase (Set1p, Set2p, Dot1p, and Set5p) and demethylase (Jhd1p, Jhd2p, Rph1p, and Gis1p) enzymes that are known to control histone lysine methylation in budding yeast cells. Specifically, we illustrate the domain architecture of the methylation enzymes and highlight the structural features that are required for their respective functions and molecular interactions. Finally, we discuss the prevalence of post-translational modifications on yeast histone methylation enzymes and how phosphorylation, acetylation, and ubiquitination in particular are emerging as key regulators of enzyme function. We note that it will be possible to completely connect the histone methylation network to the cell's signaling system, given that all methylation sites and cognate enzymes are known, most phosphosites on the enzymes are known, and the mapping of kinases to phosphosites is tractable owing to the modest set of protein kinases in yeast. Moving forward, we expect that the rich variety of post-translational modifications that decorates the histone methylation machinery will explain many of the unresolved questions surrounding the function and dynamics of this intricate epigenetic network.
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Affiliation(s)
- Ryan J Separovich
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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8
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Identification of Candida glabrata Transcriptional Regulators That Govern Stress Resistance and Virulence. Infect Immun 2021; 89:IAI.00146-20. [PMID: 33318139 DOI: 10.1128/iai.00146-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 12/04/2020] [Indexed: 12/16/2022] Open
Abstract
The mechanisms by which Candida glabrata resists host defense peptides and caspofungin are incompletely understood. To identify transcriptional regulators that enable C. glabrata to withstand these classes of stressors, a library of 215 C. glabrata transcriptional regulatory deletion mutants was screened for susceptibility to both protamine and caspofungin. We identified eight mutants that had increased susceptibility to both host defense peptides and caspofungin. Of these mutants, six were deleted for genes that were predicted to specify proteins involved in histone modification. These genes were ADA2, GCN5, SPT8, HOS2, RPD3, and SPP1 Deletion of ADA2, GCN5, and RPD3 also increased susceptibility to mammalian host defense peptides. The Δada2 and Δgcn5 mutants had increased susceptibility to other stressors, such as H2O2 and SDS. In the Galleria mellonella model of disseminated infection, the Δada2 and Δgcn5 mutants had attenuated virulence, whereas in neutropenic mice, the virulence of the Δada2 and Δrpd3 mutants was decreased. Thus, histone modification plays a central role in enabling C. glabrata to survive host defense peptides and caspofungin, and Ada2 and Rpd3 are essential for the maximal virulence of this organism during disseminated infection.
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The Set1 N-terminal domain and Swd2 interact with RNA polymerase II CTD to recruit COMPASS. Nat Commun 2020; 11:2181. [PMID: 32358498 PMCID: PMC7195483 DOI: 10.1038/s41467-020-16082-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/14/2020] [Indexed: 12/24/2022] Open
Abstract
Methylation of histone H3 lysine 4 (H3K4) by Set1/COMPASS occurs co-transcriptionally, and is important for gene regulation. Set1/COMPASS associates with the RNA polymerase II C-terminal domain (CTD) to establish proper levels and distribution of H3K4 methylations. However, details of CTD association remain unclear. Here we report that the Set1 N-terminal region and the COMPASS subunit Swd2, which interact with each other, are both needed for efficient CTD binding in Saccharomyces cerevisiae. Moreover, a single point mutation in Swd2 that affects its interaction with Set1 also impairs COMPASS recruitment to chromatin and H3K4 methylation. A CTD interaction domain (CID) from the protein Nrd1 can partially substitute for the Set1 N-terminal region to restore CTD interactions and histone methylation. However, even when Set1/COMPASS is recruited via the Nrd1 CID, histone H2B ubiquitylation is still required for efficient H3K4 methylation, indicating that H2Bub acts after the initial recruitment of COMPASS to chromatin.
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10
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Jiang H. The complex activities of the SET1/MLL complex core subunits in development and disease. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194560. [PMID: 32302696 DOI: 10.1016/j.bbagrm.2020.194560] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 01/14/2020] [Accepted: 04/09/2020] [Indexed: 12/14/2022]
Abstract
In mammalian cells, the SET1/MLL complexes are the main writers of the H3K4 methyl mark that is associated with active gene expression. The activities of these complexes are critically dependent on the association of the catalytic subunit with their shared core subunits, WDR5, RBBP5, ASH2L, and DPY30, collectively referred as WRAD. In addition, some of these core subunits can bind to proteins other than the SET1/MLL complex components. This review starts with discussion of the molecular activities of these core subunits, with an emphasis on DPY30 in organizing the assembly of the SET1/MLL complexes with other associated factors. This review then focuses on the roles of the core subunits in stem cells and development, as well as in diseased cell states, mainly cancer, and ends with discussion on dissecting the responsible activities of the core subunits and how we may target them for potential disease treatment. This article is part of a Special Issue entitled: The MLL family of proteins in normal development and disease edited by Thomas A Milne.
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Affiliation(s)
- Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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11
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Liu Y, Zhang M, Xie R, Zhang F, Wang S, Pan X, Wang S, Zhuang Z. The Methyltransferase AflSet1 Is Involved in Fungal Morphogenesis, AFB1 Biosynthesis, and Virulence of Aspergillus flavus. Front Microbiol 2020; 11:234. [PMID: 32132990 PMCID: PMC7040179 DOI: 10.3389/fmicb.2020.00234] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/31/2020] [Indexed: 11/17/2022] Open
Abstract
The filament fungal pathogen, Aspergillus flavus, spreads worldwide and contaminates several important crops. Histone posttranslational modifications are deeply involved in fungal development and virulence, but the biological function of the histone methyltransferase AflSet1 in A. flavus is still unknown. In the study, Aflset1 deletion strain was constructed through homologous recombination, and it was found that AflSet1 up-regulates hyphae growth, and promotes conidiation by sporulation regulation genes: abaA and brlA. It was also found that AflSet1 involves in sclerotia formation and AFB1 biosynthesis via sclerotia related transcriptional factors and orthodox AFB1 synthesis pathway, respectively. Crop models revealed that AflSet1 plays critical roles in colonization and AFB1 production on crop kernels. Lipase activity analysis suggested that AflSet1 affects fungal virulence to crops via digestive enzymes. Stresses tests revealed that AflSet1 is deeply involved in fungal resistance against osmotic, oxidative and cell membrane stress. The preparation of N_SET, SET domain deletion mutants and H988K mutant revealed that both domains play critical roles in fungal development and AFB1 production, and that H988 is very important in executing biological functions on morphogenesis and AFB1 synthesis. Subcellular location analysis revealed that AflSet1 is stably accumulated in nuclei in both spore germination and hyphae growth stages, even under the stress of SDS. Through immunoblot analysis, it was found that AflSet1 methylates H3K4me2 and me3 as well as H3K9me2. This study provides a solid evidence to discover the biological functions of histone methyltransferase in pathogenic fungi.
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Affiliation(s)
- Yaju Liu
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mengjuan Zhang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rui Xie
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Feng Zhang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sen Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaohua Pan
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhenhong Zhuang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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12
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Yang Y, Joshi M, Takahashi YH, Ning Z, Qu Q, Brunzelle JS, Skiniotis G, Figeys D, Shilatifard A, Couture JF. A non-canonical monovalent zinc finger stabilizes the integration of Cfp1 into the H3K4 methyltransferase complex COMPASS. Nucleic Acids Res 2020; 48:421-431. [PMID: 31724694 PMCID: PMC7145517 DOI: 10.1093/nar/gkz1037] [Citation(s) in RCA: 4] [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: 07/16/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 12/28/2022] Open
Abstract
COMPlex ASsociating with SET1 (COMPASS) is a histone H3 Lys-4 methyltransferase that typically marks the promoter region of actively transcribed genes. COMPASS is a multi-subunit complex in which the catalytic unit, SET1, is required for H3K4 methylation. An important subunit known to regulate SET1 methyltransferase activity is the CxxC zinc finger protein 1 (Cfp1). Cfp1 binds to COMPASS and is critical to maintain high level of H3K4me3 in cells but the mechanisms underlying its stimulatory activity is poorly understood. In this study, we show that Cfp1 only modestly activates COMPASS methyltransferase activity in vitro. Binding of Cfp1 to COMPASS is in part mediated by a new type of monovalent zinc finger (ZnF). This ZnF interacts with the COMPASS's subunits RbBP5 and disruption of this interaction blunts its methyltransferase activity in cells and in vivo. Collectively, our studies reveal that a novel form of ZnF on Cfp1 enables its integration into COMPASS and contributes to epigenetic signaling.
