1
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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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2
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Connacher J, von Grüning H, Birkholtz L. Histone Modification Landscapes as a Roadmap for Malaria Parasite Development. Front Cell Dev Biol 2022; 10:848797. [PMID: 35433676 PMCID: PMC9010790 DOI: 10.3389/fcell.2022.848797] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/04/2022] [Indexed: 12/26/2022] Open
Abstract
Plasmodium falciparum remains the deadliest parasite species in the world, responsible for 229 million cases of human malaria in 2019. The ability of the P. falciparum parasite to progress through multiple life cycle stages and thrive in diverse host and vector species hinges on sophisticated mechanisms of epigenetic regulation of gene expression. Emerging evidence indicates such epigenetic control exists in concentric layers, revolving around core histone post-translational modification (PTM) landscapes. Here, we provide a necessary update of recent epigenome research in malaria parasites, focusing specifically on the ability of dynamic histone PTM landscapes to orchestrate the divergent development and differentiation pathways in P. falciparum parasites. In addition to individual histone PTMs, we discuss recent findings that imply functional importance for combinatorial PTMs in P. falciparum parasites, representing an operational histone code. Finally, this review highlights the remaining gaps and provides strategies to address these to obtain a more thorough understanding of the histone modification landscapes that are at the center of epigenetic regulation in human malaria parasites.
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Li J, Bergmann L, Rafael de Almeida A, Webb KM, Gogol M, Voigt P, Liu Y, Liang H, Smolle M. H3K36 methylation and DNA-binding both promote Ioc4 recruitment and Isw1b remodeler function. Nucleic Acids Res 2022; 50:2549-2565. [PMID: 35188579 PMCID: PMC8934638 DOI: 10.1093/nar/gkac077] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 01/20/2022] [Accepted: 02/15/2022] [Indexed: 11/23/2022] Open
Abstract
The Isw1b chromatin-remodeling complex is specifically recruited to gene bodies to help retain pre-existing histones during transcription by RNA polymerase II. Recruitment is dependent on H3K36 methylation and the Isw1b subunit Ioc4, which contains an N-terminal PWWP domain. Here, we present the crystal structure of the Ioc4-PWWP domain, including a detailed functional characterization of the domain on its own as well as in the context of full-length Ioc4 and the Isw1b remodeler. The Ioc4-PWWP domain preferentially binds H3K36me3-containing nucleosomes. Its ability to bind DNA is required for nucleosome binding. It is also furthered by the unique insertion motif present in Ioc4-PWWP. The ability to bind H3K36me3 and DNA promotes the interaction of full-length Ioc4 with nucleosomes in vitro and they are necessary for its recruitment to gene bodies in vivo. Furthermore, a fully functional Ioc4-PWWP domain promotes efficient remodeling by Isw1b and the maintenance of ordered chromatin in vivo, thereby preventing the production of non-coding RNAs.
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Affiliation(s)
- Jian Li
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Lena Bergmann
- Physiological Chemistry, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
| | - Andreia Rafael de Almeida
- Physiological Chemistry, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
| | - Kimberly M Webb
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Madelaine M Gogol
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64110, USA
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Yingfang Liu
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
- School of Medicine, Sun Yat-Sen University, Guangzhou 510275, China
| | - Huanhuan Liang
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
- Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510275, China
| | - Michaela M Smolle
- Physiological Chemistry, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
- BioPhysics Core Facility, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
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4
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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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Structure and Function of Chromatin Remodelers. J Mol Biol 2021; 433:166929. [PMID: 33711345 PMCID: PMC8184634 DOI: 10.1016/j.jmb.2021.166929] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/27/2021] [Accepted: 03/04/2021] [Indexed: 12/25/2022]
Abstract
Chromatin remodelers act to regulate multiple cellular processes, such as transcription and DNA repair, by controlling access to genomic DNA. Four families of chromatin remodelers have been identified in yeast, each with non-redundant roles within the cell. There has been a recent surge in structural models of chromatin remodelers in complex with their nucleosomal substrate. These structural studies provide new insight into the mechanism of action for individual chromatin remodelers. In this review, we summarize available data for the structure and mechanism of action of the four chromatin remodeling complex families.
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Ferraro AR, Ameri AJ, Lu Z, Kamei M, Schmitz RJ, Lewis ZA. Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin. BMC Genomics 2021; 22:459. [PMID: 34147068 PMCID: PMC8214302 DOI: 10.1186/s12864-021-07774-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 06/04/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Regulation of chromatin accessibility and transcription are tightly coordinated processes. Studies in yeast and higher eukaryotes have described accessible chromatin regions, but little work has been done in filamentous fungi. RESULTS Here we present a genome-scale characterization of accessible chromatin regions in Neurospora crassa, which revealed characteristic molecular features of accessible and inaccessible chromatin. We present experimental evidence of inaccessibility within heterochromatin regions in Neurospora, and we examine features of both accessible and inaccessible chromatin, including the presence of histone modifications, types of transcription, transcription factor binding, and relative nucleosome turnover rates. Chromatin accessibility is not strictly correlated with expression level. Accessible chromatin regions in the model filamentous fungus Neurospora are characterized the presence of H3K27 acetylation and commonly associated with pervasive non-coding transcription. Conversely, methylation of H3 lysine-36 catalyzed by ASH1 is correlated with inaccessible chromatin within promoter regions. CONCLUSIONS In N. crassa, H3K27 acetylation is the most predictive histone modification for open chromatin. Conversely, our data show that H3K36 methylation is a key marker of inaccessible chromatin in gene-rich regions of the genome. Our data are consistent with an expanded role for H3K36 methylation in intergenic regions of filamentous fungi compared to the model yeasts, S. cerevisiae and S. pombe, which lack homologs of the ASH1 methyltransferase.
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Affiliation(s)
- Aileen R Ferraro
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - Abigail J Ameri
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - Zefu Lu
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Masayuki Kamei
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Zachary A Lewis
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
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Clapier CR. Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer. Int J Mol Sci 2021; 22:5578. [PMID: 34070411 PMCID: PMC8197500 DOI: 10.3390/ijms22115578] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 01/13/2023] Open
Abstract
The establishment and maintenance of genome packaging into chromatin contribute to define specific cellular identity and function. Dynamic regulation of chromatin organization and nucleosome positioning are critical to all DNA transactions-in particular, the regulation of gene expression-and involve the cooperative action of sequence-specific DNA-binding factors, histone modifying enzymes, and remodelers. Remodelers are molecular machines that generate various chromatin landscapes, adjust nucleosome positioning, and alter DNA accessibility by using ATP binding and hydrolysis to perform DNA translocation, which is highly regulated through sophisticated structural and functional conversations with nucleosomes. In this review, I first present the functional and structural diversity of remodelers, while emphasizing the basic mechanism of DNA translocation, the common regulatory aspects, and the hand-in-hand progressive increase in complexity of the regulatory conversations between remodelers and nucleosomes that accompanies the increase in challenges of remodeling processes. Next, I examine how, through nucleosome positioning, remodelers guide the regulation of gene expression. Finally, I explore various aspects of how alterations/mutations in remodelers introduce dissonance into the conversations between remodelers and nucleosomes, modify chromatin organization, and contribute to oncogenesis.
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Affiliation(s)
- Cedric R Clapier
- Department of Oncological Sciences & Howard Hughes Medical Institute, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
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The yeast ISW1b ATP-dependent chromatin remodeler is critical for nucleosome spacing and dinucleosome resolution. Sci Rep 2021; 11:4195. [PMID: 33602956 PMCID: PMC7892562 DOI: 10.1038/s41598-021-82842-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/25/2021] [Indexed: 12/15/2022] Open
Abstract
Isw1 and Chd1 are ATP-dependent nucleosome-spacing enzymes required to establish regular arrays of phased nucleosomes near transcription start sites of yeast genes. Cells lacking both Isw1 and Chd1 have extremely disrupted chromatin, with weak phasing, irregular spacing and a propensity to form close-packed dinucleosomes. The Isw1 ATPase subunit occurs in two different remodeling complexes: ISW1a (composed of Isw1 and Ioc3) and ISW1b (composed of Isw1, Ioc2 and Ioc4). The Ioc4 subunit of ISW1b binds preferentially to the H3-K36me3 mark. Here we show that ISW1b is primarily responsible for setting nucleosome spacing and resolving close-packed dinucleosomes, whereas ISW1a plays only a minor role. ISW1b and Chd1 make additive contributions to dinucleosome resolution, such that neither enzyme is capable of resolving all dinucleosomes on its own. Loss of the Set2 H3-K36 methyltransferase partly phenocopies loss of Ioc4, resulting in increased dinucleosome levels with only a weak effect on nucleosome spacing, suggesting that Set2-mediated H3-K36 trimethylation contributes to ISW1b-mediated dinucleosome separation. The H4 tail domain is required for normal nucleosome spacing but not for dinucleosome resolution. We conclude that the nucleosome spacing and dinucleosome resolving activities of ISW1b and Chd1 are critical for normal global chromatin organisation.
