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Ahmed IA, Liu M, Gomez D. Nuclear Control of Vascular Smooth Muscle Cell Plasticity during Vascular Remodeling. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:525-538. [PMID: 37820925 PMCID: PMC10988766 DOI: 10.1016/j.ajpath.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/18/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023]
Abstract
Control of vascular smooth muscle cell (SMC) gene expression is an essential process for establishing and maintaining lineage identity, contractility, and plasticity. Most mechanisms (epigenetic, transcriptional, and post-transcriptional) implicated in gene regulation occur in the nucleus. Still, intranuclear pathways are directly impacted by modifications in the extracellular environment in conditions of adaptive or maladaptive remodeling. Integration of extracellular, cellular, and genomic information into the nucleus through epigenetic and transcriptional control of genome organization plays a major role in regulating SMC functions and phenotypic transitions during vascular remodeling and diseases. This review aims to provide a comprehensive update on nuclear mechanisms, their interactions, and their integration in controlling SMC homeostasis and dysfunction. It summarizes and discusses the main nuclear mechanisms preponderant in SMCs in the context of vascular disease, such as atherosclerosis, with an emphasis on studies employing in vivo cell-specific loss-of-function and single-cell omics approaches.
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Affiliation(s)
- Ibrahim A Ahmed
- Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania; Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mingjun Liu
- Department of Pathology, New York University, New York, New York
| | - Delphine Gomez
- Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania; Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.
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2
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Zhao H, Wu H, Guseman A, Abeykoon D, Camara CM, Dalal Y, Fushman D, Papoian GA. The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea. PLoS Comput Biol 2024; 20:e1011721. [PMID: 38181064 PMCID: PMC10796010 DOI: 10.1371/journal.pcbi.1011721] [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: 08/15/2023] [Revised: 01/18/2024] [Accepted: 11/28/2023] [Indexed: 01/07/2024] Open
Abstract
Histones compact and store DNA in both Eukarya and Archaea, forming heterodimers in Eukarya and homodimers in Archaea. Despite this, the folding mechanism of histones across species remains unclear. Our study addresses this gap by investigating 11 types of histone and histone-like proteins across humans, Drosophila, and Archaea through multiscale molecular dynamics (MD) simulations, complemented by NMR and circular dichroism experiments. We confirm and elaborate on the widely applied "folding upon binding" mechanism of histone dimeric proteins and report a new alternative conformation, namely, the inverted non-native dimer, which may be a thermodynamically metastable configuration. Protein sequence analysis indicated that the inverted conformation arises from the hidden ancestral head-tail sequence symmetry underlying all histone proteins, which is congruent with the previously proposed histone evolution hypotheses. Finally, to explore the potential formations of homodimers in Eukarya, we utilized MD-based AWSEM and AI-based AlphaFold-Multimer models to predict their structures and conducted extensive all-atom MD simulations to examine their respective structural stabilities. Our results suggest that eukaryotic histones may also form stable homodimers, whereas their disordered tails bring significant structural asymmetry and tip the balance towards the formation of commonly observed heterotypic dimers.
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Affiliation(s)
- Haiqing Zhao
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Hao Wu
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
| | - Alex Guseman
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
| | - Dulith Abeykoon
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
| | - Christina M. Camara
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David Fushman
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
| | - Garegin A. Papoian
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
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Kikuchi M, Takase S, Konuma T, Noritsugu K, Sekine S, Ikegami T, Ito A, Umehara T. GAS41 promotes H2A.Z deposition through recognition of the N terminus of histone H3 by the YEATS domain. Proc Natl Acad Sci U S A 2023; 120:e2304103120. [PMID: 37844223 PMCID: PMC10614846 DOI: 10.1073/pnas.2304103120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 09/11/2023] [Indexed: 10/18/2023] Open
Abstract
Glioma amplified sequence 41 (GAS41), which has the Yaf9, ENL, AF9, Taf14, and Sas5 (YEATS) domain that recognizes lysine acetylation (Kac), regulates gene expression as a subunit of the SRCAP (SNF2-related CREBBP activator protein) complex that deposits histone H2A.Z at promoters in eukaryotes. The YEATS domains of the proteins AF9 and ENL recognize Kac by hydrogen bonding the aromatic cage to arginine situated just before K9ac or K27ac in the N-terminal tail of histone H3. Curiously, the YEATS domain of GAS41 binds most preferentially to the sequence that contains K14ac of H3 (H3K14ac) but lacks the corresponding arginine. Here, we biochemically and structurally elucidated the molecular mechanism by which GAS41 recognizes H3K14ac. First, stable binding of the GAS41 YEATS domain to H3K14ac required the N terminus of H3 (H3NT). Second, we revealed a pocket in the GAS41 YEATS domain responsible for the H3NT binding by crystallographic and NMR analyses. This pocket is away from the aromatic cage that recognizes Kac and is unique to GAS41 among the YEATS family. Finally, we showed that E109 of GAS41, a residue essential for the formation of the H3NT-binding pocket, was crucial for chromatin occupancy of H2A.Z and GAS41 at H2A.Z-enriched promoter regions. These data suggest that binding of GAS41 to H3NT via its YEATS domain is essential for its intracellular function.