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Affiliation(s)
- Yidai Yang
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
| | - Monika Joshi
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
| | - Yoh-hei Takahashi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Zhibin Ning
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
| | - Qianhui Qu
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph S Brunzelle
- Northwestern Synchrotron Research Centers, Life Science Collaborative Access Team, Northwestern University, Evanston, IL, USA
| | - Georgios Skiniotis
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel Figeys
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Jean-François Couture
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
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13
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Structural basis for histone H3K4me3 recognition by the N-terminal domain of the PHD finger protein Spp1. Biochem J 2019; 476:1957-1973. [PMID: 31253666 DOI: 10.1042/bcj20190091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/21/2019] [Accepted: 06/28/2019] [Indexed: 02/07/2023]
Abstract
Saccharomyces cerevisiae Spp1, a plant homeodomain (PHD) finger containing protein, is a critical subunit of the histone H3K4 methyltransferase complex of proteins associated with Set1 (COMPASS). The chromatin binding affinity of the PHD finger of Spp1 has been proposed to modulate COMPASS activity. During meiosis, Spp1 plays another role in promoting programmed double-strand break (DSB) formation by binding H3K4me3 via its PHD finger and interacting with a DSB protein, Mer2. However, how the Spp1 PHD finger performs site-specific readout of H3K4me3 is still not fully understood. In the present study, we determined the crystal structure of the highly conserved Spp1 N-terminal domain (Sc_Spp1NTD) in complex with the H3K4me3 peptide. The structure shows that Sc_Spp1NTD comprises a PHD finger responsible for methylated H3K4 recognition and a C3H-type zinc finger necessary to ensure the overall structural stability. Our isothermal titration calorimetry results show that binding of H3K4me3 to Sc_Spp1NTD is mildly inhibited by H3R2 methylation, weakened by H3T6 phosphorylation, and abrogated by H3T3 phosphorylation. This histone modification cross-talk, which is conserved in the Saccharomyces pombe and mammalian orthologs of Sc_Spp1 in vitro, can be rationalized structurally and might contribute to the roles of Spp1 in COMPASS activity regulation and meiotic recombination.
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14
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Jeon J, McGinty RK, Muir TW, Kim JA, Kim J. Crosstalk among Set1 complex subunits involved in H2B ubiquitylation-dependent H3K4 methylation. Nucleic Acids Res 2019; 46:11129-11143. [PMID: 30325428 PMCID: PMC6265457 DOI: 10.1093/nar/gky920] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/07/2018] [Indexed: 02/06/2023] Open
Abstract
H2B ubiquitylation (H2Bub)-dependent H3K4 methylation is mediated by the multisubunit Set1 complex (Set1C) in yeast, but precisely how Set1C subunits contribute to this histone modification remains unclear. Here, using reconstituted Set1Cs and recombinant H2Bub chromatin, we identified Set1C subunits and domains involved in the H2Bub-dependent H3K4 methylation process, showing that the Spp1 PHDL domain, in conjunction with the Set1 n-SET domain, interacts with Swd1/Swd3 and that this interaction is essential for H2Bub-dependent H3K4 methylation. Importantly, Set1C containing an Spp1-Swd1 fusion bypasses the requirement for H2Bub for H3K4 methylation, suggesting that the role of H2Bub is to induce allosteric rearrangements of the subunit-interaction network within the active site of Set1C that are necessary for methylation activity. Moreover, the interaction between the Set1 N-terminal region and Swd1 renders the Spp1-lacking Set1C competent for H2Bub-dependent H3K4 methylation. Collectively, our results suggest that H2Bub induces conformational changes in Set1C that support H3K4 methylation activity.
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Affiliation(s)
- Jongcheol Jeon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Robert K McGinty
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Tom W Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, NJ 08544, USA
| | - Jung-Ae Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea.,Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, South Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
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15
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Alsulami M, Munawar N, Dillon E, Oliviero G, Wynne K, Alsolami M, Moss C, Ó Gaora P, O'Meara F, Cotter D, Cagney G. SETD1A Methyltransferase Is Physically and Functionally Linked to the DNA Damage Repair Protein RAD18. Mol Cell Proteomics 2019; 18:1428-1436. [PMID: 31076518 PMCID: PMC6601208 DOI: 10.1074/mcp.ra119.001518] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Indexed: 12/13/2022] Open
Abstract
SETD1A is a SET domain-containing methyltransferase involved in epigenetic regulation of transcription. It is the main catalytic component of a multiprotein complex that methylates lysine 4 of histone H3, a histone mark associated with gene activation. In humans, six related protein complexes with partly nonredundant cellular functions share several protein subunits but are distinguished by unique catalytic SET-domain proteins. We surveyed physical interactions of the SETD1A-complex using endogenous immunoprecipitation followed by label-free quantitative proteomics on three subunits: SETD1A, RBBP5, and ASH2L. Surprisingly, SETD1A, but not RBBP5 or ASH2L, was found to interact with the DNA damage repair protein RAD18. Reciprocal RAD18 immunoprecipitation experiments confirmed the interaction with SETD1A, whereas size exclusion and protein network analysis suggested an interaction independent of the main SETD1A complex. We found evidence of SETD1A and RAD18 influence on mutual gene expression levels. Further, knockdown of the genes individually showed a DNA damage repair phenotype, whereas simultaneous knockdown resulted in an epistatic effect. This adds to a growing body of work linking epigenetic enzymes to processes involved in genome stability.
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Affiliation(s)
- Manal Alsulami
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nayla Munawar
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; ¶Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
| | - Eugene Dillon
- §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Giorgio Oliviero
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kieran Wynne
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; ‖Maine Medical Center Research Institute, 81 Research Drive, Scarborough, Maine 04074
| | - Mona Alsolami
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Catherine Moss
- §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Peadar Ó Gaora
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Fergal O'Meara
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - David Cotter
- **Department of Psychiatry, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Gerard Cagney
- From the ‡School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, IRELAND;; §Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland;.
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16
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Alsulami M, Munawar N, Dillon E, Oliviero G, Wynne K, Alsolami M, Moss C, Ó Gaora P, O'Meara F, Cotter D, Cagney G. SETD1A Methyltransferase Is Physically and Functionally Linked to the DNA Damage Repair Protein RAD18. Mol Cell Proteomics 2019. [DOI: https://doi.org/10.1074/mcp.ra119.001518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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17
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Fiorucci AS, Bourbousse C, Concia L, Rougée M, Deton-Cabanillas AF, Zabulon G, Layat E, Latrasse D, Kim SK, Chaumont N, Lombard B, Stroebel D, Lemoine S, Mohammad A, Blugeon C, Loew D, Bailly C, Bowler C, Benhamed M, Barneche F. Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in H3K4me3 independently from histone H2B monoubiquitination. Genome Biol 2019; 20:100. [PMID: 31113491 PMCID: PMC6528313 DOI: 10.1186/s13059-019-1705-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/02/2019] [Indexed: 12/19/2022] Open
Abstract
Background The functional determinants of H3K4me3, their potential dependency on histone H2B monoubiquitination, and their contribution to defining transcriptional regimes are poorly defined in plant systems. Unlike in Saccharomyces cerevisiae, where a single SET1 protein catalyzes H3K4me3 as part of COMPlex of proteins ASsociated with Set1 (COMPASS), in Arabidopsis thaliana, this activity involves multiple histone methyltransferases. Among these, the plant-specific SET DOMAIN GROUP 2 (SDG2) has a prominent role. Results We report that SDG2 co-regulates hundreds of genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of yeast COMPASS. We show that S2Lb co-purifies with the AtCOMPASS core subunit WDR5, and both S2Lb and SDG2 directly influence H3K4me3 enrichment over highly transcribed genes. S2Lb knockout triggers pleiotropic developmental phenotypes at the vegetative and reproductive stages, including reduced fertility and seed dormancy. However, s2lb seedlings display little transcriptomic defects as compared to the large repertoire of genes targeted by S2Lb, SDG2, or H3K4me3, suggesting that H3K4me3 enrichment is important for optimal gene induction during cellular transitions rather than for determining on/off transcriptional status. Moreover, unlike in budding yeast, most of the S2Lb and H3K4me3 genomic distribution does not rely on a trans-histone crosstalk with histone H2B monoubiquitination. Conclusions Collectively, this study unveils that the evolutionarily conserved COMPASS-like complex has been co-opted by the plant-specific SDG2 histone methyltransferase and mediates H3K4me3 deposition through an H2B monoubiquitination-independent pathway in Arabidopsis. Electronic supplementary material The online version of this article (10.1186/s13059-019-1705-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anne-Sophie Fiorucci
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France.,Present address: Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Clara Bourbousse
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Lorenzo Concia
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Martin Rougée
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Anne-Flore Deton-Cabanillas
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Gérald Zabulon
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Elodie Layat
- Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, 75005, Paris, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Soon Kap Kim
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Nicole Chaumont
- Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, 75005, Paris, France
| | - Bérangère Lombard
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - David Stroebel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Sophie Lemoine
- Genomic Facility, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, Paris, 75005, France
| | - Ammara Mohammad
- Genomic Facility, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, Paris, 75005, France
| | - Corinne Blugeon
- Genomic Facility, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, Paris, 75005, France
| | - Damarys Loew
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Christophe Bailly
- Laboratoire de Biologie du Développement, Sorbonne Université, CNRS, 75005, Paris, France
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005, Paris, France.