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9
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Marr LT, Ocampo J, Clark DJ, Hayes JJ. Global histone protein surface accessibility in yeast indicates a uniformly loosely packed genome with canonical nucleosomes. Epigenetics Chromatin 2021; 14:5. [PMID: 33430969 PMCID: PMC7802155 DOI: 10.1186/s13072-020-00381-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/28/2020] [Indexed: 01/09/2023] Open
Abstract
Background The vast majority of methods available to characterize genome-wide chromatin structure exploit differences in DNA accessibility to nucleases or chemical crosslinking. We developed a novel method to gauge genome-wide accessibility of histone protein surfaces within nucleosomes by assessing reactivity of engineered cysteine residues with a thiol-specific reagent, biotin-maleimide (BM). Results Yeast nuclei were obtained from cells expressing the histone mutant H2B S116C, in which a cysteine resides near the center of the external flat protein surface of the nucleosome. BM modification revealed that nucleosomes are generally equivalently accessible throughout the S. cerevisiae genome, including heterochromatic regions, suggesting limited, higher-order chromatin structures in which this surface is obstructed by tight nucleosome packing. However, we find that nucleosomes within 500 bp of transcription start sites exhibit the greatest range of accessibility, which correlates with the density of chromatin remodelers. Interestingly, accessibility is not well correlated with RNA polymerase density and thus the level of gene expression. We also investigated the accessibility of cysteine mutations designed to detect exposure of histone surfaces internal to the nucleosome thought to be accessible in actively transcribed genes: H3 102, is at the H2A–H2B dimer/H3–H4 tetramer interface, and H3 A110C, resides at the H3–H3 interface. However, in contrast to the external surface site, we find that neither of these internal sites were found to be appreciably exposed. Conclusions Overall, our finding that nucleosomes surfaces within S. cerevisiae chromatin are equivalently accessible genome-wide is consistent with a globally uncompacted chromatin structure lacking substantial higher-order organization. However, we find modest differences in accessibility that correlate with chromatin remodelers but not transcription, suggesting chromatin poised for transcription is more accessible than actively transcribed or intergenic regions. In contrast, we find that two internal sites remain inaccessible, suggesting that such non-canonical nucleosome species generated during transcription are rapidly and efficiently converted to canonical nucleosome structure and thus not widely present in native chromatin.
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Affiliation(s)
- Luke T Marr
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Josefina Ocampo
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI-CONICET), C1428ADN, Buenos Aires, Argentina
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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10
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Bhardwaj SK, Hailu SG, Olufemi L, Brahma S, Kundu S, Hota SK, Persinger J, Bartholomew B. Dinucleosome specificity and allosteric switch of the ISW1a ATP-dependent chromatin remodeler in transcription regulation. Nat Commun 2020; 11:5913. [PMID: 33219211 PMCID: PMC7680125 DOI: 10.1038/s41467-020-19700-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
Over the last 3 decades ATP-dependent chromatin remodelers have been thought to recognize chromatin at the level of single nucleosomes rather than higher-order organization of more than one nucleosome. We show the yeast ISW1a remodeler has such higher-order structural specificity, as manifested by large allosteric changes that activate the nucleosome remodeling and spacing activities of ISW1a when bound to dinucleosomes. Although the ATPase domain of Isw1 docks at the SHL2 position when ISW1a is bound to either mono- or di-nucleosomes, there are major differences in the interactions of the catalytic subunit Isw1 with the acidic pocket of nucleosomes and the accessory subunit Ioc3 with nucleosomal DNA. By mutational analysis and uncoupling of ISW1a's dinucleosome specificity, we find that dinucleosome recognition is required by ISW1a for proper chromatin organization at promoters; as well as transcription regulation in combination with the histone acetyltransferase NuA4 and histone H2A.Z exchanger SWR1.
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Affiliation(s)
- Saurabh K Bhardwaj
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA
- Worldwide Research and Development, Pfizer Inc, Houston, USA
| | - Solomon G Hailu
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA
- EpiCypher, Inc., Durham, USA
| | - Lola Olufemi
- National Institute of Neurological Disorders and Stroke, Bethesda, USA
| | - Sandipan Brahma
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, USA
| | - Soumyadipta Kundu
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA
- ZS Associates, Evanston, USA
| | - Swetansu K Hota
- University of California-San Francisco, Gladstone Institutes, San Francisco, USA
| | - Jim Persinger
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA
| | - Blaine Bartholomew
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA.
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA.
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11
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Lerner AM, Hepperla AJ, Keele GR, Meriesh HA, Yumerefendi H, Restrepo D, Zimmerman S, Bear JE, Kuhlman B, Davis IJ, Strahl BD. An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation. Genome Res 2020; 30:1605-1617. [PMID: 33020206 PMCID: PMC7605256 DOI: 10.1101/gr.264283.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/15/2020] [Indexed: 11/24/2022]
Abstract
Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification associated with transcription and DNA repair. Although the effects of H3K36 methylation have been studied, the genome-wide dynamics of H3K36me deposition and removal are not known. We established rapid and reversible optogenetic control for Set2, the sole H3K36 methyltransferase in yeast, by fusing the enzyme with the light-activated nuclear shuttle (LANS) domain. Light activation resulted in efficient Set2-LANS nuclear localization followed by H3K36me3 deposition in vivo, with total H3K36me3 levels correlating with RNA abundance. Although genes showed disparate levels of H3K36 methylation, relative rates of H3K36me3 accumulation were largely linear and consistent across genes, suggesting that H3K36me3 deposition occurs in a directed fashion on all transcribed genes regardless of their overall transcription frequency. Removal of H3K36me3 was highly dependent on the demethylase Rph1. However, the per-gene rate of H3K36me3 loss weakly correlated with RNA abundance and followed exponential decay, suggesting H3K36 demethylases act in a global, stochastic manner. Altogether, these data provide a detailed temporal view of H3K36 methylation and demethylation that suggests transcription-dependent and -independent mechanisms for H3K36me deposition and removal, respectively.
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Affiliation(s)
- Andrew M Lerner
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Austin J Hepperla
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | | | - Hashem A Meriesh
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Hayretin Yumerefendi
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Oncology Research Unit, Pfizer Worldwide Research and Development, Pearl River, New York 10965, USA
| | - David Restrepo
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Seth Zimmerman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - James E Bear
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Ian J Davis
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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12
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DiFiore JV, Ptacek TS, Wang Y, Li B, Simon JM, Strahl BD. Unique and Shared Roles for Histone H3K36 Methylation States in Transcription Regulation Functions. Cell Rep 2020; 31:107751. [PMID: 32521276 PMCID: PMC7334899 DOI: 10.1016/j.celrep.2020.107751] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 01/21/2020] [Accepted: 05/19/2020] [Indexed: 12/19/2022] Open
Abstract
Set2 co-transcriptionally methylates lysine 36 of histone H3 (H3K36), producing mono-, di-, and trimethylation (H3K36me1/2/3). These modifications recruit or repel chromatin effector proteins important for transcriptional fidelity, mRNA splicing, and DNA repair. However, it was not known whether the different methylation states of H3K36 have distinct biological functions. Here, we use engineered forms of Set2 that produce different lysine methylation states to identify unique and shared functions for H3K36 modifications. Although H3K36me1/2 and H3K36me3 are functionally redundant in many SET2 deletion phenotypes, we found that H3K36me3 has a unique function related to Bur1 kinase activity and FACT (facilitates chromatin transcription) complex function. Further, during nutrient stress, either H3K36me1/2 or H3K36me3 represses high levels of histone acetylation and cryptic transcription that arises from within genes. Our findings uncover the potential for the regulation of diverse chromatin functions by different H3K36 methylation states.
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Affiliation(s)
- Julia V DiFiore
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Travis S Ptacek
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yi Wang
- Research Unit of Infection and Immunity, Department of Pathophysiology, West China College of Basic and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Bing Li
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jeremy M Simon
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Brian D Strahl
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.
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13
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McDevitt PJ, Schneck JL, Diaz E, Hou W, Huddleston MJ, Matico RE, McCormick PM, Kirkpatrick RB. A Scalable Platform for Producing Recombinant Nucleosomes with Codified Histone Methyltransferase Substrate Preferences. Protein Expr Purif 2019; 164:105455. [PMID: 31306746 DOI: 10.1016/j.pep.2019.105455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 11/15/2022]
Abstract
Wolf-Hirschhorn Syndrome Candidate 1 (WHSC1; also known as NSD2) is a SET domain-containing histone lysine methyltransferase. A chromosomal translocation occurs in 15-20% of multiple myeloma patients and is associated with increased production of WHSC1 and poor clinical prognosis. To define the substrate requirements of NSD2, we established a platform for the large-scale production of recombinant polynucleosomes, based on authentic human histone proteins, expressed in E. coli, and complexed with linearized DNA. A brief survey of methyltransferases whose substrate requirements are recorded in the literature yielded expected results, lending credence to the fitness of our approach. This platform was readily 'codified' with respect to both position and extent of methylation at histone 3 lysines 18 and 36 and led to the conclusion that the most readily discernible activity of NSD2 in contact with a nucleosome substrate is dimethylation of histone 3 lysine 36. We further explored reaction mechanism, and conclude a processive, rather than distributive mechanism best describes the interaction of NSD2 with intact nucleosome substrates. The methods developed feature scale and flexibility and are suited to thorough pharmaceutical-scale drug discovery campaigns.
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Affiliation(s)
- Patrick J McDevitt
- GlaxoSmithKline Pharmaceutical Company, 1250 South Collegeville Road, Collegeville, PA, 19426-0989, USA.
| | - Jessica L Schneck
- GlaxoSmithKline Pharmaceutical Company, 1250 South Collegeville Road, Collegeville, PA, 19426-0989, USA
| | - Elsie Diaz
- Janssen Pharmaceutical Companies of Johnson and Johnson, Philadelphia, PA, USA
| | - Wangfang Hou
- GlaxoSmithKline Pharmaceutical Company, 1250 South Collegeville Road, Collegeville, PA, 19426-0989, USA
| | - Michael J Huddleston
- GlaxoSmithKline Pharmaceutical Company, 1250 South Collegeville Road, Collegeville, PA, 19426-0989, USA
| | - Rosalie E Matico
- Janssen Pharmaceutical Companies of Johnson and Johnson, Philadelphia, PA, USA
| | - Patricia M McCormick
- GlaxoSmithKline Pharmaceutical Company, 1250 South Collegeville Road, Collegeville, PA, 19426-0989, USA
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14
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Klein BJ, Krajewski K, Restrepo S, Lewis PW, Strahl BD, Kutateladze TG. Recognition of cancer mutations in histone H3K36 by epigenetic writers and readers. Epigenetics 2018; 13:683-692. [PMID: 30045670 DOI: 10.1080/15592294.2018.1503491] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Histone posttranslational modifications control the organization and function of chromatin. In particular, methylation of lysine 36 in histone H3 (H3K36me) has been shown to mediate gene transcription, DNA repair, cell cycle regulation, and pre-mRNA splicing. Notably, mutations at or near this residue have been causally linked to the development of several human cancers. These observations have helped to illuminate the role of histones themselves in disease and to clarify the mechanisms by which they acquire oncogenic properties. This perspective focuses on recent advances in discovery and characterization of histone H3 mutations that impact H3K36 methylation. We also highlight findings that the common cancer-related substitution of H3K36 to methionine (H3K36M) disturbs functions of not only H3K36me-writing enzymes but also H3K36me-specific readers. The latter case suggests that the oncogenic effects could also be linked to the inability of readers to engage H3K36M.
