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Goto N, Suke K, Yonezawa N, Nishihara H, Handa T, Sato Y, Kujirai T, Kurumizaka H, Yamagata K, Kimura H. ISWI chromatin remodeling complexes recruit NSD2 and H3K36me2 in pericentromeric heterochromatin. J Cell Biol 2024; 223:e202310084. [PMID: 38709169 PMCID: PMC11076809 DOI: 10.1083/jcb.202310084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/04/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024] Open
Abstract
Histone H3 lysine36 dimethylation (H3K36me2) is generally distributed in the gene body and euchromatic intergenic regions. However, we found that H3K36me2 is enriched in pericentromeric heterochromatin in some mouse cell lines. We here revealed the mechanism of heterochromatin targeting of H3K36me2. Among several H3K36 methyltransferases, NSD2 was responsible for inducing heterochromatic H3K36me2. Depletion and overexpression analyses of NSD2-associating proteins revealed that NSD2 recruitment to heterochromatin was mediated through the imitation switch (ISWI) chromatin remodeling complexes, such as BAZ1B-SMARCA5 (WICH), which directly binds to AT-rich DNA via a BAZ1B domain-containing AT-hook-like motifs. The abundance and stoichiometry of NSD2, SMARCA5, and BAZ1B could determine the localization of H3K36me2 in different cell types. In mouse embryos, H3K36me2 heterochromatin localization was observed at the two- to four-cell stages, suggesting its physiological relevance.
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Affiliation(s)
- Naoki Goto
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Kazuma Suke
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Japan
| | - Nao Yonezawa
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Japan
| | - Hidenori Nishihara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
| | - Tetsuya Handa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuko Sato
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Tomoya Kujirai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Kazuo Yamagata
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Japan
| | - Hiroshi Kimura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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2
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Jabeena CA, Rajavelu A. Histone globular domain epigenetic modifications: The regulators of chromatin dynamics in malaria parasite. Chembiochem 2024; 25:e202300596. [PMID: 38078518 DOI: 10.1002/cbic.202300596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 12/09/2023] [Indexed: 01/31/2024]
Abstract
Plasmodium species adapt a complex lifecycle with multiple phenotypes to survive inside various cell types of humans and mosquitoes. Stage-specific gene expression in the developmental stages of parasites is tightly controlled in Plasmodium species; however, the underlying mechanisms have yet to be explored. Genome organization and gene expression for each stage of the malaria parasite need to be better characterized. Recent studies indicated that epigenetic modifications of histone proteins play a vital role in chromatin plasticity. Like other eukaryotes, Plasmodium species N-terminal tail modifications form a distinct "histone code," which creates the docking sites for histone reader proteins, including gene activator/repressor complexes, to regulate gene expression. The emerging research findings shed light on various unconventional epigenetic changes in histone proteins' core/globular domain regions, which might contribute to the chromatin organization in different developmental stages of the malaria parasite. The malaria parasite lost many transcription factors during evolution, and it is proposed that the nature of local chromatin structure essentially regulates the stage-specific gene expression. This review highlights recent discoveries of unconventional histone globular domain epigenetic modifications and their functions in regulating chromatin structure dynamics in various developmental stages of malaria parasites.
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Affiliation(s)
- C A Jabeena
- Pathogen Biology Group, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud P O, Thiruvananthapuram, Kerala, 695014, India
| | - Arumugam Rajavelu
- Pathogen Biology Group, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud P O, Thiruvananthapuram, Kerala, 695014, India
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology, Madras, Chennai, Tamil Nadu, 600 036, India
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3
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Roy A, Niharika, Chakraborty S, Mishra J, Singh SP, Patra SK. Mechanistic aspects of reversible methylation modifications of arginine and lysine of nuclear histones and their roles in human colon cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:261-302. [PMID: 37019596 DOI: 10.1016/bs.pmbts.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Developmental proceedings and maintenance of cellular homeostasis are regulated by the precise orchestration of a series of epigenetic events that eventually control gene expression. DNA methylation and post-translational modifications (PTMs) of histones are well-characterized epigenetic events responsible for fine-tuning gene expression. PTMs of histones bear molecular logic of gene expression at chromosomal territory and have become a fascinating field of epigenetics. Nowadays, reversible methylation on histone arginine and lysine is gaining increasing attention as a significant PTM related to reorganizing local nucleosomal structure, chromatin dynamics, and transcriptional regulation. It is now well-accepted and reported that histone marks play crucial roles in colon cancer initiation and progression by encouraging abnormal epigenomic reprogramming. It is becoming increasingly clear that multiple PTM marks at the N-terminal tails of the core histones cross-talk with one another to intricately regulate DNA-templated biological processes such as replication, transcription, recombination, and damage repair in several malignancies, including colon cancer. These functional cross-talks provide an additional layer of message, which spatiotemporally fine-tunes the overall gene expression regulation. Nowadays, it is evident that several PTMs instigate colon cancer development. How colon cancer-specific PTM patterns or codes are generated and how they affect downstream molecular events are uncovered to some extent. Future studies would address more about epigenetic communication, and the relationship between histone modification marks to define cellular functions in depth. This chapter will comprehensively highlight the importance of histone arginine and lysine-based methylation modifications and their functional cross-talk with other histone marks from the perspective of colon cancer development.
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Jiang Y, Liu L, Yang ZQ. KDM4 Demethylases: Structure, Function, and Inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:87-111. [PMID: 37751137 DOI: 10.1007/978-3-031-38176-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
KDM4 histone demethylases mainly catalyze the removal of methyl marks from H3K9 and H3K36 to epigenetically regulate chromatin structure and gene expression. KDM4 expression is strictly regulated to ensure proper function in a myriad of biological processes, including transcription, cellular proliferation and differentiation, DNA damage repair, immune response, and stem cell self-renewal. Aberrant expression of KDM4 demethylase has been documented in many types of blood and solid tumors, and thus, KDM4s represent promising therapeutic targets. In this chapter, we summarize the current knowledge of the structures and regulatory mechanisms of KDM4 proteins and our understanding of their alterations in human pathological processes with a focus on development and cancer. We also review the reported KDM4 inhibitors and discuss their potential as therapeutic agents.
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Affiliation(s)
- Yuanyuan Jiang
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, 4100 John R Street, HWCRC 815, Detroit, MI, 48201, USA
| | - Lanxin Liu
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, 4100 John R Street, HWCRC 815, Detroit, MI, 48201, USA
| | - Zeng-Quan Yang
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, 4100 John R Street, HWCRC 815, Detroit, MI, 48201, USA.
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5
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Levinsky AJ, McEdwards G, Sethna N, Currie MA. Targets of histone H3 lysine 9 methyltransferases. Front Cell Dev Biol 2022; 10:1026406. [PMID: 36568972 PMCID: PMC9768651 DOI: 10.3389/fcell.2022.1026406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/05/2022] [Indexed: 12/12/2022] Open
Abstract
Histone H3 lysine 9 di- and trimethylation are well-established marks of constitutively silenced heterochromatin domains found at repetitive DNA elements including pericentromeres, telomeres, and transposons. Loss of heterochromatin at these sites causes genomic instability in the form of aberrant DNA repair, chromosome segregation defects, replication stress, and transposition. H3K9 di- and trimethylation also regulate cell type-specific gene expression during development and form a barrier to cellular reprogramming. However, the role of H3K9 methyltransferases extends beyond histone methylation. There is a growing list of non-histone targets of H3K9 methyltransferases including transcription factors, steroid hormone receptors, histone modifying enzymes, and other chromatin regulatory proteins. Additionally, two classes of H3K9 methyltransferases modulate their own function through automethylation. Here we summarize the structure and function of mammalian H3K9 methyltransferases, their roles in genome regulation and constitutive heterochromatin, as well as the current repertoire of non-histone methylation targets including cases of automethylation.
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Affiliation(s)
- Aidan J. Levinsky
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Gregor McEdwards
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Nasha Sethna
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Mark A. Currie
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada,Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada,*Correspondence: Mark A. Currie,
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Millán-Zambrano G, Burton A, Bannister AJ, Schneider R. Histone post-translational modifications - cause and consequence of genome function. Nat Rev Genet 2022; 23:563-580. [PMID: 35338361 DOI: 10.1038/s41576-022-00468-7] [Citation(s) in RCA: 214] [Impact Index Per Article: 107.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2022] [Indexed: 12/16/2022]
Abstract
Much has been learned since the early 1960s about histone post-translational modifications (PTMs) and how they affect DNA-templated processes at the molecular level. This understanding has been bolstered in the past decade by the identification of new types of histone PTM, the advent of new genome-wide mapping approaches and methods to deposit or remove PTMs in a locally and temporally controlled manner. Now, with the availability of vast amounts of data across various biological systems, the functional role of PTMs in important processes (such as transcription, recombination, replication, DNA repair and the modulation of genomic architecture) is slowly emerging. This Review explores the contribution of histone PTMs to the regulation of genome function by discussing when these modifications play a causative (or instructive) role in DNA-templated processes and when they are deposited as a consequence of such processes, to reinforce and record the event. Important advances in the field showing that histone PTMs can exert both direct and indirect effects on genome function are also presented.
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Affiliation(s)
- Gonzalo Millán-Zambrano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Adam Burton
- Institute of Epigenetics and Stem Cells, Helmholtz Center Munich, Munich, Germany
| | - Andrew J Bannister
- Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Center Munich, Munich, Germany.