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18
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Architecture and subunit arrangement of the complete Saccharomyces cerevisiae COMPASS complex. Sci Rep 2018; 8:17405. [PMID: 30479350 PMCID: PMC6258710 DOI: 10.1038/s41598-018-35609-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/17/2018] [Indexed: 01/08/2023] Open
Abstract
Methylation of histone H3 lysine 4 (H3K4) is catalyzed by the multi-component COMPASS or COMPASS-like complex, which is highly conserved from yeast to human, and plays essential roles in gene expression and transcription, cell cycle progression, and DNA repair. Here we present a cryo-EM map of the complete S. cerevisiae COMPASS complex. Through tag or Fab labeling strategy combined with cryo-EM 3D reconstruction and cross-linking and mass spectrometry (XL-MS) analysis, we uncovered new information on the subunit arrangement: Cps50, Cps35, and Cps30 were determined to group together to form the face region in the head of the complex, and Cps40 and the N-terminal portion of Set1 reside on the top of the head. Our map reveals the location of the active center and a canyon in the back of the head. Together, our study provides the first snapshot of the complete architecture of yeast COMPASS and a picture of its subunit interaction network, which could facilitate our understanding of the COMPASS machinery and its functionality.
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19
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Cruz C, Della Rosa M, Krueger C, Gao Q, Horkai D, King M, Field L, Houseley J. Tri-methylation of histone H3 lysine 4 facilitates gene expression in ageing cells. eLife 2018; 7:34081. [PMID: 30274593 PMCID: PMC6168286 DOI: 10.7554/elife.34081] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 09/17/2018] [Indexed: 12/21/2022] Open
Abstract
Transcription of protein coding genes is accompanied by recruitment of COMPASS to promoter-proximal chromatin, which methylates histone H3 lysine 4 (H3K4) to form H3K4me1, H3K4me2 and H3K4me3. Here, we determine the importance of COMPASS in maintaining gene expression across lifespan in budding yeast. We find that COMPASS mutations reduce replicative lifespan and cause expression defects in almost 500 genes. Although H3K4 methylation is reported to act primarily in gene repression, particularly in yeast, repressive functions are progressively lost with age while hundreds of genes become dependent on H3K4me3 for full expression. Basal and inducible expression of these genes is also impaired in young cells lacking COMPASS components Swd1 or Spp1. Gene induction during ageing is associated with increasing promoter H3K4me3, but H3K4me3 also accumulates in non-promoter regions and the ribosomal DNA. Our results provide clear evidence that H3K4me3 is required to maintain normal expression of many genes across organismal lifespan.
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Affiliation(s)
- Cristina Cruz
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Monica Della Rosa
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Christel Krueger
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Qian Gao
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Dorottya Horkai
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Michelle King
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Lucy Field
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Jonathan Houseley
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
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20
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Haddad JF, Yang Y, Takahashi YH, Joshi M, Chaudhary N, Woodfin AR, Benyoucef A, Yeung S, Brunzelle JS, Skiniotis G, Brand M, Shilatifard A, Couture JF. Structural Analysis of the Ash2L/Dpy-30 Complex Reveals a Heterogeneity in H3K4 Methylation. Structure 2018; 26:1594-1603.e4. [PMID: 30270175 DOI: 10.1016/j.str.2018.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/28/2018] [Accepted: 08/08/2018] [Indexed: 01/09/2023]
Abstract
Dpy-30 is a regulatory subunit controlling the histone methyltransferase activity of the KMT2 enzymes in vivo. Paradoxically, in vitro methyltransferase assays revealed that Dpy-30 only modestly participates in the positive heterotypic allosteric regulation of these methyltransferases. Detailed genome-wide, molecular and structural studies reveal that an extensive network of interactions taking place at the interface between Dpy-30 and Ash2L are critical for the correct placement, genome-wide, of H3K4me2 and H3K4me3 but marginally contribute to the methyltransferase activity of KMT2 enzymes in vitro. Moreover, we show that H3K4me2 peaks persisting following the loss of Dpy-30 are found in regions of highly transcribed genes, highlighting an interplay between Complex of Proteins Associated with SET1 (COMPASS) kinetics and the cycling of RNA polymerase to control H3K4 methylation. Overall, our data suggest that Dpy-30 couples its modest positive heterotypic allosteric regulation of KMT2 methyltransferase activity with its ability to help the positioning of SET1/COMPASS to control epigenetic signaling.
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Affiliation(s)
- John Faissal Haddad
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Yidai Yang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Yoh-Hei Takahashi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Monika Joshi
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Nidhi Chaudhary
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Ashley R Woodfin
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Aissa Benyoucef
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Sylvain Yeung
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada
| | - Joseph S Brunzelle
- Northwestern Synchrotron Research Centers, Life Science Collaborative Access Team, Northwestern University, Evanston, IL, USA
| | - Georgios Skiniotis
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marjorie Brand
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8L6, Canada
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Roger Guindon Hall, Ottawa, ON K1H 8M5, Canada.
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21
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Qu Q, Takahashi YH, Yang Y, Hu H, Zhang Y, Brunzelle JS, Couture JF, Shilatifard A, Skiniotis G. Structure and Conformational Dynamics of a COMPASS Histone H3K4 Methyltransferase Complex. Cell 2018; 174:1117-1126.e12. [PMID: 30100186 PMCID: PMC6108936 DOI: 10.1016/j.cell.2018.07.020] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/25/2018] [Accepted: 07/16/2018] [Indexed: 11/25/2022]
Abstract
The methylation of histone 3 lysine 4 (H3K4) is carried out by an evolutionarily conserved family of methyltransferases referred to as complex of proteins associated with Set1 (COMPASS). The activity of the catalytic SET domain (su(var)3-9, enhancer-of-zeste, and trithorax) is endowed through forming a complex with a set of core proteins that are widely shared from yeast to humans. We obtained cryo-electron microscopy (cryo-EM) maps of the yeast Set1/COMPASS core complex at overall 4.0- to 4.4-Å resolution, providing insights into its structural organization and conformational dynamics. The Cps50 C-terminal tail weaves within the complex to provide a central scaffold for assembly. The SET domain, snugly positioned at the junction of the Y-shaped complex, is extensively contacted by Cps60 (Bre2), Cps50 (Swd1), and Cps30 (Swd3). The mobile SET-I motif of the SET domain is engaged by Cps30, explaining its key role in COMPASS catalytic activity toward higher H3K4 methylation states.
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Affiliation(s)
- Qianhui Qu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yoh-Hei Takahashi
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Yidai Yang
- Department of Biochemistry, Microbiology, and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa ON K1H 8M5, Canada
| | - Hongli Hu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yan Zhang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph S Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, IL 60439, USA
| | - Jean-Francois Couture
- Department of Biochemistry, Microbiology, and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa ON K1H 8M5, Canada
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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22
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Crystal Structure of the COMPASS H3K4 Methyltransferase Catalytic Module. Cell 2018; 174:1106-1116.e9. [PMID: 30100181 PMCID: PMC6108940 DOI: 10.1016/j.cell.2018.06.038] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/08/2018] [Accepted: 06/20/2018] [Indexed: 01/07/2023]
Abstract
The SET1/MLL family of histone methyltransferases is conserved in eukaryotes and regulates transcription by catalyzing histone H3K4 mono-, di-, and tri-methylation. These enzymes form a common five-subunit catalytic core whose assembly is critical for their basal and regulated enzymatic activities through unknown mechanisms. Here, we present the crystal structure of the intact yeast COMPASS histone methyltransferase catalytic module consisting of Swd1, Swd3, Bre2, Sdc1, and Set1. The complex is organized by Swd1, whose conserved C-terminal tail not only nucleates Swd3 and a Bre2-Sdc1 subcomplex, but also joins Set1 to construct a regulatory pocket next to the catalytic site. This inter-subunit pocket is targeted by a previously unrecognized enzyme-modulating motif in Swd3 and features a doorstop-style mechanism dictating substrate selectivity among SET1/MLL family members. By spatially mapping the functional components of COMPASS, our results provide a structural framework for understanding the multifaceted functions and regulation of the H3K4 methyltransferase family.