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Affiliation(s)
- Brianna J Klein
- a Department of Pharmacology , University of Colorado School of Medicine , Aurora , CO , USA
| | - Krzysztof Krajewski
- b Department of Biochemistry & Biophysics , The University of North Carolina School of Medicine , Chapel Hill , NC , USA
| | - Susana Restrepo
- a Department of Pharmacology , University of Colorado School of Medicine , Aurora , CO , USA
| | - Peter W Lewis
- c Wisconsin Institute for Discovery , University of Wisconsin , Madison , WI , USA
| | - Brian D Strahl
- b Department of Biochemistry & Biophysics , The University of North Carolina School of Medicine , Chapel Hill , NC , USA
| | - Tatiana G Kutateladze
- a Department of Pharmacology , University of Colorado School of Medicine , Aurora , CO , USA
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15
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Coursey T, Milutinovic M, Regedanz E, Brkljacic J, Bisaro DM. Arabidopsis Histone Reader EMSY-LIKE 1 Binds H3K36 and Suppresses Geminivirus Infection. J Virol 2018. [PMID: 29875242 DOI: 10.1128/jvi.00219-218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Histone posttranslational modifications (PTMs) impart information that regulates chromatin structure and activity. Their effects are mediated by histone reader proteins that bind specific PTMs to modify chromatin and/or recruit appropriate effectors to alter the chromatin landscape. Despite their crucial juxtaposition between information and functional outcome, relatively few plant histone readers have been identified, and nothing is known about their impact on viral chromatin and pathogenesis. We used the geminivirus Cabbage leaf curl virus (CaLCuV) as a model to functionally characterize two recently identified reader proteins, EMSY-LIKE 1 (EML1) and EML3, which contain Tudor-like Agenet domains predictive of histone PTM binding function. Here, we show that mutant Arabidopsis plants exhibit contrasting hypersusceptible (eml1) and tolerant (eml3) responses to CaLCuV infection and that EML1 deficiency correlates with RNA polymerase II (Pol II) enrichment on viral chromatin and upregulated viral gene expression. Consistent with reader activity, EML1 and EML3 associate with nucleosomes and with CaLCuV chromatin, suggesting a direct impact on pathogenesis. We also demonstrate that EML1 and EML3 bind peptides containing histone H3 lysine 36 (H3K36), a PTM usually associated with active gene expression. The interaction encompasses multiple H3K36 PTMs, including methylation and acetylation, suggesting nuanced regulation. Furthermore, EML1 and EML3 associate with similar regions of viral chromatin, implying possible competition between the two readers. Regions of EML1 and EML3 association correlate with sites of trimethylated H3K36 (H3K36me3) enrichment, consistent with regulation of geminivirus chromatin by direct EML targeting.IMPORTANCE Histone PTMs convey information that regulates chromatin compaction and DNA accessibility. Histone reader proteins bind specific PTMs and translate their effects by modifying chromatin and/or by recruiting effectors that alter chromatin structure or activity. In this study, CaLCuV was used to characterize the activities of two Arabidopsis Agenet domain histone readers, EML1 and EML3. We show that eml1 mutants are hypersusceptible to CaLCuV, whereas eml3 plants are more tolerant of infection than wild-type plants. We also demonstrate that EML1 and EML3 associate with histones and viral chromatin in planta and that both proteins bind peptides containing H3K36, a PTM associated with active gene expression. Consistent with antiviral activity, EML1 suppresses CaLCuV gene expression and reduces Pol II access to viral chromatin. By linking EML1 and EML3 to pathogenesis, these studies have expanded our knowledge of histone reader proteins and uncovered an additional level of viral chromatin regulation.
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Affiliation(s)
- Tami Coursey
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, Ohio, USA
| | - Milica Milutinovic
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio, USA
- Institute for Biological Research Siniša Stanković, University of Belgrade, Belgrade, Serbia
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, Ohio, USA
| | - Elizabeth Regedanz
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Jelena Brkljacic
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio, USA
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, Ohio, USA
| | - David M Bisaro
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, Ohio, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, Ohio, USA
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16
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Arabidopsis Histone Reader EMSY-LIKE 1 Binds H3K36 and Suppresses Geminivirus Infection. J Virol 2018; 92:JVI.00219-18. [PMID: 29875242 DOI: 10.1128/jvi.00219-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/27/2018] [Indexed: 11/20/2022] Open
Abstract
Histone posttranslational modifications (PTMs) impart information that regulates chromatin structure and activity. Their effects are mediated by histone reader proteins that bind specific PTMs to modify chromatin and/or recruit appropriate effectors to alter the chromatin landscape. Despite their crucial juxtaposition between information and functional outcome, relatively few plant histone readers have been identified, and nothing is known about their impact on viral chromatin and pathogenesis. We used the geminivirus Cabbage leaf curl virus (CaLCuV) as a model to functionally characterize two recently identified reader proteins, EMSY-LIKE 1 (EML1) and EML3, which contain Tudor-like Agenet domains predictive of histone PTM binding function. Here, we show that mutant Arabidopsis plants exhibit contrasting hypersusceptible (eml1) and tolerant (eml3) responses to CaLCuV infection and that EML1 deficiency correlates with RNA polymerase II (Pol II) enrichment on viral chromatin and upregulated viral gene expression. Consistent with reader activity, EML1 and EML3 associate with nucleosomes and with CaLCuV chromatin, suggesting a direct impact on pathogenesis. We also demonstrate that EML1 and EML3 bind peptides containing histone H3 lysine 36 (H3K36), a PTM usually associated with active gene expression. The interaction encompasses multiple H3K36 PTMs, including methylation and acetylation, suggesting nuanced regulation. Furthermore, EML1 and EML3 associate with similar regions of viral chromatin, implying possible competition between the two readers. Regions of EML1 and EML3 association correlate with sites of trimethylated H3K36 (H3K36me3) enrichment, consistent with regulation of geminivirus chromatin by direct EML targeting.IMPORTANCE Histone PTMs convey information that regulates chromatin compaction and DNA accessibility. Histone reader proteins bind specific PTMs and translate their effects by modifying chromatin and/or by recruiting effectors that alter chromatin structure or activity. In this study, CaLCuV was used to characterize the activities of two Arabidopsis Agenet domain histone readers, EML1 and EML3. We show that eml1 mutants are hypersusceptible to CaLCuV, whereas eml3 plants are more tolerant of infection than wild-type plants. We also demonstrate that EML1 and EML3 associate with histones and viral chromatin in planta and that both proteins bind peptides containing H3K36, a PTM associated with active gene expression. Consistent with antiviral activity, EML1 suppresses CaLCuV gene expression and reduces Pol II access to viral chromatin. By linking EML1 and EML3 to pathogenesis, these studies have expanded our knowledge of histone reader proteins and uncovered an additional level of viral chromatin regulation.
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17
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McDaniel SL, Hepperla AJ, Huang J, Dronamraju R, Adams AT, Kulkarni VG, Davis IJ, Strahl BD. H3K36 Methylation Regulates Nutrient Stress Response in Saccharomyces cerevisiae by Enforcing Transcriptional Fidelity. Cell Rep 2018; 19:2371-2382. [PMID: 28614721 DOI: 10.1016/j.celrep.2017.05.057] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 04/10/2017] [Accepted: 05/17/2017] [Indexed: 10/25/2022] Open
Abstract
Set2-mediated histone methylation at H3K36 regulates diverse activities, including DNA repair, mRNA splicing, and suppression of inappropriate (cryptic) transcription. Although failure of Set2 to suppress cryptic transcription has been linked to decreased lifespan, the extent to which cryptic transcription influences other cellular functions is poorly understood. Here, we uncover a role for H3K36 methylation in the regulation of the nutrient stress response pathway. We found that the transcriptional response to nutrient stress was dysregulated in SET2-deleted (set2Δ) cells and was correlated with genome-wide bi-directional cryptic transcription that originated from within gene bodies. Antisense transcripts arising from these cryptic events extended into the promoters of the genes from which they arose and were associated with decreased sense transcription under nutrient stress conditions. These results suggest that Set2-enforced transcriptional fidelity is critical to the proper regulation of inducible and highly regulated transcription programs.
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Affiliation(s)
- Stephen L McDaniel
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Austin J Hepperla
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jie Huang
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Raghuvar Dronamraju
- Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexander T Adams
- Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Vidyadhar G Kulkarni
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ian J Davis
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Departments of Pediatrics and Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Brian D Strahl
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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18
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Li J, Duns G, Westers H, Sijmons R, van den Berg A, Kok K. SETD2: an epigenetic modifier with tumor suppressor functionality. Oncotarget 2018; 7:50719-50734. [PMID: 27191891 PMCID: PMC5226616 DOI: 10.18632/oncotarget.9368] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/05/2016] [Indexed: 11/25/2022] Open
Abstract
In the past decade important progress has been made in our understanding of the epigenetic regulatory machinery. It has become clear that genetic aberrations in multiple epigenetic modifier proteins are associated with various types of cancer. Moreover, targeting the epigenome has emerged as a novel tool to treat cancer patients. Recently, the first drugs have been reported that specifically target SETD2-negative tumors. In this review we discuss the studies on the associated protein, Set domain containing 2 (SETD2), a histone modifier for which mutations have only recently been associated with cancer development. Our review starts with the structural characteristics of SETD2 and extends to its corresponding function by combining studies on SETD2 function in yeast, Drosophila, Caenorhabditis elegans, mice, and humans. SETD2 is now generally known as the single human gene responsible for trimethylation of lysine 36 of Histone H3 (H3K36). H3K36me3 readers that recruit protein complexes to carry out specific processes, including transcription elongation, RNA processing, and DNA repair, determine the impact of this histone modification. Finally, we describe the prevalence of SETD2-inactivating mutations in cancer, with the highest frequency in clear cell Renal Cell Cancer, and explore how SETD2-inactivation might contribute to tumor development.