- Faculty of Biology, Ludwig Maximilian University (LMU) of Munich, Munich, Germany.
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7
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Zhang C, Tian Y, Song S, Zhang L, Dang Y, He Q. H3K56 deacetylation and H2A.Z deposition are required for aberrant heterochromatin spreading. Nucleic Acids Res 2022; 50:3852-3866. [PMID: 35333354 PMCID: PMC9023284 DOI: 10.1093/nar/gkac196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 03/10/2022] [Accepted: 03/15/2022] [Indexed: 11/21/2022] Open
Abstract
Crucial mechanisms are required to restrict self-propagating heterochromatin spreading within defined boundaries and prevent euchromatic gene silencing. In the filamentous fungus Neurospora crassa, the JmjC domain protein DNA METHYLATION MODULATOR-1 (DMM-1) prevents aberrant spreading of heterochromatin, but the molecular details remain unknown. Here, we revealed that DMM-1 is highly enriched in a well-defined 5-kb heterochromatin domain upstream of the cat-3 gene, hereby called 5H-cat-3 domain, to constrain aberrant heterochromatin spreading. Interestingly, aberrant spreading of the 5H-cat-3 domain observed in the dmm-1KO strain is accompanied by robust deposition of histone variant H2A.Z, and deletion of H2A.Z abolishes aberrant spreading of the 5H-cat-3 domain into adjacent euchromatin. Furthermore, lysine 56 of histone H3 is deacetylated at the expanded heterochromatin regions, and mimicking H3K56 acetylation with an H3K56Q mutation effectively blocks H2A.Z-mediated aberrant spreading of the 5H-cat-3 domain. Importantly, genome-wide analyses demonstrated the general roles of H3K56 deacetylation and H2A.Z deposition in aberrant spreading of heterochromatin. Together, our results illustrate a previously unappreciated regulatory process that mediates aberrant heterochromatin spreading.
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Affiliation(s)
- Chengcheng Zhang
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yuan Tian
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shuang Song
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
| | - Lu Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
| | - Yunkun Dang
- State Key Laboratory for Conservation and Utilization of Bio-Resources and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
| | - Qun He
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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8
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Zhang P, Guergues J, Alleyne AR, Cirino TJ, Nadeau O, Figueroa AM, Stacy HM, Suzuki T, McLaughlin JP, Stevens SM, Liu B. Novel Histone Modifications in Microglia Derived from a Mouse Model of Chronic Pain. Proteomics 2022; 22:e2100137. [PMID: 35081661 DOI: 10.1002/pmic.202100137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 11/06/2022]
Abstract
As the resident immune cells in the central nervous system, microglia play an important role in the maintenance of its homeostasis. Dysregulation of microglia has been associated with the development and maintenance of chronic pain. However, the relevant molecular pathways remain poorly defined. In this study, we used a mass spectrometry-based proteomic approach to screen potential changes of histone protein modifications in microglia isolated from the brain of control and cisplatin-induced neuropathic pain adult C57BL/6J male mice. We identified several novel microglial histone modifications associated with pain including statistically significantly decreased histone H3.1 lysine 27 mono-methylation (H3.1K27me1, 54.8% of control) and lysine 56 tri-methylation (7.5% of control), as well as a trend suggesting increased histone 3 tyrosine 41 nitration. We further investigated the functional role of H3.1K27me1 and found that treatment of cultured microglial cells for 4 consecutive days with 1-10 μM of NCDM-64, a potent and selective inhibitor of lysine demethylase 7A, an enzyme responsible for the demethylation of H3K27me1, dose-dependently elevated its levels with a greater than a 2-fold increase observed at 10 μM compared to vehicle-treated control cells. Moreover, pre-treatment of mice with NCDM-64 (10 or 25 mg/kg/day, i.p.) prior to cisplatin treatment prevented the development of neuropathic pain in mice. The identification of specific chromatin marks in microglia associated with chronic pain may yield critical insight into the contribution of microglia to the development and maintenance of pain, and opens new avenues for the development of novel non-opioid therapeutics for the effective management of chronic pain. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ping Zhang
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Jennifer Guergues
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, USA
| | - Amy R Alleyne
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Thomas J Cirino
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Owen Nadeau
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT, USA
| | - Ariana M Figueroa
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Heather M Stacy
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Takayoshi Suzuki
- The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Jay P McLaughlin
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Stanley M Stevens
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, USA
| | - Bin Liu
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
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9
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Özdemir I, Steiner FA. Transmission of chromatin states across generations in C. elegans. Semin Cell Dev Biol 2021; 127:133-141. [PMID: 34823984 DOI: 10.1016/j.semcdb.2021.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/18/2022]
Abstract
Epigenetic inheritance refers to the transmission of phenotypes across generations without affecting the genomic DNA sequence. Even though it has been documented in many species in fungi, animals and plants, the mechanisms underlying epigenetic inheritance are not fully uncovered. Epialleles, the heritable units of epigenetic information, can take the form of several biomolecules, including histones and their post-translational modifications (PTMs). Here, we review the recent advances in the understanding of the transmission of histone variants and histone PTM patterns across generations in C. elegans. We provide a general overview of the intergenerational and transgenerational inheritance of histone PTMs and their modifiers and discuss the interplay among different histone PTMs. We also evaluate soma-germ line communication and its impact on the inheritance of epigenetic traits.
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Affiliation(s)
- Isa Özdemir
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Florian A Steiner
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva, Section of Biology, Faculty of Sciences, University of Geneva, 1211 Geneva, Switzerland.
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10
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Chen YC, Hsu PY, Chin CH, Hsiao CC, Liou CW, Wang TY, Lin YY, Lee CP, Lin HC, Lin MC, Su MC. H3K23/H3K36 hypoacetylation and HDAC1 up-regulation are associated with adverse consequences in obstructive sleep apnea patients. Sci Rep 2021; 11:20697. [PMID: 34667186 PMCID: PMC8526826 DOI: 10.1038/s41598-021-00052-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 09/20/2021] [Indexed: 12/23/2022] Open
Abstract
The aim of this study is to determine the roles of global histone acetylation (Ac)/methylation (me), their modifying enzymes, and gene-specific histone enrichment in obstructive sleep apnea (OSA). Global histone modifications, and their modifying enzyme expressions were assessed in peripheral blood mononuclear cells from 56 patients with OSA and 16 matched subjects with primary snoring (PS). HIF-1α gene promoter-specific H3K36Ac enrichment was assessed in another cohort (28 OSA, 8 PS). Both global histone H3K23Ac and H3K36Ac expressions were decreased in OSA patients versus PS subjects. H3K23Ac expressions were further decreased in OSA patients with prevalent hypertension. HDAC1 expressions were higher in OSA patients, especially in those with excessive daytime sleepiness, and reduced after more than 6 months of continuous positive airway pressure treatment. H3K79me3 expression was increased in those with high C-reactive protein levels. Decreased KDM6B protein expressions were noted in those with a high hypoxic load, and associated with a higher risk for incident cardiovascular events or hypertension. HIF-1α gene promoter-specific H3K36Ac enrichment was decreased in OSA patients versus PS subjects. In vitro intermittent hypoxia with re-oxygenation stimuli resulted in HDAC1 over-expression and HIF-1α gene promoter-specific H3K36Ac under-expression, while HDAC1 inhibitor, SAHA, reversed oxidative stress through inhibiting NOX1. In conclusions, H3K23/H3K36 hypoacetylation is associated with the development of hypertension and disease severity in sleep-disordered breathing patients, probably through up-regulation of HDAC1, while H3K79 hypermethylation is associated with higher risk of cardiovascular diseases, probably through down-regulation of KDM6B.
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Affiliation(s)
- Yung-Che Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan.,Sleep Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Po-Yuan Hsu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan.,Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chien-Hung Chin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan.,Sleep Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chang-Chun Hsiao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan. .,Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taouyan, 33302, Taiwan.
| | - Chia-Wei Liou
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ting-Ya Wang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan
| | - Yong-Yong Lin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan
| | - Chiu-Ping Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan
| | - Hsin-Ching Lin
- Sleep Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Department of Otolaryngology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Meng-Chih Lin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan. .,Sleep Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan. .,Department of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Mao-Chang Su
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd, Niao-Sung District, Kaohsiung City, Taiwan. .,Sleep Center, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan. .,Chang Gung University of Science and Technology, Chia-yi, Taiwan.
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11
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High-spatial and colourimetric imaging of histone modifications in single senescent cells using plasmonic nanoprobes. Nat Commun 2021; 12:5899. [PMID: 34625566 PMCID: PMC8501099 DOI: 10.1038/s41467-021-26224-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 09/21/2021] [Indexed: 02/08/2023] Open
Abstract
Histones are closely related to the state of chromatin, and epigenetic modification of their tail results in regulation in cells. Therefore, developing various analytical tools to map the changes in position and distribution of histone modifications is helpful in studying underlying mechanisms. Herein, we propose a high-spatial and colourimetric imaging method using plasmonic nanoparticles as probes to visualize heterochromatin histone markers in a single nucleus. We visualized the reorganization between repressive histone markers, H3K9me3 and H3K27me3, caused by oncogene-induced senescence based on the scattering colours and spectral shift of plasmonic nanoprobes to longer wavelengths using their distance-dependent coupling effect. The measured scattering profiles were correlated with the computation results simulating the scattering spectra according to the arrangements and distances among the plasmonic nanoprobes. The plasmonic nanoprobe-based high-spatial hyperspectral imaging provides an advanced way to study the dynamics of histone modifications for predicting the progression of diseases or senescence.