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Stricker G, Galinier M, Gagneur J. GenoGAM 2.0: scalable and efficient implementation of genome-wide generalized additive models for gigabase-scale genomes. BMC Bioinformatics 2018; 19:247. [PMID: 29945559 PMCID: PMC6020310 DOI: 10.1186/s12859-018-2238-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/12/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND GenoGAM (Genome-wide generalized additive models) is a powerful statistical modeling tool for the analysis of ChIP-Seq data with flexible factorial design experiments. However large runtime and memory requirements of its current implementation prohibit its application to gigabase-scale genomes such as mammalian genomes. RESULTS Here we present GenoGAM 2.0, a scalable and efficient implementation that is 2 to 3 orders of magnitude faster than the previous version. This is achieved by exploiting the sparsity of the model using the SuperLU direct solver for parameter fitting, and sparse Cholesky factorization together with the sparse inverse subset algorithm for computing standard errors. Furthermore the HDF5 library is employed to store data efficiently on hard drive, reducing memory footprint while keeping I/O low. Whole-genome fits for human ChIP-seq datasets (ca. 300 million parameters) could be obtained in less than 9 hours on a standard 60-core server. GenoGAM 2.0 is implemented as an open source R package and currently available on GitHub. A Bioconductor release of the new version is in preparation. CONCLUSIONS We have vastly improved the performance of the GenoGAM framework, opening up its application to all types of organisms. Moreover, our algorithmic improvements for fitting large GAMs could be of interest to the statistical community beyond the genomics field.
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Affiliation(s)
- Georg Stricker
- Department of Informatics, Technical University Munich, Boltzmannstr. 3, Garching, Germany
| | - Mathilde Galinier
- Department of Informatics, Technical University Munich, Boltzmannstr. 3, Garching, Germany
| | - Julien Gagneur
- Department of Informatics, Technical University Munich, Boltzmannstr. 3, Garching, Germany
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24
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Abstract
Protein lysine methylation is a distinct posttranslational modification that causes minimal changes in the size and electrostatic status of lysine residues. Lysine methylation plays essential roles in regulating fates and functions of target proteins in an epigenetic manner. As a result, substrates and degrees (free versus mono/di/tri) of protein lysine methylation are orchestrated within cells by balanced activities of protein lysine methyltransferases (PKMTs) and demethylases (KDMs). Their dysregulation is often associated with neurological disorders, developmental abnormalities, or cancer. Methyllysine-containing proteins can be recognized by downstream effector proteins, which contain methyllysine reader domains, to relay their biological functions. While numerous efforts have been made to annotate biological roles of protein lysine methylation, limited work has been done to uncover mechanisms associated with this modification at a molecular or atomic level. Given distinct biophysical and biochemical properties of methyllysine, this review will focus on chemical and biochemical aspects in addition, recognition, and removal of this posttranslational mark. Chemical and biophysical methods to profile PKMT substrates will be discussed along with classification of PKMT inhibitors for accurate perturbation of methyltransferase activities. Semisynthesis of methyllysine-containing proteins will also be covered given the critical need for these reagents to unambiguously define functional roles of protein lysine methylation.
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Affiliation(s)
- Minkui Luo
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Program of Pharmacology, Weill Graduate School of Medical Science , Cornell University , New York , New York 10021 , United States
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25
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Stricker G, Engelhardt A, Schulz D, Schmid M, Tresch A, Gagneur J. GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis. Bioinformatics 2018; 33:2258-2265. [PMID: 28369277 DOI: 10.1093/bioinformatics/btx150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 03/20/2017] [Indexed: 11/14/2022] Open
Abstract
Motivation Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is a widely used approach to study protein-DNA interactions. Often, the quantities of interest are the differential occupancies relative to controls, between genetic backgrounds, treatments, or combinations thereof. Current methods for differential occupancy of ChIP-Seq data rely however on binning or sliding window techniques, for which the choice of the window and bin sizes are subjective. Results Here, we present GenoGAM (Genome-wide Generalized Additive Model), which brings the well-established and flexible generalized additive models framework to genomic applications using a data parallelism strategy. We model ChIP-Seq read count frequencies as products of smooth functions along chromosomes. Smoothing parameters are objectively estimated from the data by cross-validation, eliminating ad hoc binning and windowing needed by current approaches. GenoGAM provides base-level and region-level significance testing for full factorial designs. Application to a ChIP-Seq dataset in yeast showed increased sensitivity over existing differential occupancy methods while controlling for type I error rate. By analyzing a set of DNA methylation data and illustrating an extension to a peak caller, we further demonstrate the potential of GenoGAM as a generic statistical modeling tool for genome-wide assays. Availability and Implementation Software is available from Bioconductor: https://www.bioconductor.org/packages/release/bioc/html/GenoGAM.html . Contact gagneur@in.tum.de. Supplementary information Supplementary information is available at Bioinformatics online.
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Affiliation(s)
- Georg Stricker
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 80333 Munich, Germany.,Department of Informatics, Technische Universität München, 85748 Garching, Germany
| | - Alexander Engelhardt
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Daniel Schulz
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Matthias Schmid
- Institut für Medizinische Biometrie, Informatik und Epidemiologie, University Hospital Bonn, 53105 Bonn, Germany
| | - Achim Tresch
- Institute for Genetics, University of Cologne, 50647 Cologne, Germany
| | - Julien Gagneur
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 80333 Munich, Germany.,Department of Informatics, Technische Universität München, 85748 Garching, Germany
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26
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Li D, Sun H, Sun WJ, Bao HB, Si SH, Fan JL, Lin P, Cui RJ, Pan YJ, Wen SM, Zheng XL, Yu XG. Role of RbBP5 and H3K4me3 in the vicinity of Snail transcription start site during epithelial-mesenchymal transition in prostate cancer cell. Oncotarget 2018; 7:65553-65567. [PMID: 27566588 PMCID: PMC5323174 DOI: 10.18632/oncotarget.11549] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/13/2016] [Indexed: 01/09/2023] Open
Abstract
EMT (epithelial-mesenchymal transition) occurs in a wide range of tumor types, and has been shown to be crucial for metastasis. Epigenetic modifications of histones contribute to chromatin structure and result in the alterations in gene expression. Tri-methylation of histone H3 lysine 4 (H3K4me3) is associated with the promoters of actively transcribed genes and can serve as a transcriptional on/off switch. RbBP5 is a component of the COMPASS/ -like complex, which catalyzes H3K4me3 formation. In this study, we found that in the process of TGF-Beta1 induced EMT in the prostate cancer cell line DU145, H3K4me3 enrichment and RbBP5 binding increased in the vicinity of Snail (SNAI1) transcription start site. Knocking-down of RbBP5 notably decreased Snail expression and EMT. Recruitment of RbBP5 and formation of H3K4me3 at Snail TSS during EMT depend on binding of SMAD2/3 and CBP at Snail TSS. This study links the SMAD2/3 signal with Snail transcription via a histone modification - H3K4me3. Furthermore, our research also demonstrates that RbBP5 and even WRAD may be a promising therapeutic candidates in treating prostate cancer metastasis, and that DU145 cells maintain their incomplete mesenchymal state in an auto/paracrine manner.