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Affiliation(s)
- Jun Li
- Department of Genetics, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Gerben Duns
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
| | - Helga Westers
- Department of Genetics, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Rolf Sijmons
- Department of Genetics, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Klaas Kok
- Department of Genetics, University of Groningen, University Medical Center Groningen, The Netherlands
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19
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The Chromatin Remodeler Isw1 Prevents CAG Repeat Expansions During Transcription in Saccharomyces cerevisiae. Genetics 2018; 208:963-976. [PMID: 29305386 PMCID: PMC5844344 DOI: 10.1534/genetics.117.300529] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 01/02/2018] [Indexed: 12/23/2022] Open
Abstract
CAG/CTG trinucleotide repeat expansions cause several degenerative neurological and muscular diseases. Koch et al. show that the chromatin remodeling... CAG/CTG trinucleotide repeats are unstable sequences that are difficult to replicate, repair, and transcribe due to their structure-forming nature. CAG repeats strongly position nucleosomes; however, little is known about the chromatin remodeling needed to prevent repeat instability. In a Saccharomyces cerevisiae model system with CAG repeats carried on a YAC, we discovered that the chromatin remodeler Isw1 is required to prevent CAG repeat expansions during transcription. CAG repeat expansions in the absence of Isw1 were dependent on both transcription-coupled repair (TCR) and base-excision repair (BER). Furthermore, isw1∆ mutants are sensitive to methyl methanesulfonate (MMS) and exhibit synergistic MMS sensitivity when combined with BER or TCR pathway mutants. We conclude that CAG expansions in the isw1∆ mutant occur during a transcription-coupled excision repair process that involves both TCR and BER pathways. We observed increased RNA polymerase II (RNAPII) occupancy at the CAG repeat when transcription of the repeat was induced, but RNAPII binding did not change in isw1∆ mutants, ruling out a role for Isw1 remodeling in RNAPII progression. However, nucleosome occupancy over a transcribed CAG tract was altered in isw1∆ mutants. Based on the known role of Isw1 in the reestablishment of nucleosomal spacing after transcription, we suggest that a defect in this function allows DNA structures to form within repetitive DNA tracts, resulting in inappropriate excision repair and repeat-length changes. These results establish a new function for Isw1 in directly maintaining the chromatin structure at the CAG repeat, thereby limiting expansions that can occur during transcription-coupled excision repair.
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20
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Hohenstatt ML, Mikulski P, Komarynets O, Klose C, Kycia I, Jeltsch A, Farrona S, Schubert D. PWWP-DOMAIN INTERACTOR OF POLYCOMBS1 Interacts with Polycomb-Group Proteins and Histones and Regulates Arabidopsis Flowering and Development. THE PLANT CELL 2018; 30:117-133. [PMID: 29330200 PMCID: PMC5810566 DOI: 10.1105/tpc.17.00117] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 11/28/2017] [Accepted: 01/09/2018] [Indexed: 05/10/2023]
Abstract
Polycomb-group (PcG) proteins mediate epigenetic gene regulation by setting H3K27me3 via Polycomb Repressive Complex 2 (PRC2). In plants, it is largely unclear how PcG proteins are recruited to their target genes. Here, we identified the PWWP-DOMAIN INTERACTOR OF POLYCOMBS1 (PWO1) protein, which interacts with all three Arabidopsis thaliana PRC2 histone methyltransferases and is required for maintaining full H3 occupancy at several Arabidopsis genes. PWO1 localizes and recruits CURLY LEAF to nuclear speckles in Nicotiana benthamiana nuclei, suggesting a role in spatial organization of PcG regulation. PWO1 belongs to a gene family with three members having overlapping activities: pwo1 pwo2 pwo3 triple mutants are seedling lethal and show shoot and root meristem arrest, while pwo1 single mutants are early flowering. Interestingly, the PWWP domain of PWO1 confers binding to histones, which is reduced by a point mutation in a highly conserved residue of this domain and blocked by phosphorylation of H3S28. PWO1 carrying this mutation is not able to fully complement the pwo1 pwo2 pwo3 triple mutant, indicating the requirement of this domain for PWO1 in vivo activity. Thus, the PWO family may present a novel class of histone readers that are involved in recruiting PcG proteins to subnuclear domains and in promoting Arabidopsis development.
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Affiliation(s)
| | - Pawel Mikulski
- Institute for Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany
- Institute of Biology, Freie Universität, 14195 Berlin, Germany
| | - Olga Komarynets
- Institute for Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany
- Université de Genève, 1205 Geneva, Switzerland
| | - Constanze Klose
- Institute for Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany
| | - Ina Kycia
- Institute for Biochemistry, University of Stuttgart, 70174 Stuttgart, Germany
| | - Albert Jeltsch
- Institute for Biochemistry, University of Stuttgart, 70174 Stuttgart, Germany
| | - Sara Farrona
- Institute for Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany
- Plant and AgriBiosciences Centre, National University Ireland, Galway H91 TK33, Ireland
| | - Daniel Schubert
- Institute for Genetics, Heinrich-Heine-University, 40225 Duesseldorf, Germany
- Institute of Biology, Freie Universität, 14195 Berlin, Germany
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21
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Goodwin LR, Picketts DJ. The role of ISWI chromatin remodeling complexes in brain development and neurodevelopmental disorders. Mol Cell Neurosci 2017; 87:55-64. [PMID: 29249292 DOI: 10.1016/j.mcn.2017.10.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/04/2017] [Accepted: 10/26/2017] [Indexed: 10/18/2022] Open
Abstract
The mammalian ISWI (Imitation Switch) genes SMARCA1 and SMARCA5 encode the ATP-dependent chromatin remodeling proteins SNF2L and SNF2H. The ISWI proteins interact with BAZ (bromodomain adjacent to PHD zinc finger) domain containing proteins to generate eight distinct remodeling complexes. ISWI complex-mediated nucleosome positioning within genes and gene regulatory elements is proving important for the transition from a committed progenitor state to a differentiated cell state. Genetic studies have implicated the involvement of many ATP-dependent chromatin remodeling proteins in neurodevelopmental disorders (NDDs), including SMARCA1. Here we review the characterization of mice inactivated for ISWI and their interacting proteins, as it pertains to brain development and disease. A better understanding of chromatin dynamics during neural development is a prerequisite to understanding disease pathologies and the development of therapeutics for these complex disorders.
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Affiliation(s)
- Laura R Goodwin
- Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology & Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology & Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Department of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada.
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22
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Systematic Identification of Determinants for Single-Strand Annealing-Mediated Deletion Formation in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2017; 7:3269-3279. [PMID: 28818866 PMCID: PMC5633378 DOI: 10.1534/g3.117.300165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
To ensure genomic integrity, living organisms have evolved diverse molecular processes for sensing and repairing damaged DNA. If improperly repaired, DNA damage can give rise to different types of mutations, an important class of which are genomic structural variants (SVs). In spite of their importance for phenotypic variation and genome evolution, potential contributors to SV formation in Saccharomyces cerevisiae (budding yeast), a highly tractable model organism, are not fully recognized. Here, we developed and applied a genome-wide assay to identify yeast gene knockout mutants associated with de novo deletion formation, in particular single-strand annealing (SSA)-mediated deletion formation, in a systematic manner. In addition to genes previously linked to genome instability, our approach implicates novel genes involved in chromatin remodeling and meiosis in affecting the rate of SSA-mediated deletion formation in the presence or absence of stress conditions induced by DNA-damaging agents. We closely examined two candidate genes, the chromatin remodeling gene IOC4 and the meiosis-related gene MSH4, which when knocked-out resulted in gene expression alterations affecting genes involved in cell division and chromosome organization, as well as DNA repair and recombination, respectively. Our high-throughput approach facilitates the systematic identification of processes linked to the formation of a major class of genetic variation.
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23
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Gu Q, Wang Z, Sun X, Ji T, Huang H, Yang Y, Zhang H, Tahir HAS, Wu L, Wu H, Gao X. FvSet2 regulates fungal growth, pathogenicity, and secondary metabolism in Fusarium verticillioides. Fungal Genet Biol 2017; 107:24-30. [PMID: 28778753 DOI: 10.1016/j.fgb.2017.07.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 07/26/2017] [Accepted: 07/31/2017] [Indexed: 01/12/2023]
Abstract
Histone H3 lysine 36 methylation (H3K36me) is generally associated with activation of gene expression in most eukaryotic cells. However, the function of H3K36me in filamentous fungi is largely unknown. Set2 is the sole lysine histone methyltransferase (KHMTase) enzyme responsible for the methylation of H3K36 in Saccharomyces cerevisiae. In the current study, we identified a single ortholog of S. cerevisiae Set2 in Fusarium verticillioides. We report that FvSet2 is responsible for the trimethylation of H3K36 (H3K36me3). The FvSET2 deletion mutant (ΔFvSet2) showed significant defects in vegetative growth, FB1 biosynthesis, pigmentation, and fungal virulence. Furthermore, trimethylation of H3K36 was found to be important for active transcription of genes involved in FB1 and bikaverin biosyntheses. These data indicate that FvSet2 plays an important role in the regulation of secondary metabolism, vegetative growth and fungal virulence in F. verticillioides.