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12
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Caron P, Pobega E, Polo SE. DNA Double-Strand Break Repair: All Roads Lead to HeterochROMAtin Marks. Front Genet 2021; 12:730696. [PMID: 34539757 PMCID: PMC8440905 DOI: 10.3389/fgene.2021.730696] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/06/2021] [Indexed: 12/21/2022] Open
Abstract
In response to DNA double-strand breaks (DSBs), chromatin modifications orchestrate DNA repair pathways thus safeguarding genome integrity. Recent studies have uncovered a key role for heterochromatin marks and associated factors in shaping DSB repair within the nucleus. In this review, we present our current knowledge of the interplay between heterochromatin marks and DSB repair. We discuss the impact of heterochromatin features, either pre-existing in heterochromatin domains or de novo established in euchromatin, on DSB repair pathway choice. We emphasize how heterochromatin decompaction and mobility further support DSB repair, focusing on recent mechanistic insights into these processes. Finally, we speculate about potential molecular players involved in the maintenance or the erasure of heterochromatin marks following DSB repair, and their implications for restoring epigenome function and integrity.
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Affiliation(s)
- Pierre Caron
- Epigenetics and Cell Fate Centre, CNRS, University of Paris, Paris, France
| | - Enrico Pobega
- Epigenetics and Cell Fate Centre, CNRS, University of Paris, Paris, France
| | - Sophie E Polo
- Epigenetics and Cell Fate Centre, CNRS, University of Paris, Paris, France
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13
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Mechanistic insights into KDM4A driven genomic instability. Biochem Soc Trans 2021; 49:93-105. [PMID: 33492339 PMCID: PMC7925003 DOI: 10.1042/bst20191219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 12/19/2022]
Abstract
Alterations in global epigenetic signatures on chromatin are well established to contribute to tumor initiation and progression. Chromatin methylation status modulates several key cellular processes that maintain the integrity of the genome. KDM4A, a demethylase that belongs to the Fe-II dependent dioxygenase family that uses α-ketoglutarate and molecular oxygen as cofactors, is overexpressed in several cancers and is associated with an overall poor prognosis. KDM4A demethylates lysine 9 (H3K9me2/3) and lysine 36 (H3K36me3) methyl marks on histone H3. Given the complexity that exists with these marks on chromatin and their effects on transcription and proliferation, it naturally follows that demethylation serves an equally important role in these cellular processes. In this review, we highlight the role of KDM4A in transcriptional modulation, either dependent or independent of its enzymatic activity, arising from the amplification of this demethylase in cancer. KDM4A modulates re-replication of distinct genomic loci, activates cell cycle inducers, and represses proteins involved in checkpoint control giving rise to proliferative damage, mitotic disturbances and chromosomal breaks, ultimately resulting in genomic instability. In parallel, emerging evidence of non-nuclear substrates of epigenetic modulators emphasize the need to investigate the role of KDM4A in regulating non-nuclear substrates and evaluate their contribution to genomic instability in this context. The existence of promising KDM-specific inhibitors makes these demethylases an attractive target for therapeutic intervention in cancers.
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14
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Shadle SC, Bennett SR, Wong CJ, Karreman NA, Campbell AE, van der Maarel SM, Bass BL, Tapscott SJ. DUX4-induced bidirectional HSATII satellite repeat transcripts form intranuclear double-stranded RNA foci in human cell models of FSHD. Hum Mol Genet 2020; 28:3997-4011. [PMID: 31630170 DOI: 10.1093/hmg/ddz242] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/19/2019] [Accepted: 10/03/2019] [Indexed: 12/29/2022] Open
Abstract
The DUX4 transcription factor is normally expressed in the cleavage-stage embryo and regulates genes involved in embryonic genome activation. Misexpression of DUX4 in skeletal muscle, however, is toxic and causes facioscapulohumeral muscular dystrophy (FSHD). We recently showed DUX4-induced toxicity is due, in part, to the activation of the double-stranded RNA (dsRNA) response pathway and the accumulation of intranuclear dsRNA foci. Here, we determined the composition of DUX4-induced dsRNAs. We found that a subset of DUX4-induced dsRNAs originate from inverted Alu repeats embedded within the introns of DUX4-induced transcripts and from DUX4-induced dsRNA-forming intergenic transcripts enriched for endogenous retroviruses, Alu and LINE-1 elements. However, these repeat classes were also represented in dsRNAs from cells not expressing DUX4. In contrast, pericentric human satellite II (HSATII) repeats formed a class of dsRNA specific to the DUX4 expressing cells. Further investigation revealed that DUX4 can initiate the bidirectional transcription of normally heterochromatin-silenced HSATII repeats. DUX4-induced HSATII RNAs co-localized with DUX4-induced nuclear dsRNA foci and with intranuclear aggregation of EIF4A3 and ADAR1. Finally, gapmer-mediated knockdown of HSATII transcripts depleted DUX4-induced intranuclear ribonucleoprotein aggregates and decreased DUX4-induced cell death, suggesting that HSATII-formed dsRNAs contribute to DUX4 toxicity.
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Affiliation(s)
- Sean C Shadle
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA 91805, USA
| | - Sean R Bennett
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Chao-Jen Wong
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nancy A Karreman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Amy E Campbell
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Brenda L Bass
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Stephen J Tapscott
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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15
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Armache A, Yang S, Martínez de Paz A, Robbins LE, Durmaz C, Cheong JQ, Ravishankar A, Daman AW, Ahimovic DJ, Klevorn T, Yue Y, Arslan T, Lin S, Panchenko T, Hrit J, Wang M, Thudium S, Garcia BA, Korb E, Armache KJ, Rothbart SB, Hake SB, Allis CD, Li H, Josefowicz SZ. Histone H3.3 phosphorylation amplifies stimulation-induced transcription. Nature 2020; 583:852-857. [PMID: 32699416 PMCID: PMC7517595 DOI: 10.1038/s41586-020-2533-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/05/2020] [Indexed: 01/07/2023]
Abstract
Complex organisms can rapidly induce select genes in response to diverse environmental cues. This regulation occurs in the context of large genomes condensed by histone proteins into chromatin. The sensing of pathogens by macrophages engages conserved signalling pathways and transcription factors to coordinate the induction of inflammatory genes1-3. Enriched integration of histone H3.3, the ancestral histone H3 variant, is a general feature of dynamically regulated chromatin and transcription4-7. However, how chromatin is regulated at induced genes, and what features of H3.3 might enable rapid and high-level transcription, are unknown. The amino terminus of H3.3 contains a unique serine residue (Ser31) that is absent in 'canonical' H3.1 and H3.2. Here we show that this residue, H3.3S31, is phosphorylated (H3.3S31ph) in a stimulation-dependent manner along rapidly induced genes in mouse macrophages. This selective mark of stimulation-responsive genes directly engages the histone methyltransferase SETD2, a component of the active transcription machinery, and 'ejects' the elongation corepressor ZMYND118,9. We propose that features of H3.3 at stimulation-induced genes, including H3.3S31ph, provide preferential access to the transcription apparatus. Our results indicate dedicated mechanisms that enable rapid transcription involving the histone variant H3.3, its phosphorylation, and both the recruitment and the ejection of chromatin regulators.
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Affiliation(s)
- Anja Armache
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Shuang Yang
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Alexia Martínez de Paz
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lexi E Robbins
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ceyda Durmaz
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jin Q Cheong
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Arjun Ravishankar
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrew W Daman
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dughan J Ahimovic
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thaís Klevorn
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Yuan Yue
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Tanja Arslan
- Adolf-Butenandt Institute, Ludwig-Maximilians University, Munich, Germany
| | - Shu Lin
- Epigenetics Institute, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Tanya Panchenko
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Joel Hrit
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Miao Wang
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Samuel Thudium
- Department of Genetics, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Adolf-Butenandt Institute, Ludwig-Maximilians University, Munich, Germany
| | - Erica Korb
- Department of Genetics, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Karim-Jean Armache
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Sandra B Hake
- Adolf-Butenandt Institute, Ludwig-Maximilians University, Munich, Germany
- Institute for Genetics, Justus-Liebig-University, Giessen, Germany
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
| | - Steven Z Josefowicz
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
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16
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Guthmann M, Burton A, Torres‐Padilla M. Expression and phase separation potential of heterochromatin proteins during early mouse development. EMBO Rep 2019; 20:e47952. [PMID: 31701657 PMCID: PMC6893284 DOI: 10.15252/embr.201947952] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 10/03/2019] [Accepted: 10/16/2019] [Indexed: 12/29/2022] Open
Abstract
In most eukaryotes, constitutive heterochromatin is associated with H3K9me3 and HP1α. The latter has been shown to play a role in heterochromatin formation through liquid-liquid phase separation. However, many other proteins are known to regulate and/or interact with constitutive heterochromatic regions in several species. We postulate that some of these heterochromatic proteins may play a role in the regulation of heterochromatin formation by liquid-liquid phase separation. Indeed, an analysis of the constitutive heterochromatin proteome shows that proteins associated with constitutive heterochromatin are significantly more disordered than a random set or a full nucleome set of proteins. Interestingly, their expression begins low and increases during preimplantation development. These observations suggest that the preimplantation embryo is a useful model to address the potential role for phase separation in heterochromatin formation, anticipating exciting research in the years to come.