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Affiliation(s)
- Dong Li
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Hui Sun
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China.,Department of Clinical Laboratory, The Second Clinical Medical School of Inner Mongolia University for The Nationalities, (Inner Mongolia Forestry General Hospital), Hulunbuir, Inner Mongolia 022150, P.R. China
| | - Wen-Jing Sun
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Hong-Bo Bao
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, P.R. China
| | - Shu-Han Si
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Jia-Lin Fan
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Ping Lin
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Rong-Jun Cui
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China.,Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, Heilongjiang 157000, P.R. China
| | - Yu-Jia Pan
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Si-Min Wen
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Xiu-Lan Zheng
- Department of Ultrasonography, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150081, P.R. China
| | - Xiao-Guang Yu
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
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27
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Beckwith SL, Schwartz EK, García-Nieto PE, King DA, Gowans GJ, Wong KM, Eckley TL, Paraschuk AP, Peltan EL, Lee LR, Yao W, Morrison AJ. The INO80 chromatin remodeler sustains metabolic stability by promoting TOR signaling and regulating histone acetylation. PLoS Genet 2018; 14:e1007216. [PMID: 29462149 PMCID: PMC5834206 DOI: 10.1371/journal.pgen.1007216] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/02/2018] [Accepted: 01/23/2018] [Indexed: 12/16/2022] Open
Abstract
Chromatin remodeling complexes are essential for gene expression programs that coordinate cell function with metabolic status. However, how these remodelers are integrated in metabolic stability pathways is not well known. Here, we report an expansive genetic screen with chromatin remodelers and metabolic regulators in Saccharomyces cerevisiae. We found that, unlike the SWR1 remodeler, the INO80 chromatin remodeling complex is composed of multiple distinct functional subunit modules. We identified a strikingly divergent genetic signature for the Ies6 subunit module that links the INO80 complex to metabolic homeostasis. In particular, mitochondrial maintenance is disrupted in ies6 mutants. INO80 is also needed to communicate TORC1-mediated signaling to chromatin, as ino80 mutants exhibit defective transcriptional profiles and altered histone acetylation of TORC1-responsive genes. Furthermore, comparative analysis reveals subunits of INO80 and mTORC1 have high co-occurrence of alterations in human cancers. Collectively, these results demonstrate that the INO80 complex is a central component of metabolic homeostasis that influences histone acetylation and may contribute to disease when disrupted.
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Affiliation(s)
- Sean L. Beckwith
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | - Erin K. Schwartz
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | | | - Devin A. King
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | - Graeme J. Gowans
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | - Ka Man Wong
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | - Tessa L. Eckley
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | | | - Egan L. Peltan
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | - Laura R. Lee
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | - Wei Yao
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | - Ashby J. Morrison
- Department of Biology, Stanford University, Stanford, CA, United States of America
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28
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Soares LM, He PC, Chun Y, Suh H, Kim T, Buratowski S. Determinants of Histone H3K4 Methylation Patterns. Mol Cell 2017; 68:773-785.e6. [PMID: 29129639 DOI: 10.1016/j.molcel.2017.10.013] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 08/23/2017] [Accepted: 10/12/2017] [Indexed: 11/28/2022]
Abstract
Various factors differentially recognize trimethylated histone H3 lysine 4 (H3K4me3) near promoters, H3K4me2 just downstream, and promoter-distal H3K4me1 to modulate gene expression. This methylation "gradient" is thought to result from preferential binding of the H3K4 methyltransferase Set1/complex associated with Set1 (COMPASS) to promoter-proximal RNA polymerase II. However, other studies have suggested that location-specific cues allosterically activate Set1. Chromatin immunoprecipitation sequencing (ChIP-seq) experiments show that H3K4 methylation patterns on active genes are not universal or fixed and change in response to both transcription elongation rate and frequency as well as reduced COMPASS activity. Fusing Set1 to RNA polymerase II results in H3K4me2 throughout transcribed regions and similarly extended H3K4me3 on highly transcribed genes. Tethered Set1 still requires histone H2B ubiquitylation for activity. These results show that higher-level methylations reflect not only Set1/COMPASS recruitment but also multiple rounds of transcription. This model provides a simple explanation for non-canonical methylation patterns at some loci or in certain COMPASS mutants.
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Affiliation(s)
- Luis M Soares
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - P Cody He
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yujin Chun
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Hyunsuk Suh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - TaeSoo Kim
- Department of Life Science, Ewha Womans University, Seoul 03760, Korea
| | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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29
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Vosnakis N, Koch M, Scheer E, Kessler P, Mély Y, Didier P, Tora L. Coactivators and general transcription factors have two distinct dynamic populations dependent on transcription. EMBO J 2017; 36:2710-2725. [PMID: 28724529 PMCID: PMC5599802 DOI: 10.15252/embj.201696035] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 06/08/2017] [Accepted: 06/15/2017] [Indexed: 12/29/2022] Open
Abstract
SAGA and ATAC are two distinct chromatin modifying co‐activator complexes with distinct enzymatic activities involved in RNA polymerase II (Pol II) transcription regulation. To investigate the mobility of co‐activator complexes and general transcription factors in live‐cell nuclei, we performed imaging experiments based on photobleaching. SAGA and ATAC, but also two general transcription factors (TFIID and TFIIB), were highly dynamic, exhibiting mainly transient associations with chromatin, contrary to Pol II, which formed more stable chromatin interactions. Fluorescence correlation spectroscopy analyses revealed that the mobile pool of the two co‐activators, as well as that of TFIID and TFIIB, can be subdivided into “fast” (free) and “slow” (chromatin‐interacting) populations. Inhibiting transcription elongation decreased H3K4 trimethylation and reduced the “slow” population of SAGA, ATAC, TFIIB and TFIID. In addition, inhibiting histone H3K4 trimethylation also reduced the “slow” populations of SAGA and ATAC. Thus, our results demonstrate that in the nuclei of live cells the equilibrium between fast and slow population of SAGA or ATAC complexes is regulated by active transcription via changes in the abundance of H3K4me3 on chromatin.
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Affiliation(s)
- Nikolaos Vosnakis
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Marc Koch
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Pascal Kessler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Yves Mély
- Université de Strasbourg, Illkirch, France.,Laboratoire de Biophotonique et Pharmacologie, Illkirch, France
| | - Pascal Didier
- Université de Strasbourg, Illkirch, France.,Laboratoire de Biophotonique et Pharmacologie, Illkirch, France
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
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30
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D'Urso A, Takahashi YH, Xiong B, Marone J, Coukos R, Randise-Hinchliff C, Wang JP, Shilatifard A, Brickner JH. Set1/COMPASS and Mediator are repurposed to promote epigenetic transcriptional memory. eLife 2016; 5:e16691. [PMID: 27336723 DOI: 10.7554/elife.16691.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/22/2016] [Indexed: 05/21/2023] Open
Abstract
In yeast and humans, previous experiences can lead to epigenetic transcriptional memory: repressed genes that exhibit mitotically heritable changes in chromatin structure and promoter recruitment of poised RNA polymerase II preinitiation complex (RNAPII PIC), which enhances future reactivation. Here, we show that INO1 memory in yeast is initiated by binding of the Sfl1 transcription factor to the cis-acting Memory Recruitment Sequence, targeting INO1 to the nuclear periphery. Memory requires a remodeled form of the Set1/COMPASS methyltransferase lacking Spp1, which dimethylates histone H3 lysine 4 (H3K4me2). H3K4me2 recruits the SET3C complex, which plays an essential role in maintaining this mark. Finally, while active INO1 is associated with Cdk8(-) Mediator, during memory, Cdk8(+) Mediator recruits poised RNAPII PIC lacking the Kin28 CTD kinase. Aspects of this mechanism are generalizable to yeast and conserved in human cells. Thus, COMPASS and Mediator are repurposed to promote epigenetic transcriptional poising by a highly conserved mechanism.