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Affiliation(s)
- Qin Gu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | | | - Xiao Sun
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | - Tiantian Ji
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | - Hai Huang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | - Yang Yang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | - Hao Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | - Hafiz Abdul Samad Tahir
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | - Liming Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | - Huijun Wu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China.
| | - Xuewen Gao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
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Singh P, Sailu S, Palchamy E, Coumar MS, Baluchamy S. Identification of a novel leukemic-specific splice variant of DNMT3B and its stability. Med Oncol 2017; 34:145. [PMID: 28730333 DOI: 10.1007/s12032-017-1008-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 07/18/2017] [Indexed: 11/29/2022]
Abstract
DNA methyltransferases make use of alternative splicing mechanism to generate various splice variants, but their role(s) in modulating DNA methylation patterns in the cells is unclear. Notably, DNMT3B alone contains nearly 40 different splice variants. In this study, we have identified a novel splice variant of DNMT3B, which lacks exon 7 and 10 from leukemic cell lines which we termed as DNMT3B9. The exon 7 codes for the major part of PWWP domain, and exon 10 inclusion serves as a pluripotent marker. By quantitative RT-PCR using exon-exon junction-specific primers, we showed higher level of DNMT3B9 transcripts in several leukemic cell lines. However, DNMT3B9 expression was less in other tested cancer cell lines indicating that DNMT3B9 might serve as a leukemic-specific biomarker. Surprisingly, endogenous protein for DNMT3B9 was not detected in leukemic cells suggesting the unidentified RNA-related function(s) for DNMT3B9. In addition, we showed that DNMT3B9 protein lacks PWWP domain is less stable compared to other DNMT3B variants which contain PWWP domain through computational predictions and by cycloheximide half-life experiment. Taken together, we demonstrated the existence of novel leukemic-specific splice variant of DNMT3B and provide the evidence for the role of PWWP domain in the stability of DNMT3B. The findings reported here have relevance in epigenetic therapy, which is aimed to target the DNMT3B in cancer cells.
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Affiliation(s)
- Prachi Singh
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Sarvagalla Sailu
- Centre for Bioinformatics, Pondicherry Central University, Pondicherry, 605014, India
| | - Elango Palchamy
- Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | | | - Sudhakar Baluchamy
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India.
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25
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Histone Acetylation, Not Stoichiometry, Regulates Linker Histone Binding in Saccharomyces cerevisiae. Genetics 2017; 207:347-355. [PMID: 28739661 DOI: 10.1534/genetics.117.1132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 07/12/2017] [Indexed: 12/27/2022] Open
Abstract
Linker histones play a fundamental role in shaping chromatin structure, but how their interaction with chromatin is regulated is not well understood. In this study, we used a combination of genetic and genomic approaches to explore the regulation of linker histone binding in the yeast, Saccharomyces cerevisiae We found that increased expression of Hho1, the yeast linker histone, resulted in a severe growth defect, despite only subtle changes in chromatin structure. Further, this growth defect was rescued by mutations that increase histone acetylation. Consistent with this, genome-wide analysis of linker histone occupancy revealed an inverse correlation with histone tail acetylation in both yeast and mouse embryonic stem cells. Collectively, these results suggest that histone acetylation negatively regulates linker histone binding in S. cerevisiae and other organisms and provide important insight into how chromatin structure is regulated and maintained to both facilitate and repress transcription.
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26
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Shaping the cellular landscape with Set2/SETD2 methylation. Cell Mol Life Sci 2017; 74:3317-3334. [PMID: 28386724 DOI: 10.1007/s00018-017-2517-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/24/2017] [Accepted: 03/28/2017] [Indexed: 12/15/2022]
Abstract
Chromatin structure is a major barrier to gene transcription that must be disrupted and re-set during each round of transcription. Central to this process is the Set2/SETD2 methyltransferase that mediates co-transcriptional methylation to histone H3 at lysine 36 (H3K36me). Studies reveal that H3K36me not only prevents inappropriate transcriptional initiation from arising within gene bodies, but that it has other conserved functions that include the repair of damaged DNA and regulation of pre-mRNA splicing. Consistent with the importance of Set2/SETD2 in chromatin biology, mutations of SETD2, or mutations at or near H3K36 in H3.3, have recently been found to underlie cancer development. This review will summarize the latest insights into the functions of Set2/SETD2 in genome regulation and cancer development.
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27
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Li J, Zhu S, Ke XX, Cui H. Role of several histone lysine methyltransferases in tumor development. Biomed Rep 2016; 4:293-299. [PMID: 26998265 PMCID: PMC4774316 DOI: 10.3892/br.2016.574] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 12/31/2015] [Indexed: 12/17/2022] Open
Abstract
The field of cancer epigenetics has been evolving rapidly in recent decades. Epigenetic mechanisms include DNA methylation, histone modifications and microRNAs. Histone modifications are important markers of function and chromatin state. Aberrant histone methylation frequently occurs in tumor development and progression. Multiple studies have identified that histone lysine methyltransferases regulate gene transcription through the methylation of histone, which affects cell proliferation and differentiation, cell migration and invasion, and other biological characteristics. Histones have variant lysine sites for different levels of methylation, catalyzed by different lysine methyltransferases, which have numerous effects on human cancers. The present review focused on the most recent advances, described the key function sites of histone lysine methyltransferases, integrated significant quantities of data to introduce several compelling histone lysine methyltransferases in various types of human cancers, summarized their role in tumor development and discussed their potential mechanisms of action.
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Affiliation(s)
- Jifu Li
- Cell Biology Laboratory, State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, P.R. China
| | - Shunqin Zhu
- School of Life Science, Southwest University, Chongqing 400716, P.R. China
| | - Xiao-Xue Ke
- Cell Biology Laboratory, State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, P.R. China
| | - Hongjuan Cui
- Cell Biology Laboratory, State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, P.R. China
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28
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Speranzini V, Pilotto S, Sixma TK, Mattevi A. Touch, act and go: landing and operating on nucleosomes. EMBO J 2016; 35:376-88. [PMID: 26787641 DOI: 10.15252/embj.201593377] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/10/2015] [Indexed: 12/16/2022] Open
Abstract
Chromatin-associated enzymes are responsible for the installation, removal and reading of precise post-translation modifications on DNA and histone proteins. They are specifically recruited to the target gene by associated factors, and as a result of their activity, they contribute in modulating cell identity and differentiation. Structural and biophysical approaches are broadening our knowledge on these processes, demonstrating that DNA, histone tails and histone surfaces can each function as distinct yet functionally interconnected anchoring points promoting nucleosome binding and modification. The mechanisms underlying nucleosome recognition have been described for many histone modifiers and related readers. Here, we review the recent literature on the structural organization of these nucleosome-associated proteins, the binding properties that drive nucleosome modification and the methodological advances in their analysis. The overarching conclusion is that besides acting on the same substrate (the nucleosome), each system functions through characteristic modes of action, which bring about specific biological functions in gene expression regulation.
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Affiliation(s)
| | - Simona Pilotto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Titia K Sixma
- Division of Biochemistry and Cancer Genomics Center, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
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29
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Rona GB, Eleutherio ECA, Pinheiro AS. PWWP domains and their modes of sensing DNA and histone methylated lysines. Biophys Rev 2016; 8:63-74. [PMID: 28510146 DOI: 10.1007/s12551-015-0190-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/14/2015] [Indexed: 12/21/2022] Open
Abstract
Chromatin plays an important role in gene transcription control, cell cycle progression, recombination, DNA replication and repair. The fundamental unit of chromatin, the nucleosome, is formed by a DNA duplex wrapped around an octamer of histones. Histones are susceptible to various post-translational modifications, covalent alterations that change the chromatin status. Lysine methylation is one of the major post-translational modifications involved in the regulation of chromatin function. The PWWP domain is a member of the Royal superfamily that functions as a chromatin methylation reader by recognizing both DNA and histone methylated lysines. The PWWP domain three-dimensional structure is based on an N-terminal hydrophobic β-barrel responsible for histone methyl-lysine binding, and a C-terminal α-helical domain. In this review, we set out to discuss the most recent literature on PWWP domains, focusing on their structural features and the mechanisms by which they specifically recognize DNA and histone methylated lysines at the level of the nucleosome.
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Affiliation(s)
- Germana B Rona
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
| | - Elis C A Eleutherio
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil
| | - Anderson S Pinheiro
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-909, Brazil.
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30
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Baude A, Aaes TL, Zhai B, Al-Nakouzi N, Oo HZ, Daugaard M, Rohde M, Jäättelä M. Hepatoma-derived growth factor-related protein 2 promotes DNA repair by homologous recombination. Nucleic Acids Res 2015; 44:2214-26. [PMID: 26721387 PMCID: PMC4797281 DOI: 10.1093/nar/gkv1526] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 12/21/2015] [Indexed: 01/29/2023] Open
Abstract
We have recently identified lens epithelium-derived growth factor (LEDGF/p75, also known as PSIP1) as a component of the homologous recombination DNA repair machinery. Through its Pro-Trp-Trp-Pro (PWWP) domain, LEDGF/p75 binds to histone marks associated with active transcription and promotes DNA end resection by recruiting DNA endonuclease retinoblastoma-binding protein 8 (RBBP8/CtIP) to broken DNA ends. Here we show that the structurally related PWWP domain-containing protein, hepatoma-derived growth factor-related protein 2 (HDGFRP2), serves a similar function in homologous recombination repair. Its depletion compromises the survival of human U2OS osteosarcoma and HeLa cervix carcinoma cells and impairs the DNA damage-induced phosphorylation of replication protein A2 (RPA2) and the recruitment of DNA endonuclease RBBP8/CtIP to DNA double strand breaks. In contrast to LEDGF/p75, HDGFRP2 binds preferentially to histone marks characteristic for transcriptionally silent chromatin. Accordingly, HDGFRP2 is found in complex with the heterochromatin-binding chromobox homologue 1 (CBX1) and Pogo transposable element with ZNF domain (POGZ). Supporting the functionality of this complex, POGZ-depleted cells show a similar defect in DNA damage-induced RPA2 phosphorylation as HDGFRP2-depleted cells. These data suggest that HDGFRP2, possibly in complex with POGZ, recruits homologous recombination repair machinery to damaged silent genes or to active genes silenced upon DNA damage.