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Affiliation(s)
- Manuel Guthmann
- Institute of Epigenetics and Stem Cells (IES)Helmholtz Zentrum MünchenMünchenGermany
- Faculty of BiologyLudwig‐Maximilians UniversitätMünchenGermany
| | - Adam Burton
- Institute of Epigenetics and Stem Cells (IES)Helmholtz Zentrum MünchenMünchenGermany
- Faculty of BiologyLudwig‐Maximilians UniversitätMünchenGermany
| | - Maria‐Elena Torres‐Padilla
- Institute of Epigenetics and Stem Cells (IES)Helmholtz Zentrum MünchenMünchenGermany
- Faculty of BiologyLudwig‐Maximilians UniversitätMünchenGermany
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17
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Vacík T, Lađinović D, Raška I. KDM2A/B lysine demethylases and their alternative isoforms in development and disease. Nucleus 2019; 9:431-441. [PMID: 30059280 PMCID: PMC7000146 DOI: 10.1080/19491034.2018.1498707] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Aberrant levels of histone modifications lead to chromatin malfunctioning and consequently to various developmental defects and human diseases. Therefore, the proteins bearing the ability to modify histones have been extensively studied and the molecular mechanisms of their action are now fairly well understood. However, little attention has been paid to naturally occurring alternative isoforms of chromatin modifying proteins and to their biological roles. In this review, we focus on mammalian KDM2A and KDM2B, the only two lysine demethylases whose genes have been described to produce also an alternative isoform lacking the N-terminal demethylase domain. These short KDM2A/B-SF isoforms arise through alternative promoter usage and seem to play important roles in development and disease. We hypothesise about the biological significance of these alternative isoforms, which might represent a more common evolutionarily conserved regulatory mechanism.
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Affiliation(s)
- Tomáš Vacík
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University and General University Hospital in Prague , Praha 2 , Czech Republic
| | - Dijana Lađinović
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University and General University Hospital in Prague , Praha 2 , Czech Republic
| | - Ivan Raška
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University and General University Hospital in Prague , Praha 2 , Czech Republic
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18
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Duchatel RJ, Jackson ER, Alvaro F, Nixon B, Hondermarck H, Dun MD. Signal Transduction in Diffuse Intrinsic Pontine Glioma. Proteomics 2019; 19:e1800479. [DOI: 10.1002/pmic.201800479] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 05/03/2019] [Indexed: 11/12/2022]
Affiliation(s)
- Ryan J. Duchatel
- Cancer Signalling Research Group School of Biomedical Sciences and Pharmacy Faculty of Health and Medicine University of Newcastle Callaghan NSW 2308 Australia
- Priority Research Centre for Cancer Research Innovation and Translation Hunter Medical Research Institute Lambton NSW 2305 Australia
| | - Evangeline R. Jackson
- Cancer Signalling Research Group School of Biomedical Sciences and Pharmacy Faculty of Health and Medicine University of Newcastle Callaghan NSW 2308 Australia
- Priority Research Centre for Cancer Research Innovation and Translation Hunter Medical Research Institute Lambton NSW 2305 Australia
| | - Frank Alvaro
- Priority Research Centre for Cancer Research Innovation and Translation Hunter Medical Research Institute Lambton NSW 2305 Australia
- John Hunter Children's Hospital Faculty of Health and Medicine University of Newcastle New Lambton Heights NSW 2305 Australia
| | - Brett Nixon
- Priority Research Centre for Reproductive Science School of Environmental and Life Sciences University of Newcastle Callaghan NSW 2308 Australia
| | - Hubert Hondermarck
- Priority Research Centre for Cancer Research Innovation and Translation Hunter Medical Research Institute Lambton NSW 2305 Australia
- Cancer Neurobiology Group School of Biomedical Sciences and Pharmacy Faculty of Health and Medicine University of Newcastle Callaghan NSW 2308 Australia
| | - Matthew D. Dun
- Cancer Signalling Research Group School of Biomedical Sciences and Pharmacy Faculty of Health and Medicine University of Newcastle Callaghan NSW 2308 Australia
- Priority Research Centre for Cancer Research Innovation and Translation Hunter Medical Research Institute Lambton NSW 2305 Australia
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19
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Abstract
DNA double-strand breaks (DSBs) are particularly challenging to repair in pericentromeric heterochromatin because of the increased risk of aberrant recombination in highly repetitive sequences. Recent studies have identified specialized mechanisms enabling 'safe' homologous recombination (HR) repair in heterochromatin. These include striking nuclear actin filaments (F-actin) and myosins that drive the directed motion of repair sites to the nuclear periphery for 'safe' repair. Here, we summarize our current understanding of the mechanisms involved, and propose how they might operate in the context of a phase-separated environment.
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20
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Nicetto D, Zaret KS. Role of H3K9me3 heterochromatin in cell identity establishment and maintenance. Curr Opin Genet Dev 2019; 55:1-10. [PMID: 31103921 DOI: 10.1016/j.gde.2019.04.013] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 03/18/2019] [Accepted: 04/15/2019] [Indexed: 01/17/2023]
Abstract
Compacted, transcriptionally repressed chromatin, referred to as heterochromatin, represents a major fraction of the higher eukaryotic genome and exerts pivotal functions of silencing repetitive elements, maintenance of genome stability, and control of gene expression. Among the different histone post-translational modifications (PTMs) associated with heterochromatin, tri-methylation of lysine 9 on histone H3 (H3K9me3) is gaining increased attention. Besides its known role in repressing repetitive elements and non-coding portions of the genome, recent observations indicate H3K9me3 as an important player in silencing lineage-inappropriate genes. The ability of H3K9me3 to influence cell identity challenges the original concept of H3K9me3-marked heterochromatin as mainly a constitutive type of chromatin and provides a further level of understanding of how to modulate cell fate control. Here, we summarize the role of H3K9me3 marked heterochromatin and its dynamics in establishing and maintaining cellular identity.
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Affiliation(s)
- Dario Nicetto
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Dept. Cell and Developmental, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA; Dept. Cell and Developmental, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
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21
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Molina-Serrano D, Kyriakou D, Kirmizis A. Histone Modifications as an Intersection Between Diet and Longevity. Front Genet 2019; 10:192. [PMID: 30915107 PMCID: PMC6422915 DOI: 10.3389/fgene.2019.00192] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/22/2019] [Indexed: 12/12/2022] Open
Abstract
Histone modifications are key epigenetic regulators that control chromatin structure and gene transcription, thereby impacting on various important cellular phenotypes. Over the past decade, a growing number of studies have indicated that changes in various histone modifications have a significant influence on the aging process. Furthermore, it has been revealed that the abundance and localization of histone modifications are responsive to various environmental stimuli, such as diet, which can also affect gene expression and lifespan. This supports the notion that histone modifications can serve as a main cellular platform for signal integration. Hence, in this review we focus on the role of histone modifications during aging, report the data indicating that diet affects histone modification levels and explore the idea that histone modifications may function as an intersection through which diet regulates lifespan. A greater understanding of the epigenetic mechanisms that link environmental signals to longevity may provide new strategies for therapeutic intervention in age-related diseases and for promoting healthy aging.
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Affiliation(s)
- Diego Molina-Serrano
- UMR 6290, Centre National de la Recherche Scientifique, Rennes, France.,Institute of Genetics and Development of Rennes (IGDR), Université de Rennes 1, Rennes, France
| | - Dimitris Kyriakou
- Efevre Tech Ltd., Larnaca, Cyprus.,Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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22
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Janssen A, Colmenares SU, Lee T, Karpen GH. Timely double-strand break repair and pathway choice in pericentromeric heterochromatin depend on the histone demethylase dKDM4A. Genes Dev 2018; 33:103-115. [PMID: 30578303 PMCID: PMC6317320 DOI: 10.1101/gad.317537.118] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/29/2018] [Indexed: 12/22/2022]
Abstract
Repair of DNA double-strand breaks (DSBs) must be orchestrated properly within diverse chromatin domains in order to maintain genetic stability. Euchromatin and heterochromatin domains display major differences in histone modifications, biophysical properties, and spatiotemporal dynamics of DSB repair. However, it is unclear whether differential histone-modifying activities are required for DSB repair in these distinct domains. We showed previously that the Drosophila melanogaster KDM4A (dKDM4A) histone demethylase is required for heterochromatic DSB mobility. Here we used locus-specific DSB induction in Drosophila animal tissues and cultured cells to more deeply interrogate the impact of dKDM4A on chromatin changes, temporal progression, and pathway utilization during DSB repair. We found that dKDM4A promotes the demethylation of heterochromatin-associated histone marks at DSBs in heterochromatin but not euchromatin. Most importantly, we demonstrate that dKDM4A is required to complete DSB repair in a timely manner and regulate the relative utilization of homologous recombination (HR) and nonhomologous end-joining (NHEJ) repair pathways but exclusively for heterochromatic DSBs. We conclude that the temporal kinetics and pathway utilization during heterochromatic DSB repair depend on dKDM4A-dependent demethylation of heterochromatic histone marks. Thus, distinct pre-existing chromatin states require specialized epigenetic alterations to ensure proper DSB repair.