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Affiliation(s)
- Agustina D'Urso
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Yoh-Hei Takahashi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, United States
| | - Bin Xiong
- Department of Statistics, Northwestern University, Evanston, United States
| | - Jessica Marone
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Robert Coukos
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | | | - Ji-Ping Wang
- Department of Statistics, Northwestern University, Evanston, United States
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, United States
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
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31
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D'Urso A, Takahashi YH, Xiong B, Marone J, Coukos R, Randise-Hinchliff C, Wang JP, Shilatifard A, Brickner JH. Set1/COMPASS and Mediator are repurposed to promote epigenetic transcriptional memory. eLife 2016; 5. [PMID: 27336723 PMCID: PMC4951200 DOI: 10.7554/elife.16691] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/22/2016] [Indexed: 12/17/2022] Open
Abstract
In yeast and humans, previous experiences can lead to epigenetic transcriptional memory: repressed genes that exhibit mitotically heritable changes in chromatin structure and promoter recruitment of poised RNA polymerase II preinitiation complex (RNAPII PIC), which enhances future reactivation. Here, we show that INO1 memory in yeast is initiated by binding of the Sfl1 transcription factor to the cis-acting Memory Recruitment Sequence, targeting INO1 to the nuclear periphery. Memory requires a remodeled form of the Set1/COMPASS methyltransferase lacking Spp1, which dimethylates histone H3 lysine 4 (H3K4me2). H3K4me2 recruits the SET3C complex, which plays an essential role in maintaining this mark. Finally, while active INO1 is associated with Cdk8- Mediator, during memory, Cdk8+ Mediator recruits poised RNAPII PIC lacking the Kin28 CTD kinase. Aspects of this mechanism are generalizable to yeast and conserved in human cells. Thus, COMPASS and Mediator are repurposed to promote epigenetic transcriptional poising by a highly conserved mechanism. DOI:http://dx.doi.org/10.7554/eLife.16691.001 Cells respond to stressful conditions by changing which of their genes are switched on. Such stress-specific genes are typically switched off again when the conditions improve, but can remain primed and ready to be switched on again when needed. This phenomenon is known as “epigenetic transcriptional memory” and allows for a faster or stronger response to the same stress in the future. In fact, these memories can last for a long time, even after the cell divides many times. Inside cells, most of the DNA is wrapped tightly around proteins called histones. To activate – or transcribe – a gene, the DNA must be re-packaged to allow better access for specific proteins including the enzyme called RNA polymerase II. This repackaging involves a number of changes including chemical modification of the histone proteins. Genes that have been previously transcribed under stress are packaged in a different way so that they are poised and ready for the next time they are needed. However, the details of this process were not clear. Using yeast as a model, D'Urso et al. have dissected the changes that are responsible for priming genes to respond to future events. The yeast gene INO1, which shows transcriptional memory, was studied in cells by characterizing the proteins bound at and around the gene and the histone modifications in the region. D'Urso et al. found that a protein called SfI1 bound to this gene only during transcriptional memory and that this binding was critical to start the phenomenon. Further experiments showed that transcriptional memory also required altering two protein complexes that normally bind to genes when they are switched on. One complex, which includes an enzyme that modifies histones, was altered so that the histones at the INO1 gene were marked in a unique way. The other complex was responsible for recruiting an inactive, poised form of RNA polymerase II to the gene, which allowed the gene to be activated when needed. In addition, D'Urso found that other genes that show transcriptional memory in yeast, as well as such genes in human cells, were also marked in the same ways. A future challenge will be to understand how different conditions in different organisms can lead to transcriptional memory. Further studies could also explore how this memory phenomenon is inherited and how it influences an organism’s fitness. DOI:http://dx.doi.org/10.7554/eLife.16691.002
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Affiliation(s)
- Agustina D'Urso
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Yoh-Hei Takahashi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, United States
| | - Bin Xiong
- Department of Statistics, Northwestern University, Evanston, United States
| | - Jessica Marone
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Robert Coukos
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | | | - Ji-Ping Wang
- Department of Statistics, Northwestern University, Evanston, United States
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, United States
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
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32
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Bedard LG, Dronamraju R, Kerschner JL, Hunter GO, Axley ED, Boyd AK, Strahl BD, Mosley AL. Quantitative Analysis of Dynamic Protein Interactions during Transcription Reveals a Role for Casein Kinase II in Polymerase-associated Factor (PAF) Complex Phosphorylation and Regulation of Histone H2B Monoubiquitylation. J Biol Chem 2016; 291:13410-20. [PMID: 27143358 DOI: 10.1074/jbc.m116.727735] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Indexed: 11/06/2022] Open
Abstract
Using affinity purification MS approaches, we have identified a novel role for casein kinase II (CKII) in the modification of the polymerase associated factor complex (PAF-C). Our data indicate that the facilitates chromatin transcription complex (FACT) interacts with CKII and may facilitate PAF complex phosphorylation. Posttranslational modification analysis of affinity-isolated PAF-C shows extensive CKII phosphorylation of all five subunits of PAF-C, although CKII subunits were not detected as interacting partners. Consistent with this, recombinant CKII or FACT-associated CKII isolated from cells can phosphorylate PAF-C in vitro, whereas no intrinsic kinase activity was detected in PAF-C samples. Significantly, PAF-C purifications combined with stable isotope labeling in cells (SILAC) quantitation for PAF-C phosphorylation from wild-type and CKII temperature-sensitive strains (cka1Δ cka2-8) showed that PAF-C phosphorylation at consensus CKII sites is significantly reduced in cka1Δ cka2-8 strains. Consistent with a role of CKII in FACT and PAF-C function, we show that decreased CKII function in vivo results in decreased levels of histone H2B lysine 123 monoubiquitylation, a modification dependent on FACT and PAF-C. Taken together, our results define a coordinated role of CKII and FACT in the regulation of RNA polymerase II transcription through chromatin via phosphorylation of PAF-C.
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Affiliation(s)
- Lynn Glowczewski Bedard
- From the Department of Biology, DePauw University, Greencastle, Indiana 46135, the Department of Biochemistry and Molecular Biology and
| | | | - Jenny L Kerschner
- the Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, and
| | | | | | - Asha K Boyd
- From the Department of Biology, DePauw University, Greencastle, Indiana 46135, the Department of Biochemistry and Molecular Biology and
| | - Brian D Strahl
- the Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, and Curriculum in Genetics and Molecular Biology, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | - Amber L Mosley
- the Department of Biochemistry and Molecular Biology and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, and
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Corujo D, Mas G, Malinverni R, Di Croce L, Buschbeck M. Barcelona conference on epigenetics and cancer 2015: Coding and non-coding functions of the genome. Epigenetics 2016; 11:95-100. [PMID: 26996885 DOI: 10.1080/15592294.2015.1131377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The Barcelona Conference on Epigenetics and Cancer (BCEC) entitled "Coding and Non-Coding functions of the Genome" took place October 29-30, 2015 in Barcelona. The 2015 BCEC was the third edition of a series of annual conferences jointly organized by 5 leading research centers in Barcelona together with B-Debate, an initiative of BioCat. Luciano Di Croce from the Center for Genomic Regulation and Marcus Buschbeck from the Josep Carreras Leukemia Research Institute put together the scientific program with a particular focus on the role of non-coding RNAs in enhancer regulation, epigenetic control by Polycomb complexes, histone variants, and nuclear organization. In one and a half days, 22 talks and 56 posters were presented to an audience of 215 participants.
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Affiliation(s)
- David Corujo
- a Josep Carreras Leukaemia Research Institute (IJC), Campus ICO - Germans Trias i Pujol, Campus Can Ruti, Crta. Can Ruti, Cami de les Escoles , Badalona , Spain
| | - Gloria Mas
- b Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88 , Barcelona , Spain.,c Universitat Pompeu Fabra (UPF) , Barcelona , Spain
| | - Roberto Malinverni
- a Josep Carreras Leukaemia Research Institute (IJC), Campus ICO - Germans Trias i Pujol, Campus Can Ruti, Crta. Can Ruti, Cami de les Escoles , Badalona , Spain
| | - Luciano Di Croce
- b Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88 , Barcelona , Spain.,c Universitat Pompeu Fabra (UPF) , Barcelona , Spain.,d Institució Catalana de Recerca i Estudis Avançats, Passeig Lluis Companys 23 , Barcelona , Spain
| | - Marcus Buschbeck
- a Josep Carreras Leukaemia Research Institute (IJC), Campus ICO - Germans Trias i Pujol, Campus Can Ruti, Crta. Can Ruti, Cami de les Escoles , Badalona , Spain
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Huang F, Ramakrishnan S, Pokhrel S, Pflueger C, Parnell TJ, Kasten MM, Currie SL, Bhachech N, Horikoshi M, Graves BJ, Cairns BR, Bhaskara S, Chandrasekharan MB. Interaction of the Jhd2 Histone H3 Lys-4 Demethylase with Chromatin Is Controlled by Histone H2A Surfaces and Restricted by H2B Ubiquitination. J Biol Chem 2015; 290:28760-77. [PMID: 26451043 DOI: 10.1074/jbc.m115.693085] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 11/06/2022] Open
Abstract
Histone H3 lysine 4 (H3K4) methylation is a dynamic modification. In budding yeast, H3K4 methylation is catalyzed by the Set1-COMPASS methyltransferase complex and is removed by Jhd2, a JMJC domain family demethylase. The catalytic JmjC and JmjN domains of Jhd2 have the ability to remove all three degrees (mono-, di-, and tri-) of H3K4 methylation. Jhd2 also contains a plant homeodomain (PHD) finger required for its chromatin association and H3K4 demethylase functions. The Jhd2 PHD finger associates with chromatin independent of H3K4 methylation and the H3 N-terminal tail. Therefore, how Jhd2 associates with chromatin to perform H3K4 demethylation has remained unknown. We report a novel interaction between the Jhd2 PHD finger and histone H2A. Two residues in H2A (Phe-26 and Glu-57) serve as a binding site for Jhd2 in vitro and mediate its chromatin association and H3K4 demethylase functions in vivo. Using RNA sequencing, we have identified the functional target genes for Jhd2 and the H2A Phe-26 and Glu-57 residues. We demonstrate that H2A Phe-26 and Glu-57 residues control chromatin association and H3K4 demethylase functions of Jhd2 during positive or negative regulation of transcription at target genes. Importantly, we show that H2B Lys-123 ubiquitination blocks Jhd2 from accessing its binding site on chromatin, and thereby, we have uncovered a second mechanism by which H2B ubiquitination contributes to the trans-histone regulation of H3K4 methylation. Overall, our study provides novel insights into the chromatin binding dynamics and H3K4 demethylase functions of Jhd2.