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Affiliation(s)
- Annika Baude
- Unit of Cell Death and Metabolism, Center for Autophagy, Recycling and Metabolism, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Tania Løve Aaes
- Unit of Cell Death and Metabolism, Center for Autophagy, Recycling and Metabolism, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Beibei Zhai
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Nader Al-Nakouzi
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Htoo Zarni Oo
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Mads Daugaard
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Mikkel Rohde
- Unit of Cell Death and Metabolism, Center for Autophagy, Recycling and Metabolism, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Marja Jäättelä
- Unit of Cell Death and Metabolism, Center for Autophagy, Recycling and Metabolism, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
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31
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Yi X, Jiang XJ, Li XY, Jiang DS. Histone methyltransferases: novel targets for tumor and developmental defects. Am J Transl Res 2015; 7:2159-2175. [PMID: 26807165 PMCID: PMC4697697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/31/2015] [Indexed: 06/05/2023]
Abstract
Histone lysine methylation plays a critical role in epigenetic regulation of eukaryotes. To date, studies have shown that lysine residues of K4, K9, K27, K36 and K79 in histone H3 and K20 in histone H4 can be modified by histone methyltransferases (HMTs). Such histone methylation can specifically activate or repress the transcriptional activity to play a key role in gene expression/regulation and biological genetics. Importantly, abnormities of patterns or levels of histone methylation in higher eukaryotes may result in tumorigenesis and developmental defects, suggesting histone methylation will be one of the important targets or markers for treating these diseases. This review will outline the structural characteristics, active sites and specificity of HMTs, correlation between histone methylation and human diseases and lay special emphasis on the progress of the research on H3K36 methylation.
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Affiliation(s)
- Xin Yi
- Department of Cardiology, Renmin Hospital of Wuhan UniversityWuhan 430060, China
- Cardiovascular Research Institute, Wuhan UniversityWuhan 430060, China
| | - Xue-Jun Jiang
- Department of Cardiology, Renmin Hospital of Wuhan UniversityWuhan 430060, China
- Cardiovascular Research Institute, Wuhan UniversityWuhan 430060, China
| | - Xiao-Yan Li
- Department of Cardiology, Renmin Hospital of Wuhan UniversityWuhan 430060, China
- Cardiovascular Research Institute, Wuhan UniversityWuhan 430060, China
| | - Ding-Sheng Jiang
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430030, China
- Heart-Lung Transplantation Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430030, China
- Sino-Swiss Heart-Lung Transplantation Institute, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan 430030, China
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32
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Zhang T, Cooper S, Brockdorff N. The interplay of histone modifications - writers that read. EMBO Rep 2015; 16:1467-81. [PMID: 26474904 PMCID: PMC4641500 DOI: 10.15252/embr.201540945] [Citation(s) in RCA: 516] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/16/2015] [Indexed: 01/07/2023] Open
Abstract
Histones are subject to a vast array of posttranslational modifications including acetylation, methylation, phosphorylation, and ubiquitylation. The writers of these modifications play important roles in normal development and their mutation or misregulation is linked with both genetic disorders and various cancers. Readers of these marks contain protein domains that allow their recruitment to chromatin. Interestingly, writers often contain domains which can read chromatin marks, allowing the reinforcement of modifications through a positive feedback loop or inhibition of their activity by other modifications. We discuss how such positive reinforcement can result in chromatin states that are robust and can be epigenetically maintained through cell division. We describe the implications of these regulatory systems in relation to modifications including H3K4me3, H3K79me3, and H3K36me3 that are associated with active genes and H3K27me3 and H3K9me3 that have been linked to transcriptional repression. We also review the crosstalk between active and repressive modifications, illustrated by the interplay between the Polycomb and Trithorax histone-modifying proteins, and discuss how this may be important in defining gene expression states during development.
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Affiliation(s)
- Tianyi Zhang
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Sarah Cooper
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Neil Brockdorff
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, UK
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33
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Méndez C, Ahlenstiel CL, Kelleher AD. Post-transcriptional gene silencing, transcriptional gene silencing and human immunodeficiency virus. World J Virol 2015; 4:219-244. [PMID: 26279984 PMCID: PMC4534814 DOI: 10.5501/wjv.v4.i3.219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/24/2015] [Accepted: 04/29/2015] [Indexed: 02/05/2023] Open
Abstract
While human immunodeficiency virus 1 (HIV-1) infection is controlled through continuous, life-long use of a combination of drugs targeting different steps of the virus cycle, HIV-1 is never completely eradicated from the body. Despite decades of research there is still no effective vaccine to prevent HIV-1 infection. Therefore, the possibility of an RNA interference (RNAi)-based cure has become an increasingly explored approach. Endogenous gene expression is controlled at both, transcriptional and post-transcriptional levels by non-coding RNAs, which act through diverse molecular mechanisms including RNAi. RNAi has the potential to control the turning on/off of specific genes through transcriptional gene silencing (TGS), as well as fine-tuning their expression through post-transcriptional gene silencing (PTGS). In this review we will describe in detail the canonical RNAi pathways for PTGS and TGS, the relationship of TGS with other silencing mechanisms and will discuss a variety of approaches developed to suppress HIV-1 via manipulation of RNAi. We will briefly compare RNAi strategies against other approaches developed to target the virus, highlighting their potential to overcome the major obstacle to finding a cure, which is the specific targeting of the HIV-1 reservoir within latently infected cells.
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34
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Histone exchange, chromatin structure and the regulation of transcription. Nat Rev Mol Cell Biol 2015; 16:178-89. [DOI: 10.1038/nrm3941] [Citation(s) in RCA: 650] [Impact Index Per Article: 72.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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35
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Wozniak GG, Strahl BD. Hitting the ‘mark’: Interpreting lysine methylation in the context of active transcription. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1353-61. [DOI: 10.1016/j.bbagrm.2014.03.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 03/01/2014] [Accepted: 03/03/2014] [Indexed: 12/31/2022]
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36
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Qin S, Min J. Structure and function of the nucleosome-binding PWWP domain. Trends Biochem Sci 2014; 39:536-47. [PMID: 25277115 DOI: 10.1016/j.tibs.2014.09.001] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/26/2014] [Accepted: 09/08/2014] [Indexed: 12/11/2022]
Abstract
PWWP domain-containing proteins are often involved in chromatin-associated biological processes, such as transcriptional regulation and DNA repair, and recent studies have shown that the PWWP domain specifies chromatin localization. Mutations in the PWWP domain, a 100-150 amino acid motif, have been linked to various human diseases, emphasizing its importance. Structural studies reveal that PWWP domains possess a conserved aromatic cage for histone methyl-lysine recognition, and synergistically bind both histone and DNA, which contributes to their nucleosome-binding ability and chromatin localization. Furthermore, the PWWP domain often cooperates with other histone and DNA 'reader' or 'modifier' domains to evoke crosstalk between various epigenetic marks. Here, we discuss these recent advances in understanding the structure and function of the PWWP domain.
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Affiliation(s)
- Su Qin
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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37
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Shmakova A, Batie M, Druker J, Rocha S. Chromatin and oxygen sensing in the context of JmjC histone demethylases. Biochem J 2014; 462:385-95. [PMID: 25145438 PMCID: PMC4147966 DOI: 10.1042/bj20140754] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/07/2014] [Accepted: 07/09/2014] [Indexed: 01/22/2023]
Abstract
Responding appropriately to changes in oxygen availability is essential for multicellular organism survival. Molecularly, cells have evolved intricate gene expression programmes to handle this stressful condition. Although it is appreciated that gene expression is co-ordinated by changes in transcription and translation in hypoxia, much less is known about how chromatin changes allow for transcription to take place. The missing link between co-ordinating chromatin structure and the hypoxia-induced transcriptional programme could be in the form of a class of dioxygenases called JmjC (Jumonji C) enzymes, the majority of which are histone demethylases. In the present review, we will focus on the function of JmjC histone demethylases, and how these could act as oxygen sensors for chromatin in hypoxia. The current knowledge concerning the role of JmjC histone demethylases in the process of organism development and human disease will also be reviewed.