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Affiliation(s)
- Aniek Janssen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA.,Innovative Genomics Institute, Berkeley, California 94720, USA
| | - Serafin U Colmenares
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA.,Innovative Genomics Institute, Berkeley, California 94720, USA
| | - Timothy Lee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Gary H Karpen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA.,Innovative Genomics Institute, Berkeley, California 94720, USA
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23
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Abstract
Constitutive heterochromatin is a major component of the eukaryotic nucleus and is essential for the maintenance of genome stability. Highly concentrated at pericentromeric and telomeric domains, heterochromatin is riddled with repetitive sequences and has evolved specific ways to compartmentalize, silence, and repair repeats. The delicate balance between heterochromatin epigenetic maintenance and cellular processes such as mitosis and DNA repair and replication reveals a highly dynamic and plastic chromatin domain that can be perturbed by multiple mechanisms, with far-reaching consequences for genome integrity. Indeed, heterochromatin dysfunction provokes genetic turmoil by inducing aberrant repeat repair, chromosome segregation errors, transposon activation, and replication stress and is strongly implicated in aging and tumorigenesis. Here, we summarize the general principles of heterochromatin structure and function, discuss the importance of its maintenance for genome integrity, and propose that more comprehensive analyses of heterochromatin roles in tumorigenesis will be integral to future innovations in cancer treatment.
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Affiliation(s)
- Aniek Janssen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Serafin U. Colmenares
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Gary H. Karpen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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24
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Chromatin dynamics at the core of kidney fibrosis. Matrix Biol 2018; 68-69:194-229. [DOI: 10.1016/j.matbio.2018.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 02/16/2018] [Accepted: 02/17/2018] [Indexed: 02/06/2023]
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25
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Levin M, Stark M, Assaraf YG. The JmjN domain as a dimerization interface and a targeted inhibitor of KDM4 demethylase activity. Oncotarget 2018; 9:16861-16882. [PMID: 29682190 PMCID: PMC5908291 DOI: 10.18632/oncotarget.24717] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 02/25/2018] [Indexed: 12/14/2022] Open
Abstract
Histone methylation is regulated to shape the epigenome by modulating DNA compaction, thus playing central roles in fundamental chromatin-based processes including transcriptional regulation, DNA repair and cell proliferation. Histone methylation is erased by demethylases including the well-established KDM4 subfamily members, however, little is known about their dimerization capacity and its impact on their demethylase activity. Using the powerful bimolecular fluorescence complementation technique, we herein show the in situ formation of human KDM4A and KDM4C homodimers and heterodimers in nuclei of live transfectant cells and evaluate their H3K9me3 demethylation activity. Using size exclusion HPLC as well as Western blot analysis, we show that endogenous KDM4C undergoes dimerization under physiological conditions. Importantly, we identify the JmjN domain as the KDM4C dimerization interface and pin-point specific charged residues therein to be essential for this dimerization. We further demonstrate that KDM4A/C dimerization is absolutely required for their demethylase activity which was abolished by the expression of free JmjN peptides. In contrast, KDM4B does not dimerize and functions as a monomer, and hence was not affected by free JmjN expression. KDM4 proteins are overexpressed in numerous malignancies and their pharmacological inhibition or depletion in cancer cells was shown to impair tumor cell proliferation, invasion and metastasis. Thus, the KDM4 dimer-interactome emerging from the present study bears potential implications for cancer therapeutics via selective inhibition of KDM4A/C demethylase activity using JmjN-based peptidomimetics.
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Affiliation(s)
- May Levin
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Michal Stark
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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26
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Drosophila Histone Demethylase KDM4A Has Enzymatic and Non-enzymatic Roles in Controlling Heterochromatin Integrity. Dev Cell 2017; 42:156-169.e5. [PMID: 28743002 DOI: 10.1016/j.devcel.2017.06.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 03/21/2017] [Accepted: 06/16/2017] [Indexed: 11/23/2022]
Abstract
Eukaryotic genomes are broadly divided between gene-rich euchromatin and the highly repetitive heterochromatin domain, which is enriched for proteins critical for genome stability and transcriptional silencing. This study shows that Drosophila KDM4A (dKDM4A), previously characterized as a euchromatic histone H3 K36 demethylase and transcriptional regulator, predominantly localizes to heterochromatin and regulates heterochromatin position-effect variegation (PEV), organization of repetitive DNAs, and DNA repair. We demonstrate that dKDM4A demethylase activity is dispensable for PEV. In contrast, dKDM4A enzymatic activity is required to relocate heterochromatic double-strand breaks outside the domain, as well as for organismal survival when DNA repair is compromised. Finally, DNA damage triggers dKDM4A-dependent changes in the levels of H3K56me3, suggesting that dKDM4A demethylates this heterochromatic mark to facilitate repair. We conclude that dKDM4A, in addition to its previously characterized role in euchromatin, utilizes both enzymatic and structural mechanisms to regulate heterochromatin organization and functions.
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27
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Quantitative chromatin proteomics reveals a dynamic histone post-translational modification landscape that defines asexual and sexual Plasmodium falciparum parasites. Sci Rep 2017; 7:607. [PMID: 28377601 PMCID: PMC5428830 DOI: 10.1038/s41598-017-00687-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 03/08/2017] [Indexed: 01/24/2023] Open
Abstract
Gene expression in Plasmodia integrates post-transcriptional regulation with epigenetic marking of active genomic regions through histone post-translational modifications (PTMs). To generate insights into the importance of histone PTMs to the entire asexual and sexual developmental cycles of the parasite, we used complementary and comparative quantitative chromatin proteomics to identify and functionally characterise histone PTMs in 8 distinct life cycle stages of P. falciparum parasites. ~500 individual histone PTMs were identified of which 106 could be stringently validated. 46 individual histone PTMs and 30 co-existing PTMs were fully quantified with high confidence. Importantly, 15 of these histone PTMs are novel for Plasmodia (e.g. H3K122ac, H3K27me3, H3K56me3). The comparative nature of the data revealed a highly dynamic histone PTM landscape during life cycle development, with a set of histone PTMs (H3K4ac, H3K9me1 and H3K36me2) displaying a unique and conserved abundance profile exclusively during gametocytogenesis (P < 0.001). Euchromatic histone PTMs are abundant during schizogony and late gametocytes; heterochromatic PTMs mark early gametocytes. Collectively, this data provides the most accurate, complete and comparative chromatin proteomic analyses of the entire life cycle development of malaria parasites. A substantial association between histone PTMs and stage-specific transition provides insights into the intricacies characterising Plasmodial developmental biology.
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Abstract
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Post-translational
modifications of histones by protein methyltransferases
(PMTs) and histone demethylases (KDMs) play an important role in the
regulation of gene expression and transcription and are implicated
in cancer and many other diseases. Many of these enzymes also target
various nonhistone proteins impacting numerous crucial biological
pathways. Given their key biological functions and implications in
human diseases, there has been a growing interest in assessing these
enzymes as potential therapeutic targets. Consequently, discovering
and developing inhibitors of these enzymes has become a very active
and fast-growing research area over the past decade. In this review,
we cover the discovery, characterization, and biological application
of inhibitors of PMTs and KDMs with emphasis on key advancements in
the field. We also discuss challenges, opportunities, and future directions
in this emerging, exciting research field.
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Affiliation(s)
- H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Michael L Martini
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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Snyder MJ, Lau AC, Brouhard EA, Davis MB, Jiang J, Sifuentes MH, Csankovszki G. Anchoring of Heterochromatin to the Nuclear Lamina Reinforces Dosage Compensation-Mediated Gene Repression. PLoS Genet 2016; 12:e1006341. [PMID: 27690361 PMCID: PMC5045178 DOI: 10.1371/journal.pgen.1006341] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 09/06/2016] [Indexed: 12/21/2022] Open
Abstract
Higher order chromosome structure and nuclear architecture can have profound effects on gene regulation. We analyzed how compartmentalizing the genome by tethering heterochromatic regions to the nuclear lamina affects dosage compensation in the nematode C. elegans. In this organism, the dosage compensation complex (DCC) binds both X chromosomes of hermaphrodites to repress transcription two-fold, thus balancing gene expression between XX hermaphrodites and XO males. X chromosome structure is disrupted by mutations in DCC subunits. Using X chromosome paint fluorescence microscopy, we found that X chromosome structure and subnuclear localization are also disrupted when the mechanisms that anchor heterochromatin to the nuclear lamina are defective. Strikingly, the heterochromatic left end of the X chromosome is less affected than the gene-rich middle region, which lacks heterochromatic anchors. These changes in X chromosome structure and subnuclear localization are accompanied by small, but significant levels of derepression of X-linked genes as measured by RNA-seq, without any observable defects in DCC localization and DCC-mediated changes in histone modifications. We propose a model in which heterochromatic tethers on the left arm of the X cooperate with the DCC to compact and peripherally relocate the X chromosomes, contributing to gene repression.
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Affiliation(s)
- Martha J. Snyder
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alyssa C. Lau
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Elizabeth A. Brouhard
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Michael B. Davis
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jianhao Jiang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Margarita H. Sifuentes
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Györgyi Csankovszki
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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30
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Stejskal S, Stepka K, Tesarova L, Stejskal K, Matejkova M, Simara P, Zdrahal Z, Koutna I. Cell cycle-dependent changes in H3K56ac in human cells. Cell Cycle 2016; 14:3851-63. [PMID: 26645646 DOI: 10.1080/15384101.2015.1106760] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The incorporation of histone H3 with an acetylated lysine 56 (H3K56ac) into the nucleosome is important for chromatin remodeling and serves as a marker of new nucleosomes during DNA replication and repair in yeast. However, in human cells, the level of H3K56ac is greatly reduced, and its role during the cell cycle is controversial. Our aim was to determine the potential of H3K56ac to regulate cell cycle progression in different human cell lines. A significant increase in the number of H3K56ac foci, but not in H3K56ac protein levels, was observed during the S and G2 phases in cancer cell lines, but was not observed in embryonic stem cell lines. Despite this increase, the H3K56ac signal was not present in late replication chromatin, and H3K56ac protein levels did not decrease after the inhibition of DNA replication. H3K56ac was not tightly associated with the chromatin and was primarily localized to active chromatin regions. Our results support the role of H3K56ac in transcriptionally active chromatin areas but do not confirm H3K56ac as a marker of newly synthetized nucleosomes in DNA replication.