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Affiliation(s)
- Masaki Kikuchi
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama230-0045, Japan
| | - Shohei Takase
- Laboratory of Cell Signaling, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo192-0392, Japan
| | - Tsuyoshi Konuma
- Structural Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama230-0045, Japan
| | - Kota Noritsugu
- Laboratory of Cell Signaling, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo192-0392, Japan
| | - Saaya Sekine
- Laboratory of Cell Signaling, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo192-0392, Japan
| | - Takahisa Ikegami
- Structural Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama230-0045, Japan
| | - Akihiro Ito
- Laboratory of Cell Signaling, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo192-0392, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama230-0045, Japan
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Gòdia M, Lian Y, Naval-Sanchez M, Ponte I, Rodríguez-Gil JE, Sanchez A, Clop A. Micrococcal nuclease sequencing of porcine sperm suggests enriched co-location between retained histones and genomic regions related to semen quality and early embryo development. PeerJ 2023; 11:e15520. [PMID: 37361042 PMCID: PMC10290446 DOI: 10.7717/peerj.15520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 05/16/2023] [Indexed: 06/28/2023] Open
Abstract
The mammalian spermatozoon has a unique chromatin structure in which the majority of histones are replaced by protamines during spermatogenesis and a small fraction of nucleosomes are retained at specific locations of the genome. The sperm's chromatin structure remains unresolved in most animal species, including the pig. However, mapping the genomic locations of retained nucleosomes in sperm could help understanding the molecular basis of both sperm development and function as well as embryo development. This information could then be useful to identify molecular markers for sperm quality and fertility traits. Here, micrococcal nuclease digestion coupled with high throughput sequencing was performed on pig sperm to map the genomic location of mono- and sub-nucleosomal chromatin fractions in relation to a set of diverse functional elements of the genome, some of which were related to semen quality and early embryogenesis. In particular, the investigated elements were promoters, the different sections of the gene body, coding and non-coding RNAs present in the pig sperm, potential transcription factor binding sites, genomic regions associated to semen quality traits and repeat elements. The analysis yielded 25,293 and 4,239 peaks in the mono- and sub-nucleosomal fractions, covering 0.3% and 0.02% of the porcine genome, respectively. A cross-species comparison revealed positional conservation of the nucleosome retention in sperm between the pig data and a human dataset that found nucleosome enrichment in genomic regions of importance in development. Both gene ontology analysis of the genes mapping nearby the mono-nucleosomal peaks and the identification of putative transcription factor binding motifs within the mono- and the sub- nucleosomal peaks showed enrichment for processes related to sperm function and embryo development. There was significant motif enrichment for Znf263, which in humans was suggested to be a key regulator of genes with paternal preferential expression during early embryogenesis. Moreover, enriched positional intersection was found in the genome between the mono-nucleosomal peaks and both the RNAs present in pig sperm and the RNAs related to sperm quality. There was no co-location between GWAS hits for semen quality in swine and the nucleosomal sites. Finally, the data evidenced depletion of mono-nucleosomes in long interspersed nuclear elements and enrichment of sub-nucleosomes in short interspersed repeat elements.These results suggest that retained nucleosomes in sperm could both mark regulatory elements or genes expressed during spermatogenesis linked to semen quality and fertility and act as transcriptional guides during early embryogenesis. The results of this study support the undertaking of ambitious research using a larger number of samples to robustly assess the positional relationship between histone retention in sperm and the reproductive ability of boars.