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Affiliation(s)
- Fu Huang
- the Stowers Institute for Medical Research, Kansas City, Missouri 64110, and
| | - Saravanan Ramakrishnan
- From the Departments of Radiation Oncology and the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112
| | - Srijana Pokhrel
- From the Departments of Radiation Oncology and the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112
| | - Christian Pflueger
- the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, Oncological Sciences and
| | - Timothy J Parnell
- the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112
| | - Margaret M Kasten
- the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, Oncological Sciences and
| | - Simon L Currie
- the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, Oncological Sciences and
| | - Niraja Bhachech
- the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, Oncological Sciences and
| | - Masami Horikoshi
- the Laboratory of Developmental Biology, Institute of Molecular and Cellular Biosciences, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Barbara J Graves
- the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, Oncological Sciences and
| | - Bradley R Cairns
- the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, Oncological Sciences and
| | - Srividya Bhaskara
- From the Departments of Radiation Oncology and the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, Oncological Sciences and
| | - Mahesh B Chandrasekharan
- From the Departments of Radiation Oncology and the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112,
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Tajima K, Yae T, Javaid S, Tam O, Comaills V, Morris R, Wittner BS, Liu M, Engstrom A, Takahashi F, Black JC, Ramaswamy S, Shioda T, Hammell M, Haber DA, Whetstine JR, Maheswaran S. SETD1A modulates cell cycle progression through a miRNA network that regulates p53 target genes. Nat Commun 2015; 6:8257. [PMID: 26394836 PMCID: PMC4667427 DOI: 10.1038/ncomms9257] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 08/03/2015] [Indexed: 01/28/2023] Open
Abstract
Expression of the p53-inducible antiproliferative gene BTG2 is suppressed in many cancers in the absence of inactivating gene mutations, suggesting alternative mechanisms of silencing. Using a shRNA screen targeting 43 histone lysine methyltransferases (KMTs), we show that SETD1A suppresses BTG2 expression through its induction of several BTG2-targeting miRNAs. This indirect but highly specific mechanism, by which a chromatin regulator that mediates transcriptional activating marks can lead to the downregulation of a critical effector gene, is shared with multiple genes in the p53 pathway. Through such miRNA-dependent effects, SETD1A regulates cell cycle progression in vitro and modulates tumorigenesis in mouse xenograft models. Together, these observations help explain the remarkably specific genetic consequences associated with alterations in generic chromatin modulators in cancer. The p53-inducible antiproliferative gene BTG2 is suppressed in many cancers, in the absence of inactivating gene mutations. Here the authors show that the histone lysine methyltransferase SETD1A suppresses the expression of several p53 target genes including BTG2 by inducing a network of microRNAs.
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Affiliation(s)
- Ken Tajima
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Toshifumi Yae
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Sarah Javaid
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Oliver Tam
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Valentine Comaills
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Robert Morris
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Ben S Wittner
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Mingzhu Liu
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Amanda Engstrom
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Fumiyuki Takahashi
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Joshua C Black
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Sridhar Ramaswamy
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Toshihiro Shioda
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Johnathan R Whetstine
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA.,Department of Surgery, Harvard Medical School, Charlestown, Massachusetts 02129, USA
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36
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Chen FX, Woodfin AR, Gardini A, Rickels RA, Marshall SA, Smith ER, Shiekhattar R, Shilatifard A. PAF1, a Molecular Regulator of Promoter-Proximal Pausing by RNA Polymerase II. Cell 2015; 162:1003-15. [PMID: 26279188 DOI: 10.1016/j.cell.2015.07.042] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 05/16/2015] [Accepted: 07/02/2015] [Indexed: 10/25/2022]
Abstract
The control of promoter-proximal pausing and the release of RNA polymerase II (Pol II) is a widely used mechanism for regulating gene expression in metazoans, especially for genes that respond to environmental and developmental cues. Here, we identify that Pol-II-associated factor 1 (PAF1) possesses an evolutionarily conserved function in metazoans in the regulation of promoter-proximal pausing. Reduction in PAF1 levels leads to an increased release of paused Pol II into gene bodies at thousands of genes. PAF1 depletion results in increased nascent and mature transcripts and increased levels of phosphorylation of Pol II's C-terminal domain on serine 2 (Ser2P). These changes can be explained by the recruitment of the Ser2P kinase super elongation complex (SEC) effecting increased release of paused Pol II into productive elongation, thus establishing PAF1 as a regulator of promoter-proximal pausing by Pol II.
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Affiliation(s)
- Fei Xavier Chen
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Ashley R Woodfin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Alessandro Gardini
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1501 NW 10(th) Avenue, Miami, FL 33136, USA
| | - Ryan A Rickels
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Stacy A Marshall
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Edwin R Smith
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Ramin Shiekhattar
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1501 NW 10(th) Avenue, Miami, FL 33136, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 E. Superior Street, Chicago, IL 60611, USA; Stowers Institute for Medical Research, 1000 East 50(th) Street, Kansas City, MO 64110, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA.
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37
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Cucinotta CE, Young AN, Klucevsek KM, Arndt KM. The Nucleosome Acidic Patch Regulates the H2B K123 Monoubiquitylation Cascade and Transcription Elongation in Saccharomyces cerevisiae. PLoS Genet 2015; 11:e1005420. [PMID: 26241481 PMCID: PMC4524731 DOI: 10.1371/journal.pgen.1005420] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 07/05/2015] [Indexed: 02/06/2023] Open
Abstract
Eukaryotes regulate gene expression and other nuclear processes through the posttranslational modification of histones. In S. cerevisiae, the mono-ubiquitylation of histone H2B on lysine 123 (H2B K123ub) affects nucleosome stability, broadly influences gene expression and other DNA-templated processes, and is a prerequisite for additional conserved histone modifications that are associated with active transcription, namely the methylation of lysine residues in H3. While the enzymes that promote these chromatin marks are known, regions of the nucleosome required for the recruitment of these enzymes are undefined. To identify histone residues required for H2B K123ub, we exploited a functional interaction between the ubiquitin-protein ligase, Rkr1/Ltn1, and H2B K123ub in S. cerevisiae. Specifically, we performed a synthetic lethal screen with cells lacking RKR1 and a comprehensive library of H2A and H2B residue substitutions, and identified H2A residues that are required for H2B K123ub. Many of these residues map to the nucleosome acidic patch. The substitutions in the acidic patch confer varying histone modification defects downstream of H2B K123ub, indicating that this region contributes differentially to multiple histone modifications. Interestingly, substitutions in the acidic patch result in decreased recruitment of H2B K123ub machinery to active genes and defects in transcription elongation and termination. Together, our findings reveal a role for the nucleosome acidic patch in recruitment of histone modification machinery and maintenance of transcriptional integrity. Chromatin, a complex of DNA wrapped around histone proteins, impacts all DNA-templated processes, including gene expression. Cells employ various strategies to alter chromatin structure and control access to the genetic material. Nucleosomes, the building blocks of chromatin, are subject to a myriad of modifications on their constituent histone proteins. One highly conserved modification with important connections to human health is the addition of ubiquitin to histone H2B. H2B ubiquitylation modulates chromatin structure during gene transcription and acts as a master regulator for downstream histone modifications. The proteins that promote H2B ubiquitylation have been identified; however, little is known about how these proteins interface with the nucleosome. Here, we exploited the genetic tools of budding yeast to reveal features of the nucleosome that are required for H2B ubiquitylation. Our genetic screen identified amino acids on the nucleosome acidic patch, a negatively charged region on the nucleosome surface, as being important for this process. The acidic patch is critical for regulating chromatin transactions, and, in our study, we identified roles for the acidic patch throughout transcription. Our data reveal that the acidic patch recruits histone modifiers, regulates histone modifications within the H2B ubiquitylation cascade, and maintains transcriptional fidelity.