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Affiliation(s)
- Stanislav Stejskal
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
| | - Karel Stepka
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
| | - Lenka Tesarova
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
| | - Karel Stejskal
- b Research Group - Proteomics; Central European Institute of Technology; Masaryk University ; Brno , Czech Republic.,c National Centre for Biomolecular Research; Faculty of Science; Masaryk University ; Brno , Czech Republic
| | - Martina Matejkova
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
| | - Pavel Simara
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
| | - Zbynek Zdrahal
- b Research Group - Proteomics; Central European Institute of Technology; Masaryk University ; Brno , Czech Republic.,c National Centre for Biomolecular Research; Faculty of Science; Masaryk University ; Brno , Czech Republic
| | - Irena Koutna
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
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31
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Kang MK, Mehrazarin S, Park NH, Wang CY. Epigenetic gene regulation by histone demethylases: emerging role in oncogenesis and inflammation. Oral Dis 2016; 23:709-720. [PMID: 27514027 DOI: 10.1111/odi.12569] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 08/05/2016] [Accepted: 08/09/2016] [Indexed: 12/11/2022]
Abstract
Histone N-terminal tails of nucleosomes are the sites of complex regulation of gene expression through post-translational modifications. Among these modifications, histone methylation had long been associated with permanent gene inactivation until the discovery of Lys-specific demethylase (LSD1), which is responsible for dynamic gene regulation. There are more than 30 members of the Lys demethylase (KDM) family, and with exception of LSD1 and LSD2, all other KDMs possess the Jumonji C (JmjC) domain exhibiting demethylase activity and require unique cofactors, for example, Fe(II) and α-ketoglutarate. These cofactors have been targeted when devising KDM inhibitors, which may yield therapeutic benefit. KDMs and their counterpart Lys methyltransferases (KMTs) regulate multiple biological processes, including oncogenesis and inflammation. KDMs' functional interactions with retinoblastoma (Rb) and E2 factor (E2F) target promoters illustrate their regulatory role in cell cycle progression and oncogenesis. Recent findings also demonstrate the control of inflammation and immune functions by KDMs, such as KDM6B that regulates the pro-inflammatory gene expression and CD4+ T helper (Th) cell lineage determination. This review will highlight the mechanisms by which KDMs and KMTs regulate the target gene expression and how epigenetic mechanisms may be applied to our understanding of oral inflammation.
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Affiliation(s)
- M K Kang
- Shapiro Laboratory of Viral Oncology and Aging Research, Los Angeles, CA, USA
| | - S Mehrazarin
- Shapiro Laboratory of Viral Oncology and Aging Research, Los Angeles, CA, USA
| | - N-H Park
- Shapiro Laboratory of Viral Oncology and Aging Research, Los Angeles, CA, USA.,David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - C-Y Wang
- Laboratory of Molecular Signaling, UCLA School of Dentistry, Los Angeles, CA, USA
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32
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Gibeault RL, Conn KL, Bildersheim MD, Schang LM. An Essential Viral Transcription Activator Modulates Chromatin Dynamics. PLoS Pathog 2016; 12:e1005842. [PMID: 27575707 PMCID: PMC5004865 DOI: 10.1371/journal.ppat.1005842] [Citation(s) in RCA: 16] [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: 05/20/2016] [Accepted: 08/03/2016] [Indexed: 12/02/2022] Open
Abstract
Although ICP4 is the only essential transcription activator of herpes simplex virus 1 (HSV-1), its mechanisms of action are still only partially understood. We and others propose a model in which HSV-1 genomes are chromatinized as a cellular defense to inhibit HSV-1 transcription. To counteract silencing, HSV-1 would have evolved proteins that prevent or destabilize chromatinization to activate transcription. These proteins should act as HSV-1 transcription activators. We have shown that HSV-1 genomes are organized in highly dynamic nucleosomes and that histone dynamics increase in cells infected with wild type HSV-1. We now show that whereas HSV-1 mutants encoding no functional ICP0 or VP16 partially enhanced histone dynamics, mutants encoding no functional ICP4 did so only minimally. Transient expression of ICP4 was sufficient to enhance histone dynamics in the absence of other HSV-1 proteins or HSV-1 DNA. The dynamics of H3.1 were increased in cells expressing ICP4 to a greater extent than those of H3.3. The dynamics of H2B were increased in cells expressing ICP4, whereas those of canonical H2A were not. ICP4 preferentially targets silencing H3.1 and may also target the silencing H2A variants. In infected cells, histone dynamics were increased in the viral replication compartments, where ICP4 localizes. These results suggest a mechanism whereby ICP4 activates transcription by disrupting, or preventing the formation of, stable silencing nucleosomes on HSV-1 genomes. The nuclear-replicating DNA viruses of the family herpesviridae cause a variety of diseases. Eight herpesviruses infect humans. Three of them, including herpes simplex virus 1 (HSV-1), belong to the alpha-herpesvirus sub-family. Viruses in this family have the fastest replication cycles of all herpesviruses, producing acute symptoms. During lytic infection, the genomes of HSV-1 associate with histones in more dynamic chromatin than those of the beta- and gamma- herpesviruses. The transcription activator ICP4 is conserved only among alpha-herpesviruses. Although ICP4 is essential, relatively little is known about its mechanisms of action. We have shown that histone dynamics are enhanced in HSV-1 lytically infected cells. Here we show that HSV-1 mutants in ICP4 are deficient in their ability to enhance histone dynamics. ICP4 was sufficient to enhance histone dynamics in the absence of other HSV-1 proteins or DNA. The dynamics of histones were greater in the viral replication compartments, where ICP4 localizes, than in the cellular chromatin. ICP4 may thus mobilize histones away from HSV-1 genomes to activate transcription. Such a mechanism of transcription activation would result in the highly dynamic nature of the viral chromatin and the fast replication cycles, and the acute pathologies, of the alpha-herpesviruses.
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Affiliation(s)
- Rebecca L. Gibeault
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Kristen L. Conn
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Luis M. Schang
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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33
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The Commercial Antibodies Widely Used to Measure H3 K56 Acetylation Are Non-Specific in Human and Drosophila Cells. PLoS One 2016; 11:e0155409. [PMID: 27187594 PMCID: PMC4871326 DOI: 10.1371/journal.pone.0155409] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/28/2016] [Indexed: 12/26/2022] Open
Abstract
Much of our understanding of the function of histone post-translational modifications in metazoans is inferred from their genomic localization and / or extrapolated from yeast studies. For example, acetylation of histone H3 lysine 56 (H3 K56Ac) is assumed to be important for transcriptional regulation in metazoan cells based on its occurrence at promoters and its function in yeast. Here we directly assess the function of H3 K56Ac during chromatin disassembly from gene regulatory regions during transcriptional induction in human cells by using mutations that either mimic or prevent H3 K56Ac. Although there is rapid histone H3 disassembly during induction of some estrogen receptor responsive genes, depletion of the histone chaperone ASF1A/B, which is required for H3 K56 acetylation, has no effect on chromatin disassembly at these regions. During the course of this work, we found that all the commercially available antibodies to H3 K56Ac are non-specific in human cells and in Drosophila. We used H3-YFP fusions to show that the H3 K56Q mutation can promote chromatin disassembly from regulatory regions of some estrogen responsive genes in the context of transcriptional induction. However, neither the H3 K56R nor K56Q mutation significantly altered chromatin disassembly dynamics by FRAP analysis. These results indicate that unlike the situation in yeast, human cells do not use H3 K56Ac to promote chromatin disassembly from regulatory regions or from the genome in general. Furthermore, our work highlights the need for rigorous characterization of the specificity of antibodies to histone post-translational modifications in vivo.