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Affiliation(s)
- Marta Gòdia
- Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Cerdanyola del Vallés, Catalonia, Spain
- Animal Breeding and Genomics, Wageningen University and Research, Wageninger, Netherlands
| | - Yu Lian
- Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Cerdanyola del Vallés, Catalonia, Spain
| | | | - Inma Ponte
- Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, Catalonia, Spain
| | - Joan Enric Rodríguez-Gil
- Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, Catalonia, Spain
| | - Armand Sanchez
- Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Cerdanyola del Vallés, Catalonia, Spain
- Animal and food sciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, Catalonia, Spain
| | - Alex Clop
- Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Cerdanyola del Vallés, Catalonia, Spain
- Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia, Spain
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Clatterbuck Soper SF, Meltzer PS. ATRX/DAXX: Guarding the Genome against the Hazards of ALT. Genes (Basel) 2023; 14:genes14040790. [PMID: 37107548 PMCID: PMC10137841 DOI: 10.3390/genes14040790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Proliferating cells must enact a telomere maintenance mechanism to ensure genomic stability. In a subset of tumors, telomeres are maintained not by telomerase, but through a homologous recombination-based mechanism termed Alternative Lengthening of Telomeres or ALT. The ALT process is linked to mutations in the ATRX/DAXX/H3.3 histone chaperone complex. This complex is responsible for depositing non-replicative histone variant H3.3 at pericentric and telomeric heterochromatin but has also been found to have roles in ameliorating replication in repeat sequences and in promoting DNA repair. In this review, we will discuss ways in which ATRX/DAXX helps to protect the genome, and how loss of this complex allows ALT to take hold.
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6
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Aagaard A, Liu S, Tregenza T, Braad Lund M, Schramm A, Verhoeven KJF, Bechsgaard J, Bilde T. Adapting to climate with limited genetic diversity: Nucleotide, DNA methylation and microbiome variation among populations of the social spider Stegodyphus dumicola. Mol Ecol 2022; 31:5765-5783. [PMID: 36112081 PMCID: PMC9827990 DOI: 10.1111/mec.16696] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 02/06/2023]
Abstract
Understanding the role of genetic and nongenetic variants in modulating phenotypes is central to our knowledge of adaptive responses to local conditions and environmental change, particularly in species with such low population genetic diversity that it is likely to limit their evolutionary potential. A first step towards uncovering the molecular mechanisms underlying population-specific responses to the environment is to carry out environmental association studies. We associated climatic variation with genetic, epigenetic and microbiome variation in populations of a social spider with extremely low standing genetic diversity. We identified genetic variants that are associated strongly with environmental variation, particularly with average temperature, a pattern consistent with local adaptation. Variation in DNA methylation in many genes was strongly correlated with a wide set of climate parameters, thereby revealing a different pattern of associations than that of genetic variants, which show strong correlations to a more restricted range of climate parameters. DNA methylation levels were largely independent of cis-genetic variation and of overall genetic population structure, suggesting that DNA methylation can work as an independent mechanism. Microbiome composition also correlated with environmental variation, but most strong associations were with precipitation-related climatic factors. Our results suggest a role for both genetic and nongenetic mechanisms in shaping phenotypic responses to local environments.
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Affiliation(s)
- Anne Aagaard
- Section for Genetics, Ecology & Evolution, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Shenglin Liu
- Section for Genetics, Ecology & Evolution, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Tom Tregenza
- Centre for Ecology & Conservation, School of BiosciencesUniversity of ExeterPenryn CampusUK
| | - Marie Braad Lund
- Section for Microbiology, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Andreas Schramm
- Section for Microbiology, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Koen J. F. Verhoeven
- Terrestrial Ecology DepartmentNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Jesper Bechsgaard
- Section for Genetics, Ecology & Evolution, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Trine Bilde
- Section for Genetics, Ecology & Evolution, Department of BiologyAarhus UniversityAarhus CDenmark
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7
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George S, Cassidy RN, Saintilnord WN, Fondufe-Mittendorf Y. Epigenomic reprogramming in iAs-mediated carcinogenesis. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 96:319-365. [PMID: 36858778 DOI: 10.1016/bs.apha.2022.08.004] [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: 03/03/2023]
Abstract
Arsenic is a naturally occurring metal carcinogen found in the Earth's crust. Millions of people worldwide are chronically exposed to arsenic through drinking water and food. Exposure to inorganic arsenic has been implicated in many diseases ranging from acute toxicities to malignant transformations. Despite the well-known deleterious health effects of arsenic exposure, the molecular mechanisms in arsenic-mediated carcinogenesis are not fully understood. Since arsenic is non-mutagenic, the mechanism by which arsenic causes carcinogenesis is via alterations in epigenetic-regulated gene expression. There are two possible ways by which arsenic may modify the epigenome-indirectly through an arsenic-induced generation of reactive oxygen species which then impacts chromatin remodelers, or directly through interaction and modulation of chromatin remodelers. Whether directly or indirectly, arsenic modulates epigenetic gene regulation and our understanding of the direct effect of this modulation on chromatin structure is limited. In this chapter we will discuss the various ways by which inorganic arsenic affects the epigenome with consequences in health and disease.