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Key Words
- chromatin
- chromatin remodeller
- histone methylation
- hypoxia
- hypoxia-inducible factor (hif)
- jumonji c (jmjc)
- transcription
- cd, chromodomain
- chd, chromodomain helicase dna binding
- crc, chromatin-remodelling complex
- fih, factor inhibiting hif
- hif, hypoxia-inducible factor
- iswi, imitation-swi protein
- jmjc, jumonji c
- kdm, lysine-specific demethylase
- lsd, lysine-specific demethylase
- nurd, nucleosome-remodelling deacetylase
- phd, plant homeodomain
- phf, phd finger protein
- rest, repressor element 1-silencing transcription factor
- vhl, von hippel–lindau protein
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Affiliation(s)
- Alena Shmakova
- *Centre for Gene Regulation and Expression, MSI/WTB/JBC Complex, Dow Street, University of Dundee, Dundee DD1 5EH, Scotland, U.K
| | - Michael Batie
- *Centre for Gene Regulation and Expression, MSI/WTB/JBC Complex, Dow Street, University of Dundee, Dundee DD1 5EH, Scotland, U.K
| | - Jimena Druker
- *Centre for Gene Regulation and Expression, MSI/WTB/JBC Complex, Dow Street, University of Dundee, Dundee DD1 5EH, Scotland, U.K
| | - Sonia Rocha
- *Centre for Gene Regulation and Expression, MSI/WTB/JBC Complex, Dow Street, University of Dundee, Dundee DD1 5EH, Scotland, U.K
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38
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Gilbert TM, McDaniel SL, Byrum SD, Cades JA, Dancy BCR, Wade H, Tackett AJ, Strahl BD, Taverna SD. A PWWP domain-containing protein targets the NuA3 acetyltransferase complex via histone H3 lysine 36 trimethylation to coordinate transcriptional elongation at coding regions. Mol Cell Proteomics 2014; 13:2883-95. [PMID: 25104842 DOI: 10.1074/mcp.m114.038224] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Post-translational modifications of histones, such as acetylation and methylation, are differentially positioned in chromatin with respect to gene organization. For example, although histone H3 is often trimethylated on lysine 4 (H3K4me3) and acetylated on lysine 14 (H3K14ac) at active promoter regions, histone H3 lysine 36 trimethylation (H3K36me3) occurs throughout the open reading frames of transcriptionally active genes. The conserved yeast histone acetyltransferase complex, NuA3, specifically binds H3K4me3 through a plant homeodomain (PHD) finger in the Yng1 subunit, and subsequently catalyzes the acetylation of H3K14 through the histone acetyltransferase domain of Sas3, leading to transcription initiation at a subset of genes. We previously found that Ylr455w (Pdp3), an uncharacterized proline-tryptophan-tryptophan-proline (PWWP) domain-containing protein, copurifies with stable members of NuA3. Here, we employ mass-spectrometric analysis of affinity purified Pdp3, biophysical binding assays, and genetic analyses to classify NuA3 into two functionally distinct forms: NuA3a and NuA3b. Although NuA3a uses the PHD finger of Yng1 to interact with H3K4me3 at the 5'-end of open reading frames, NuA3b contains the unique member, Pdp3, which regulates an interaction between NuA3b and H3K36me3 at the transcribed regions of genes through its PWWP domain. We find that deletion of PDP3 decreases NuA3-directed transcription and results in growth defects when combined with transcription elongation mutants, suggesting NuA3b acts as a positive elongation factor. Finally, we determine that NuA3a, but not NuA3b, is synthetically lethal in combination with a deletion of the histone acetyltransferase GCN5, indicating NuA3b has a specialized role at coding regions that is independent of Gcn5 activity. Collectively, these studies define a new form of the NuA3 complex that associates with H3K36me3 to effect transcriptional elongation. MS data are available via ProteomeXchange with identifier PXD001156.
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Affiliation(s)
- Tonya M Gilbert
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Stephen L McDaniel
- ¶Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - Stephanie D Byrum
- ‖Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205
| | - Jessica A Cades
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Blair C R Dancy
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Herschel Wade
- **Department of Biophysics and Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
| | - Alan J Tackett
- ‖Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205
| | - Brian D Strahl
- ¶Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599; ‡‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - Sean D Taverna
- From the ‡Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205; §Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205;
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SUMV-1 antagonizes the activity of synthetic multivulva genes in Caenorhabditis elegans. Dev Biol 2014; 392:266-82. [PMID: 24882710 DOI: 10.1016/j.ydbio.2014.05.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 05/20/2014] [Accepted: 05/22/2014] [Indexed: 11/22/2022]
Abstract
Chromatin regulators contribute to the developmental control of gene expression. In the nematode Caenorhabditis elegans, the roles of chromatin regulation in development have been explored in several contexts, including vulval differentiation. The synthetic multivulva (synMuv) genes are regulators of vulval development in C. elegans and the proteins encoded by these genes include components of several histone modification and chromatin remodelling complexes. By inhibiting ectopic expression of the epidermal growth factor (LIN-3) in the nematode hypodermis, the synMuv genes prevent inappropriate vulval induction. In a forward genetic screen for modifiers of the expression of a hypodermal reporter gene, we identified a mutation that results in increased expression of the reporter. This mutation also suppresses ectopic vulval induction in synMuv mutants and we have consequently named the affected gene suppressor of synthetic multivulva-1 (sumv-1). We show that SUMV-1 is required in the hypodermis for the synMuv phenotype and that loss of sumv-1 function suppresses ectopic expression of lin-3 in synMuv mutant animals. In yeast two-hybrid assays SUMV-1 physically interacts with SUMV-2, and reduction of sumv-2 function also suppresses the synMuv phenotype. We identified similarities between SUMV-1 and SUMV-2 and mammalian proteins KAT8 NSL2 and KAT8 NSL3, respectively, which are components of the KAT8/MOF histone acetyltransferase complex. Reduction of function of mys-2, which encodes the enzymatic component of the KAT8/MOF complex, also suppresses the synMuv phenotype, and MYS-2 physically interacts with SUMV-2 in yeast two-hybrid assays. Together these observations suggest that SUMV-1 and SUMV-2 may function together with MYS-2 in a nematode KAT8/MOF-like complex to antagonise the activity of the synMuv genes.
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Musselman CA, Khorasanizadeh S, Kutateladze TG. Towards understanding methyllysine readout. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:686-93. [PMID: 24727128 DOI: 10.1016/j.bbagrm.2014.04.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 03/19/2014] [Accepted: 04/02/2014] [Indexed: 02/09/2023]
Abstract
BACKGROUND Lysine methylation is the most versatile covalent posttranslational modification (PTM) found in histones and non-histone proteins. Over the past decade a number of methyllysine-specific readers have been discovered and their interactions with histone tails have been structurally and biochemically characterized. More recently innovative experimental approaches have emerged that allow for studying reader interactions in the context of the full nucleosome and nucleosomal arrays. SCOPE OF REVIEW In this review we give a brief overview of the known mechanisms of histone lysine methylation readout, summarize progress recently made in exploring interactions with methylated nucleosomes, and discuss the latest advances in the development of small molecule inhibitors of the methyllysine-specific readers. MAJOR CONCLUSIONS New studies reveal various reader-nucleosome contacts outside the methylated histone tail, thus offering a better model for association of histone readers to chromatin and broadening our understanding of the functional implications of these interactions. In addition, some progress has been made in the design of antagonists of these interactions. GENERAL SIGNIFICANCE Specific lysine methylation patterns are commonly associated with certain chromatin states and genomic elements, and are linked to distinct biological outcomes such as transcription activation or repression. Disruption of patterns of histone modifications is associated with a number of diseases, and there is tremendous therapeutic potential in targeting histone modification pathways. Thus, investigating binding of readers of these modifications is not only important for elucidating fundamental mechanisms of chromatin regulation, but also necessary for the design of targeted therapeutics. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
| | - Sepideh Khorasanizadeh
- Diabetes and Obesity Research Center, Sanford-Burnham Medical Research Institute, Orlando, FL 32827, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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41
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Adenovirus E1A recruits the human Paf1 complex to enhance transcriptional elongation. J Virol 2014; 88:5630-7. [PMID: 24600005 DOI: 10.1128/jvi.03518-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED During infection by human adenovirus (HAdV), the proteins encoded by the early region 1A (E1A) gene bind and appropriate components of the cellular transcriptional machinery to activate the transcription of viral early genes. Previously, we identified roles for the human Bre1 (hBre1) and hPaf1 complexes in E1A-mediated transcriptional activation of HAdV early genes. Here we show that E1A binds hBre1 directly and that this complex targets the hPaf1 complex via the Rtf1 subunit. Depletion of hPaf1 reduces E1A-dependent activation of transcription from the E2e, E3, and E4 viral transcription units, and this does not result from a reduced ability of RNA polymerase II to be recruited to the promoter-proximal regions of these genes. In contrast, depletion of hPaf1 reduces the occupancy of RNA polymerase II across these transcription units. This is accompanied by reductions in the level of H3K36 trimethylation, a posttranslational histone modification associated with efficient transcriptional elongation, and the number of full-length transcripts from these genes. Together, these results indicate that E1A uses hBre1 to recruit the hPaf1 complex in order to optimally activate viral early transcription by enhancing transcriptional elongation. IMPORTANCE This work provides the mechanism by which the hPaf1 complex contributes to E1A-dependent activation of early gene transcription. The work also demonstrates that E1A induces gene expression by stimulating transcriptional elongation, in addition to its better-characterized effects on transcriptional initiation.
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Abstract
A large family of chromatin remodelers that noncovalently modify chromatin is crucial in cell development and differentiation. They are often the targets of cancer, neurological disorders, and other human diseases. These complexes alter nucleosome positioning, higher-order chromatin structure, and nuclear organization. They also assemble chromatin, exchange out histone variants, and disassemble chromatin at defined locations. We review aspects of the structural organization of these complexes, the functional properties of their protein domains, and variation between complexes. We also address the mechanistic details of these complexes in mobilizing nucleosomes and altering chromatin structure. A better understanding of these issues will be vital for further analyses of subunits of these chromatin remodelers, which are being identified as targets in human diseases by NGS (next-generation sequencing).