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34
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Graves HK, Wang P, Lagarde M, Chen Z, Tyler JK. Mutations that prevent or mimic persistent post-translational modifications of the histone H3 globular domain cause lethality and growth defects in Drosophila. Epigenetics Chromatin 2016; 9:9. [PMID: 26933451 PMCID: PMC4772521 DOI: 10.1186/s13072-016-0059-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/19/2016] [Indexed: 01/24/2023] Open
Abstract
Background
Understanding the function of histone post-translational modifications is the key to deciphering how genomic activities are regulated. Among the least well-understood histone modifications in vivo are those that occur on the surface of the globular domain of histones, despite their causing the most profound structural alterations of the nucleosome in vitro. We utilized a Drosophila system to replace the canonical histone genes with mutated histone transgenes. Results Mutations predicted to mimic or prevent acetylation on histone H3 lysine (K) 56, K115, K122, and both K115/K122, or to prevent or mimic phosphorylation on H3 threonine (T) 118 and T80, all caused lethality, with the exception of K122R mutants. T118 mutations caused profound growth defects within wing discs, while K115R, K115Q, K56Q, and the K115/K122 mutations caused more subtle growth defects. The H3 K56R and H3 K122R mutations caused no defects in growth, differentiation, or transcription within imaginal discs, indicating that H3 K56 acetylation and K122 acetylation are dispensable for these functions. In agreement, we found the antibody to H3 K122Ac, which was previously used to imply a role for H3 K122Ac in transcription in metazoans, to be non-specific in vivo. Conclusions Our data suggest that chromatin structural perturbations caused by acetylation of K56, K115, or K122 and phosphorylation of T80 or T118 are important for key developmental processes. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0059-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hillary K Graves
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Pingping Wang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA ; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065 USA
| | - Matthew Lagarde
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Zhihong Chen
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Jessica K Tyler
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA ; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY 10065 USA
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35
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Lawrence M, Daujat S, Schneider R. Lateral Thinking: How Histone Modifications Regulate Gene Expression. Trends Genet 2015; 32:42-56. [PMID: 26704082 DOI: 10.1016/j.tig.2015.10.007] [Citation(s) in RCA: 496] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 12/21/2022]
Abstract
The DNA of each cell is wrapped around histone octamers, forming so-called 'nucleosomal core particles'. These histone proteins have tails that project from the nucleosome and many residues in these tails can be post-translationally modified, influencing all DNA-based processes, including chromatin compaction, nucleosome dynamics, and transcription. In contrast to those present in histone tails, modifications in the core regions of the histones had remained largely uncharacterised until recently, when some of these modifications began to be analysed in detail. Overall, recent work has shown that histone core modifications can not only directly regulate transcription, but also influence processes such as DNA repair, replication, stemness, and changes in cell state. In this review, we focus on the most recent developments in our understanding of histone modifications, particularly those on the lateral surface of the nucleosome. This region is in direct contact with the DNA and is formed by the histone cores. We suggest that these lateral surface modifications represent a key insight into chromatin regulation in the cell. Therefore, lateral surface modifications form a key area of interest and a focal point of ongoing study in epigenetics.
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36
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Zhao Y, Garcia BA. Comprehensive Catalog of Currently Documented Histone Modifications. Cold Spring Harb Perspect Biol 2015; 7:a025064. [PMID: 26330523 DOI: 10.1101/cshperspect.a025064] [Citation(s) in RCA: 257] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Modern techniques in molecular biology, genomics, and mass spectrometry-based proteomics have identified a large number of novel histone posttranslational modifications (PTMs), many of whose functions are still under intense investigation. Here, we catalog histone PTMs under two classes: first, those whose functions have been fairly well studied and, second, those PTMs that have been more recently identified but whose functions remain unclear. We hope that this will be a useful resource for researchers from all biological or technical backgrounds, aiding in their chromatin and epigenetic pursuits.
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Affiliation(s)
- Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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37
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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38
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Awwad SW, Ayoub N. Overexpression of KDM4 lysine demethylases disrupts the integrity of the DNA mismatch repair pathway. Biol Open 2015; 4:498-504. [PMID: 25770186 PMCID: PMC4400592 DOI: 10.1242/bio.201410991] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The KDM4 family of lysine demethylases consists of five members, KDM4A, -B and -C that demethylate H3K9me2/3 and H3K36me2/3 marks, while KDM4D and -E demethylate only H3K9me2/3. Recent studies implicated KDM4 proteins in regulating genomic instability and carcinogenesis. Here, we describe a previously unrecognized pathway by which hyperactivity of KDM4 demethylases promotes genomic instability. We show that overexpression of KDM4A-C, but not KDM4D, disrupts MSH6 foci formation during S phase by demethylating its binding site, H3K36me3. Consequently, we demonstrate that cells overexpressing KDM4 members are defective in DNA mismatch repair (MMR), as evident by the instability of four microsatellite markers and the remarkable increase in the spontaneous mutations frequency at the HPRT locus. Furthermore, we show that the defective MMR in cells overexpressing KDM4C is mainly due to the increase in its demethylase activity and can be mended by KDM4C downregulation. Altogether, our data suggest that cells overexpressing KDM4A-C are defective in DNA MMR and this may contribute to genomic instability and tumorigenesis.
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Affiliation(s)
- Samah W Awwad
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Nabieh Ayoub
- Department of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
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39
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Khoury-Haddad H, Nadar-Ponniah PT, Awwad S, Ayoub N. The emerging role of lysine demethylases in DNA damage response: dissecting the recruitment mode of KDM4D/JMJD2D to DNA damage sites. Cell Cycle 2015; 14:950-8. [PMID: 25714495 PMCID: PMC4614868 DOI: 10.1080/15384101.2015.1014147] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 01/26/2015] [Accepted: 01/27/2015] [Indexed: 02/06/2023] Open
Abstract
KDM4D is a lysine demethylase that removes tri- and di- methylated residues from H3K9 and is involved in transcriptional regulation and carcinogenesis. We recently showed that KDM4D is recruited to DNA damage sites in a PARP1-dependent manner and facilitates double-strand break repair in human cells. Moreover, we demonstrated that KDM4D is an RNA binding protein and mapped its RNA-binding motifs. Interestingly, KDM4D-RNA interaction is essential for its localization on chromatin and subsequently for efficient demethylation of its histone substrate H3K9me3. Here, we provide new data that shed mechanistic insights into KDM4D accumulation at DNA damage sites. We show for the first time that KDM4D binds poly(ADP-ribose) (PAR) in vitro via its C-terminal region. In addition, we demonstrate that KDM4D-RNA interaction is required for KDM4D accumulation at DNA breakage sites. Finally, we discuss the recruitment mode and the biological functions of additional lysine demethylases including KDM4B, KDM5B, JMJD1C, and LSD1 in DNA damage response.
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Affiliation(s)
| | | | - Samah Awwad
- Department of Biology; Israel Institute of Technology; Haifa, Israel
| | - Nabieh Ayoub
- Department of Biology; Israel Institute of Technology; Haifa, Israel
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40
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Kebede AF, Schneider R, Daujat S. Novel types and sites of histone modifications emerge as players in the transcriptional regulation contest. FEBS J 2014; 282:1658-74. [DOI: 10.1111/febs.13047] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 09/03/2014] [Accepted: 09/09/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Adam F. Kebede
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS UMR 7104 - Inserm U964; Université de Strasbourg; Illkirch France
| | - Robert Schneider
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS UMR 7104 - Inserm U964; Université de Strasbourg; Illkirch France
| | - Sylvain Daujat
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; CNRS UMR 7104 - Inserm U964; Université de Strasbourg; Illkirch France
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41
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Xu YM, Du JY, Lau ATY. Posttranslational modifications of human histone H3: an update. Proteomics 2014; 14:2047-60. [PMID: 25044606 DOI: 10.1002/pmic.201300435] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 05/30/2014] [Accepted: 07/04/2014] [Indexed: 02/05/2023]
Abstract
Histone proteins, the fundamental components of chromatin, are highly conserved proteins that present in eukaryotic nuclei. They organize genomic DNA to form nucleosomes, the basic units of chromatin. PTMs of histones play essential roles in many biological processes, such as chromatin condensation, gene expression, cell differentiation, and apoptosis. With the advancement of proteomic technology, a growing number of histone PTMs have been identified, including ADP-ribosylation, biotinylation, citrullination, crotonylation, O-GlcNAcylation, glutathionylation, succinylation, and so on. Because of the fast growing list of these PTMs in just a few years, the functions of these marks are being studied intensively. As histone H3 has the most number of PTMs among the histone members, in this review, we would like to present the overall concepts of the more familiar PTMs as well as discussing all the recently identified yet less well-known PTMs on human histone H3.
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Affiliation(s)
- Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, P. R. China
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Perfus-Barbeoch L, Castagnone-Sereno P, Reichelt M, Fneich S, Roquis D, Pratx L, Cosseau C, Grunau C, Abad P. Elucidating the molecular bases of epigenetic inheritance in non-model invertebrates: the case of the root-knot nematode Meloidogyne incognita. Front Physiol 2014; 5:211. [PMID: 24936189 PMCID: PMC4047830 DOI: 10.3389/fphys.2014.00211] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 05/15/2014] [Indexed: 01/01/2023] Open
Abstract
Root-knot nematodes of the genus Meloidogyne are biotrophic plant parasites that exhibit different life cycles and reproduction modes, ranging from classical amphimixis to obligatory mitotic parthenogenesis (apomixis), depending on the species. Meloidogyne incognita, an apomictic species, exhibits a worldwide distribution and a wide host range affecting more than 3000 plant species. Furthermore, evidences suggest that apomixis does not prevent M. incognita from adapting to its environment in contrast to what is expected from mitotic parthenogenesis that should theoretically produce clonal progenies. This raises questions about mechanisms of genome plasticity leading to genetic variation and adaptive evolution in apomictic animals. We reasoned that epigenetic mechanisms might in part be responsible for the generation of phenotypic variants that provide potential for rapid adaptation. We established therefore a pipeline to investigate the principal carriers of epigenetic information, DNA methylation and post-translational histone modifications. Even if M. incognita possesses the epigenetic machinery i.e., chromatin modifying enzymes, 5-methyl-cytosine and 5-hydroxy-methyl-cytosine content is absent or very weak. In contrast, we demonstrated that the canonical histone modifications are present and chromatin shows typical nucleosome structure. This work is the first characterization of carriers of epigenetic information in M. incognita and constitutes a preamble to further investigate if M. incognita development and its adaptation to plant hosts are under epigenetic control. Our pipeline should allow performing similar types of studies in any non-model organism.