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Affiliation(s)
- Christine E. Cucinotta
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alexandria N. Young
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kristin M. Klucevsek
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Karen M. Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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38
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Shinsky SA, Monteith KE, Viggiano S, Cosgrove MS. Biochemical reconstitution and phylogenetic comparison of human SET1 family core complexes involved in histone methylation. J Biol Chem 2015; 290:6361-75. [PMID: 25561738 DOI: 10.1074/jbc.m114.627646] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mixed lineage leukemia protein-1 (MLL1) is a member of the SET1 family of histone H3 lysine 4 (H3K4) methyltransferases that are required for metazoan development. MLL1 is the best characterized human SET1 family member, which includes MLL1-4 and SETd1A/B. MLL1 assembles with WDR5, RBBP5, ASH2L, DPY-30 (WRAD) to form the MLL1 core complex, which is required for H3K4 dimethylation and transcriptional activation. Because all SET1 family proteins interact with WRAD in vivo, it is hypothesized they are regulated by similar mechanisms. However, recent evidence suggests differences among family members that may reflect unique regulatory inputs in the cell. Missing is an understanding of the intrinsic enzymatic activities of different SET1 family complexes under standard conditions. In this investigation, we reconstituted each human SET1 family core complex and compared subunit assembly and enzymatic activities. We found that in the absence of WRAD, all but one SET domain catalyzes at least weak H3K4 monomethylation. In the presence of WRAD, all SET1 family members showed stimulated monomethyltransferase activity but differed in their di- and trimethylation activities. We found that these differences are correlated with evolutionary lineage, suggesting these enzyme complexes have evolved to accomplish unique tasks within metazoan genomes. To understand the structural basis for these differences, we employed a "phylogenetic scanning mutagenesis" assay and identified a cluster of amino acid substitutions that confer a WRAD-dependent gain-of-function dimethylation activity on complexes assembled with the MLL3 or Drosophila trithorax proteins. These results form the basis for understanding how WRAD differentially regulates SET1 family complexes in vivo.
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Affiliation(s)
- Stephen A Shinsky
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Kelsey E Monteith
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Susan Viggiano
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
| | - Michael S Cosgrove
- From the Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210
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39
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Harmeyer KM, South PF, Bishop B, Ogas J, Briggs SD. Immediate chromatin immunoprecipitation and on-bead quantitative PCR analysis: a versatile and rapid ChIP procedure. Nucleic Acids Res 2014; 43:e38. [PMID: 25539918 PMCID: PMC4381045 DOI: 10.1093/nar/gku1347] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/15/2014] [Indexed: 12/12/2022] Open
Abstract
Genome-wide chromatin immunoprecipitation (ChIP) studies have brought significant insight into the genomic localization of chromatin-associated proteins and histone modifications. The large amount of data generated by these analyses, however, require approaches that enable rapid validation and analysis of biological relevance. Furthermore, there are still protein and modification targets that are difficult to detect using standard ChIP methods. To address these issues, we developed an immediate chromatin immunoprecipitation procedure which we call ZipChip. ZipChip significantly reduces the time and increases sensitivity allowing for rapid screening of multiple loci. Here we describe how ZipChIP enables detection of histone modifications (H3K4 mono- and trimethylation) and two yeast histone demethylases, Jhd2 and Rph1, which were previously difficult to detect using standard methods. Furthermore, we demonstrate the versatility of ZipChIP by analyzing the enrichment of the histone deacetylase Sir2 at heterochromatin in yeast and enrichment of the chromatin remodeler, PICKLE, at euchromatin in Arabidopsis thaliana.
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Affiliation(s)
- Kayla M Harmeyer
- Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Paul F South
- Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Brett Bishop
- Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Joe Ogas
- Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Scott D Briggs
- Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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40
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Mikheyeva IV, Grady PJR, Tamburini FB, Lorenz DR, Cam HP. Multifaceted genome control by Set1 Dependent and Independent of H3K4 methylation and the Set1C/COMPASS complex. PLoS Genet 2014; 10:e1004740. [PMID: 25356590 PMCID: PMC4214589 DOI: 10.1371/journal.pgen.1004740] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 09/08/2014] [Indexed: 12/21/2022] Open
Abstract
Histone modifiers are critical regulators of chromatin-based processes in eukaryotes. The histone methyltransferase Set1, a component of the Set1C/COMPASS complex, catalyzes the methylation at lysine 4 of histone H3 (H3K4me), a hallmark of euchromatin. Here, we show that the fission yeast Schizosaccharomyces pombe Set1 utilizes distinct domain modules to regulate disparate classes of repetitive elements associated with euchromatin and heterochromatin via H3K4me-dependent and -independent pathways. Set1 employs its RNA-binding RRM2 and catalytic SET domains to repress Tf2 retrotransposons and pericentromeric repeats while relying on its H3K4me function to maintain transcriptional repression at the silent mating type (mat) locus and subtelomeric regions. These repressive functions of Set1 correlate with the requirement of Set1C components to maintain repression at the mat locus and subtelomeres while dispensing Set1C in repressing Tf2s and pericentromeric repeats. We show that the contributions of several Set1C subunits to the states of H3K4me diverge considerably from those of Saccharomyces cerevisiae orthologs. Moreover, unlike S. cerevisiae, the regulation of Set1 protein level is not coupled to the status of H3K4me or histone H2B ubiquitination by the HULC complex. Intriguingly, we uncover a genome organization role for Set1C and H3K4me in mediating the clustering of Tf2s into Tf bodies by antagonizing the acetyltransferase Mst1-mediated H3K4 acetylation. Our study provides unexpected insights into the regulatory intricacies of a highly conserved chromatin-modifying complex with diverse roles in genome control. Methylation of histone H3 at lysine 4 (H3K4me) is a well-documented mark associated with euchromatin. In this study, we investigate the contributions of the histone methyltransferase Set1 (KMT2) and its associated Set1C/COMPASS complex in the fission yeast Schizosaccharomyces pombe to histone H3 lysine 4 methylation (H3K4me), transcriptional repression, and genome organization. We show that Set1 exhibits multiple modes of transcriptional repression at different types of repetitive elements, requiring distinct domains of Set1 and other Set1C subunits. Despite high conservation of subunits between the S. pombe and S. cerevisiae Set1C complexes, there are considerable differences in contributions to H3K4me by several individual subunits. Furthermore, unlike a recent report in S. cerevisiae, the abundance of Set1 proteins in S. pombe is generally not coupled to either the status of H3K4 methylation or H2B ubiquitination, further highlighting critical differences in Set1 regulation between the two yeast species. We describe a role for the Set1C complex in the nuclear organization of dispersed retrotransposons into Tf bodies. Set1C maintains Tf body integrity by employing H3K4me to antagonize the activities of the H3K4 acetyltransferase Mst1. Collectively, our findings dramatically expand the regulatory landscape controlled by the Set1C complex, an important and highly conserved chromatin-modifying complex with diverse roles in genome control and development.
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Affiliation(s)
- Irina V. Mikheyeva
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Patrick J. R. Grady
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Fiona B. Tamburini
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - David R. Lorenz
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Hugh P. Cam
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
- * E-mail:
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41
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Vlaming H, van Welsem T, de Graaf EL, Ontoso D, Altelaar AFM, San-Segundo PA, Heck AJR, van Leeuwen F. Flexibility in crosstalk between H2B ubiquitination and H3 methylation in vivo. EMBO Rep 2014; 15:1077-84. [PMID: 25141862 DOI: 10.15252/embr.201438793] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Histone H2B ubiquitination is a dynamic modification that promotes methylation of histone H3K79 and H3K4. This crosstalk is important for the DNA damage response and has been implicated in cancer. Here, we show that in engineered yeast strains, ubiquitins tethered to every nucleosome promote H3K79 and H3K4 methylation from a proximal as well as a more distal site, but only if in a correct orientation. This plasticity indicates that the exact location of the attachment site, the native ubiquitin-lysine linkage and ubiquitination cycles are not critical for trans-histone crosstalk in vivo. The flexibility in crosstalk also indicates that other ubiquitination events may promote H3 methylation.
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Affiliation(s)
- Hanneke Vlaming
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Erik L de Graaf
- Biomolecular Mass Spectrometry and Proteomics Group, The Netherlands Proteomics Centre Utrecht University, Utrecht, the Netherlands
| | - David Ontoso
- Instituto de Biología Funcional y Genómica CSIC/University of Salamanca, Salamanca, Spain
| | - A F Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics Group, The Netherlands Proteomics Centre Utrecht University, Utrecht, the Netherlands
| | - Pedro A San-Segundo
- Instituto de Biología Funcional y Genómica CSIC/University of Salamanca, Salamanca, Spain
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics Group, The Netherlands Proteomics Centre Utrecht University, Utrecht, the Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
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42
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Enhancer biology and enhanceropathies. Nat Struct Mol Biol 2014; 21:210-9. [DOI: 10.1038/nsmb.2784] [Citation(s) in RCA: 220] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 02/06/2014] [Indexed: 12/18/2022]
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