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Affiliation(s)
- Blaine Bartholomew
- University of Texas MD Anderson Cancer Center, Department of Molecular Carcinogenesis, Smithville, Texas 78957;
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Swygert SG, Peterson CL. Chromatin dynamics: interplay between remodeling enzymes and histone modifications. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:728-36. [PMID: 24583555 DOI: 10.1016/j.bbagrm.2014.02.013] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 02/13/2014] [Accepted: 02/20/2014] [Indexed: 01/08/2023]
Abstract
Chromatin dynamics play an essential role in regulating the accessibility of genomic DNA for a variety of nuclear processes, including gene transcription and DNA repair. The posttranslational modification of the core histones and the action of ATP-dependent chromatin remodeling enzymes represent two primary mechanisms by which chromatin dynamics are controlled and linked to nuclear events. Although there are examples in which a histone modification or a remodeling enzyme may be sufficient to drive a chromatin transition, these mechanisms typically work in concert to integrate regulatory inputs, leading to a coordinated alteration in chromatin structure and function. Indeed, site-specific histone modifications can facilitate the recruitment of chromatin remodeling enzymes to particular genomic regions, or they can regulate the efficiency or the outcome of a chromatin remodeling reaction. Conversely, chromatin remodeling enzymes can also influence, and sometimes directly modulate, the modification state of histones. These functional interactions are generally complex, frequently transient, and often require the association of myriad additional factors. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Sarah G Swygert
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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Bartholomew B. ISWI chromatin remodeling: one primary actor or a coordinated effort? Curr Opin Struct Biol 2014; 24:150-5. [PMID: 24561830 DOI: 10.1016/j.sbi.2014.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 01/14/2014] [Accepted: 01/16/2014] [Indexed: 01/20/2023]
Abstract
The ISWI family of ATP-dependent chromatin remodelers regulates transcription of coding and noncoding RNA by mobilizing nucleosomes and controlling the length of linker DNA separating nucleosomes (spacing). Nucleosome movement is tightly coupled to the DNA translocation activity of the helicase domain in the catalytic subunit. There may be other domains besides the helicase domain needed to move DNA in and out of nucleosomes. The C terminus of the ISWI catalytic subunit with the conserved HAND, SANT, and SLIDE domains may be involved in nucleosome spacing. There are several models of how the C terminus may facilitate in ISWI remodeling such as regulating the activity of the helicase domain and causing the helicase domain to translocate more efficiently on DNA or to enhance its selectivity for nucleosomes. Another possibility is that domains like SLIDE promote linker DNA entering into nucleosomes in a coordinated manner with the helicase domain.
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Affiliation(s)
- Blaine Bartholomew
- The University of Texas MD Anderson Cancer Center, Department of Molecular Carcinogenesis, Smithville, TX 78957, United States.
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45
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Morchikh M, Naughtin M, Di Nunzio F, Xavier J, Charneau P, Jacob Y, Lavigne M. TOX4 and NOVA1 proteins are partners of the LEDGF PWWP domain and affect HIV-1 replication. PLoS One 2013; 8:e81217. [PMID: 24312278 PMCID: PMC3842248 DOI: 10.1371/journal.pone.0081217] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 10/10/2013] [Indexed: 12/31/2022] Open
Abstract
PWWP domains are involved in the chromatin attachment of several proteins. They bind to both DNA and proteins and their interaction with specific histone methylation marks define them as a new class of histone code readers. The lens epithelium derived growth factor (LEDGF/p75) contains an N-terminal PWWP domain necessary for its interaction with chromatin but also a C-terminal domain which interacts with several proteins, such as lentiviral integrases. These two domains confer a chromatin-tethering function to LEDGF/p75 and in the case of lentiviral integrases, this tethering participates in the efficiency and site selectivity of integration. Although proteins interacting with LEDGF/p75 C-terminal domain have been extensively studied, no data exist about partners of its PWWP domain regulating its interaction with chromatin. In this study, we report the identification by yeast-two-hybrid of thirteen potential partners of the LEDGF PWWP domain. Five of these interactions were confirmed in mammalian cells, using both a protein complementation assay and co-immunoprecipitation approaches. Three of these partners interact with full length LEDGF/p75, they are specific for PWWP domains of the HDGF family and they require PWWP amino acids essential for the interaction with chromatin. Among them, the transcription activator TOX4 and the splicing cofactor NOVA1 were selected for a more extensive study. These two proteins or their PWWP interacting regions (PIR) colocalize with LEDGF/p75 in Hela cells and interact in vitro in the presence of DNA. Finally, single round VSV-G pseudotyped HIV-1 but not MLV infection is inhibited in cells overexpressing these two PIRs. The observed inhibition of infection can be attributed to a defect in the integration step. Our data suggest that a regulation of LEDGF interaction with chromatin by cellular partners of its PWWP domain could be involved in several processes linked to LEDGF tethering properties, such as lentiviral integration, DNA repair or transcriptional regulation.
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Affiliation(s)
- Mehdi Morchikh
- Ecole Normale Supérieure, Laboratoire Joliot-Curie, Centre National de la Recherche Scientifique, Lyon, France
- Institut Pasteur, Unité de Virologie Structurale, Centre National de la Recherche Scientifique, Unité de recherche associée, Paris, France
- Université Pierre et Marie Curie, Paris, France
| | - Monica Naughtin
- Ecole Normale Supérieure, Laboratoire Joliot-Curie, Centre National de la Recherche Scientifique, Lyon, France
| | - Francesca Di Nunzio
- Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, Centre National de la Recherche Scientifique, Paris, France
| | - Johan Xavier
- Ecole Normale Supérieure, Laboratoire Joliot-Curie, Centre National de la Recherche Scientifique, Lyon, France
| | - Pierre Charneau
- Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, Centre National de la Recherche Scientifique, Paris, France
| | - Yves Jacob
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Centre National de la Recherche Scientifique, Paris, France
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Marc Lavigne
- Ecole Normale Supérieure, Laboratoire Joliot-Curie, Centre National de la Recherche Scientifique, Lyon, France
- Institut Pasteur, Unité de Virologie Structurale, Centre National de la Recherche Scientifique, Unité de recherche associée, Paris, France
- * E-mail:
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Kato H, Okazaki K, Urano T. Spt6: two fundamentally distinct functions in the regulation of histone modification. Epigenetics 2013; 8:1249-53. [PMID: 24107707 PMCID: PMC3933485 DOI: 10.4161/epi.26487] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
As posttranslational modifications of histones H3 and H4 determine the state of chromatin in cis, these histones should remain attached to template DNA during transcription in order to maintain the state of chromatin. RNA polymerase II itself can transcribe the nucleosome template without changing nucleosome positioning. However, it was uncertain whether Spt6, a highly conserved polymerase-associated histone chaperone, prevents “preexisting” histone molecules from being dissociated from template DNA during transcription. We recently showed that Spt6 prevents transcription-coupled loss of posttranslationally modified histone H3. Taking previous studies into account, we would like to propose here that Spt6 has two fundamentally distinct functions in the regulation of histone modification: one is to act as a platform for histone modifiers and the other is to act as a molecular liaison between histone molecules and template DNA to prevent cotranscriptional dissociation of preexisting histones in order to maintain locus-specific modifications.
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Affiliation(s)
- Hiroaki Kato
- Department of Biochemistry; Shimane University School of Medicine; Izumo, Japan; PRESTO; Japan Science and Technology Agency (JST); Saitama, Japan
| | - Kosuke Okazaki
- Department of Biochemistry; Shimane University School of Medicine; Izumo, Japan
| | - Takeshi Urano
- Department of Biochemistry; Shimane University School of Medicine; Izumo, Japan
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47
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Balancing chromatin remodeling and histone modifications in transcription. Trends Genet 2013; 29:621-9. [PMID: 23870137 DOI: 10.1016/j.tig.2013.06.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 05/29/2013] [Accepted: 06/18/2013] [Indexed: 11/24/2022]
Abstract
Chromatin remodelers use the energy of ATP hydrolysis to reposition or evict nucleosomes or to replace canonical histones with histone variants. By regulating nucleosome dynamics, remodelers gate access to the underlying DNA for replication, repair, and transcription. Nucleosomes are subject to extensive post-translational modifications that can recruit regulatory proteins or alter the local chromatin structure. Just as extensive crosstalk has been observed between different histone post-translational modifications, there is growing evidence for both coordinated and antagonistic functional relations between nucleosome remodeling and modifying machineries. Defining the combined functions of the complexes that alter nucleosome interactions, position, and stability is key to understanding processes that require access to DNA, particularly with growing appreciation of their contributions to human health and disease. Here, we highlight recent advances in the interactions between histone modifications and the imitation-switch (ISWI) and chromodomain helicase DNA-binding protein 1 (CHD1) chromatin remodelers from studies in budding yeast, fission yeast, flies, and mammalian cells, with a focus on yeast.
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48
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Jeronimo C, Bataille AR, Robert F. The Writers, Readers, and Functions of the RNA Polymerase II C-Terminal Domain Code. Chem Rev 2013; 113:8491-522. [DOI: 10.1021/cr4001397] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - Alain R. Bataille
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
- Département
de Médecine,
Faculté de Médecine, Université de Montréal, Montréal, Québec,
Canada H3T 1J4
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49
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Venkatesh S, Workman JL, Smolle M. UpSETing chromatin during non-coding RNA production. Epigenetics Chromatin 2013; 6:16. [PMID: 23738864 PMCID: PMC3680234 DOI: 10.1186/1756-8935-6-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 05/10/2013] [Indexed: 01/01/2023] Open
Abstract
The packaging of eukaryotic DNA into nucleosomal arrays permits cells to tightly regulate and fine-tune gene expression. The ordered disassembly and reassembly of these nucleosomes allows RNA polymerase II (RNAPII) conditional access to the underlying DNA sequences. Disruption of nucleosome reassembly following RNAPII passage results in spurious transcription initiation events, leading to the production of non-coding RNA (ncRNA). We review the molecular mechanisms involved in the suppression of these cryptic initiation events and discuss the role played by ncRNAs in regulating gene expression.
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Affiliation(s)
- Swaminathan Venkatesh
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64110, USA.
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50
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Regulation of nucleosome dynamics by histone modifications. Nat Struct Mol Biol 2013; 20:259-66. [PMID: 23463310 DOI: 10.1038/nsmb.2470] [Citation(s) in RCA: 618] [Impact Index Per Article: 56.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 11/02/2012] [Indexed: 12/12/2022]
Abstract
Chromatin is a dynamic structure that must respond to myriad stimuli to regulate access to DNA, and chemical modification of histones is a major means by which the cell modulates nucleosome mobility and turnover. Histone modifications are linked to essentially every cellular process requiring DNA access, including transcription, replication and repair. Here we consider properties of the major types of histone modification in the context of their associated biological processes to view them in light of the cellular mechanisms that regulate nucleosome dynamics.
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