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Affiliation(s)
- Laetitia Perfus-Barbeoch
- INRA, Institut Sophia Agrobiotech, UMR 1355 ISA Sophia-Antipolis, France ; CNRS, Institut Sophia Agrobiotech, UMR 7254 ISA Sophia-Antipolis, France ; Institut Sophia Agrobiotech, Université de Nice Sophia-Antipolis, UMR ISA Sophia-Antipolis, France
| | - Philippe Castagnone-Sereno
- INRA, Institut Sophia Agrobiotech, UMR 1355 ISA Sophia-Antipolis, France ; CNRS, Institut Sophia Agrobiotech, UMR 7254 ISA Sophia-Antipolis, France ; Institut Sophia Agrobiotech, Université de Nice Sophia-Antipolis, UMR ISA Sophia-Antipolis, France
| | | | - Sara Fneich
- Ecologie et Evolution des Interactions, Université de Perpignan Via Domitia Perpignan, France ; Ecologie et Evolution des Interactions, CNRS, UMR5244 Perpignan, France
| | - David Roquis
- Ecologie et Evolution des Interactions, Université de Perpignan Via Domitia Perpignan, France ; Ecologie et Evolution des Interactions, CNRS, UMR5244 Perpignan, France
| | - Loris Pratx
- INRA, Institut Sophia Agrobiotech, UMR 1355 ISA Sophia-Antipolis, France ; CNRS, Institut Sophia Agrobiotech, UMR 7254 ISA Sophia-Antipolis, France ; Institut Sophia Agrobiotech, Université de Nice Sophia-Antipolis, UMR ISA Sophia-Antipolis, France
| | - Céline Cosseau
- Ecologie et Evolution des Interactions, Université de Perpignan Via Domitia Perpignan, France ; Ecologie et Evolution des Interactions, CNRS, UMR5244 Perpignan, France
| | - Christoph Grunau
- Ecologie et Evolution des Interactions, Université de Perpignan Via Domitia Perpignan, France ; Ecologie et Evolution des Interactions, CNRS, UMR5244 Perpignan, France
| | - Pierre Abad
- INRA, Institut Sophia Agrobiotech, UMR 1355 ISA Sophia-Antipolis, France ; CNRS, Institut Sophia Agrobiotech, UMR 7254 ISA Sophia-Antipolis, France ; Institut Sophia Agrobiotech, Université de Nice Sophia-Antipolis, UMR ISA Sophia-Antipolis, France
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Lyons DB, Lomvardas S. Repressive histone methylation: a case study in deterministic versus stochastic gene regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1373-84. [PMID: 24859457 DOI: 10.1016/j.bbagrm.2014.05.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/09/2014] [Accepted: 05/13/2014] [Indexed: 01/21/2023]
Abstract
Transcriptionally repressive histone lysine methylation is used by eukaryotes to tightly control cell fate. Here we explore the importance of this form of regulation in the control of clustered genes in the genome. Two distinctly regulated gene families with important roles in vertebrates are discussed, namely the Hox genes and olfactory receptor genes. Major recent advances in these two fields are compared and contrasted, with an emphasis on the roles of the two different forms of histone trimethylation. We discuss how this repression may impact both the transcriptional output of these loci and the way higher-order chromatin organization is related to their unique control.
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Affiliation(s)
- David B Lyons
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stavros Lomvardas
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Anatomy, University of California San Francisco, CA 94920, USA.
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44
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Getting down to the core of histone modifications. Chromosoma 2014; 123:355-71. [PMID: 24789118 DOI: 10.1007/s00412-014-0465-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/08/2014] [Accepted: 04/09/2014] [Indexed: 10/25/2022]
Abstract
The identification of an increasing number of posttranslationally modified residues within histone core domains is furthering our understanding of how nucleosome dynamics are regulated. In this review, we first discuss how the targeting of specific histone H3 core residues can directly influence the nucleosome structure and then apply this knowledge to provide functional reasoning for their localization to distinct genomic regions. While we focus mainly on transcriptional implications, the principles discussed in this review can also be applied to their roles in other cellular processes. Finally, we highlight some examples of how aberrant modifications of core histone residues can facilitate the pathogenesis of some diseases.
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Rivera C, Gurard-Levin ZA, Almouzni G, Loyola A. Histone lysine methylation and chromatin replication. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1433-9. [PMID: 24686120 DOI: 10.1016/j.bbagrm.2014.03.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/12/2014] [Accepted: 03/20/2014] [Indexed: 01/20/2023]
Abstract
In eukaryotic organisms, the replication of the DNA sequence and its organization into chromatin are critical to maintain genome integrity. Chromatin components, such as histone variants and histone post-translational modifications, along with the higher-order chromatin structure, impact several DNA metabolic processes, including replication, transcription, and repair. In this review we focus on lysine methylation and the relationships between this histone mark and chromatin replication. We first describe studies implicating lysine methylation in regulating early steps in the replication process. We then discuss chromatin reassembly following replication fork passage, where the incorporation of a combination of newly synthesized histones and parental histones can impact the inheritance of lysine methylation marks on the daughter strands. Finally, we elaborate on how the inheritance of lysine methylation can impact maintenance of the chromatin landscape, using heterochromatin as a model chromatin domain, and we discuss the potential mechanisms involved in this process.
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Affiliation(s)
| | - Zachary A Gurard-Levin
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR 3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR 3664, Paris F-75248, France; UPMC, UMR 3664, Paris F-75248, France; Paris Sciences & Lettres, PSL, France
| | - Geneviève Almouzni
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR 3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR 3664, Paris F-75248, France; UPMC, UMR 3664, Paris F-75248, France; Paris Sciences & Lettres, PSL, France.
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46
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Zheng W, Huang Y. The chemistry and biology of the α-ketoglutarate-dependent histone Nε-methyl-lysine demethylases. MEDCHEMCOMM 2014. [DOI: 10.1039/c3md00325f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
This review describes the current knowledge of the chemistry and biology of the physiologically and therapeutically important histone/protein Nε-methyl-lysine demethylation reactions catalyzed by the JMJD2 and JARID1 families of the α-ketoglutarate-dependent demethylases.
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Affiliation(s)
- Weiping Zheng
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Yajun Huang
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
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47
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Labbé RM, Holowatyj A, Yang ZQ. Histone lysine demethylase (KDM) subfamily 4: structures, functions and therapeutic potential. Am J Transl Res 2013; 6:1-15. [PMID: 24349617 PMCID: PMC3853420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 11/25/2013] [Indexed: 06/03/2023]
Abstract
KDM4 histone demethylases catalyze the removal of methyl marks from histone lysine residues to epigenetically regulate chromatin structure and gene expression. KDM4 expression is tightly regulated to insure proper function in diverse biological processes, such as cellular differentiation. Mounting evidence has shown that disrupting KDM4 expression is implicated in the establishment and progression of multiple diseases including cancer. In particular, genomic regions encoding the KDM4A, B and C genes are often amplified, disrupting normal cellular proliferation. Furthermore, KDM4 demethylases are promising druggable targets. In this review, we highlight the latest advances in characterizing the structures and regulatory mechanisms of KDM4 proteins, as well as our current understanding of their alterations and roles in tumorigenesis. We also review the reported KDM4 inhibitors and discuss their potential as therapeutic agents.
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Affiliation(s)
- Roselyne M Labbé
- Karmanos Cancer Institute, Department of Oncology, Wayne State University Detroit, MI 48201, USA
| | - Andreana Holowatyj
- Karmanos Cancer Institute, Department of Oncology, Wayne State University Detroit, MI 48201, USA
| | - Zeng-Quan Yang
- Karmanos Cancer Institute, Department of Oncology, Wayne State University Detroit, MI 48201, USA
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48
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Epigenetics of eu- and heterochromatin in inverted and conventional nuclei from mouse retina. Chromosome Res 2013; 21:535-54. [PMID: 23996328 DOI: 10.1007/s10577-013-9375-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/16/2013] [Accepted: 07/17/2013] [Indexed: 12/20/2022]
Abstract
To improve light propagation through the retina, the rod nuclei of nocturnal mammals are uniquely changed compared to the nuclei of other cells. In particular, the main classes of chromatin are segregated in them and form regular concentric shells in order; inverted in comparison to conventional nuclei. A broad study of the epigenetic landscape of the inverted and conventional mouse retinal nuclei indicated several differences between them and several features of general interest for the organization of the mammalian nuclei. In difference to nuclei with conventional architecture, the packing density of pericentromeric satellites and LINE-rich chromatin is similar in inverted rod nuclei; euchromatin has a lower packing density in both cases. A high global chromatin condensation in rod nuclei minimizes the structural difference between active and inactive X chromosome homologues. DNA methylation is observed primarily in the chromocenter, Dnmt1 is primarily associated with the euchromatic shell. Heterochromatin proteins HP1-alpha and HP1-beta localize in heterochromatic shells, whereas HP1-gamma is associated with euchromatin. For most of the 25 studied histone modifications, we observed predominant colocalization with a certain main chromatin class. Both inversions in rod nuclei and maintenance of peripheral heterochromatin in conventional nuclei are not affected by a loss or depletion of the major silencing core histone modifications in respective knock-out mice, but for different reasons. Maintenance of peripheral heterochromatin appears to be ensured by redundancy both at the level of enzymes setting the epigenetic code (writers) and the code itself, whereas inversion in rods rely on the absence of the peripheral heterochromatin tethers (absence of code readers).
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