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Affiliation(s)
- Smitha George
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, United States
| | - Richard N Cassidy
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, United States
| | - Wesley N Saintilnord
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, United States; Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States
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Amatori S, Tavolaro S, Gambardella S, Fanelli M. The dark side of histones: genomic organization and role of oncohistones in cancer. Clin Epigenetics 2021; 13:71. [PMID: 33827674 PMCID: PMC8025322 DOI: 10.1186/s13148-021-01057-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
Background The oncogenic role of histone mutations is one of the most relevant discovery in cancer epigenetics. Recurrent mutations targeting histone genes have been described in pediatric brain tumors, chondroblastoma, giant cell tumor of bone and other tumor types. The demonstration that mutant histones can be oncogenic and drive the tumorigenesis in pediatric tumors, led to the coining of the term “oncohistones.” The first identified histone mutations were localized at or near residues normally targeted by post-translational modifications (PTMs) in the histone N-terminal tails and suggested a possible interference with histone PTMs regulation and reading. Main body In this review, we describe the peculiar organization of the multiple genes that encode histone proteins, and the latter advances in both the identification and the biological role of histone mutations in cancer. Recent works show that recurrent somatic mutations target both N-terminal tails and globular histone fold domain in diverse tumor types. Oncohistones are often dominant-negative and occur at higher frequencies in tumors affecting children and adolescents. Notably, in many cases the mutations target selectively only some of the genes coding the same histone protein and are frequently associated with specific tumor types or, as documented for histone variant H3.3 in pediatric glioma, with peculiar tumors arising from specific anatomic locations. Conclusion The overview of the most recent advances suggests that the oncogenic potential of histone mutations can be exerted, together with the alteration of histone PTMs, through the destabilization of nucleosome and DNA–nucleosome interactions, as well as through the disruption of higher-order chromatin structure. However, further studies are necessary to fully elucidate the mechanism of action of oncohistones, as well as to evaluate their possible application to cancer classification, prognosis and to the identification of new therapies.
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Affiliation(s)
- Stefano Amatori
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.
| | - Simona Tavolaro
- Fredis Associazione, Via Edoardo Jenner 30, 00151, Rome, Italy
| | - Stefano Gambardella
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.,IRCCS Neuromed, Via Atinense 18, 86077, Pozzilli, IS, Italy
| | - Mirco Fanelli
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Via Arco d'Augusto 2, 61032, Fano, PU, Italy.
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Du K, Luo Q, Yin L, Wu J, Liu Y, Gan J, Dong A, Shen WH. OsChz1 acts as a histone chaperone in modulating chromatin organization and genome function in rice. Nat Commun 2020; 11:5717. [PMID: 33177521 PMCID: PMC7658359 DOI: 10.1038/s41467-020-19586-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
While the yeast Chz1 acts as a specific histone-chaperone for H2A.Z, functions of CHZ-domain proteins in multicellular eukaryotes remain obscure. Here, we report on the functional characterization of OsChz1, a sole CHZ-domain protein identified in rice. OsChz1 interacts with both the canonical H2A-H2B dimer and the variant H2A.Z-H2B dimer. Within crystal structure the C-terminal region of OsChz1 binds H2A-H2B via an acidic region, pointing to a previously unknown recognition mechanism. Knockout of OsChz1 leads to multiple plant developmental defects. At genome-wide level, loss of OsChz1 causes mis-regulations of thousands of genes and broad alterations of nucleosome occupancy as well as reductions of H2A.Z-enrichment. While OsChz1 associates with chromatin regions enriched of repressive histone marks (H3K27me3 and H3K4me2), its loss does not affect the genome landscape of DNA methylation. Taken together, it is emerging that OsChz1 functions as an important H2A/H2A.Z-H2B chaperone in dynamic regulation of chromatin for higher eukaryote development. Function of CHZ-domain proteins in multicellular eukaryotes remains unclear. Here, the authors characterize the sole CHZ-domain protein identified in rice and show that it functions as an H2A/H2A.Z-H2B chaperone in dynamic regulation of chromatin organization and genome function.
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Affiliation(s)
- Kangxi Du
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qiang Luo
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Liufan Yin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jiabing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yuhao Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jianhua Gan
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China. .,Institut de Biologie Moléculaire des Plantes, UPR2357 CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg, Cédex, France.
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10
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Yan A, Borg M, Berger F, Chen Z. The atypical histone variant H3.15 promotes callus formation in Arabidopsis thaliana. Development 2020; 147:dev184895. [PMID: 32439757 DOI: 10.1242/dev.184895] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 04/28/2020] [Indexed: 12/22/2022]
Abstract
Plants are capable of regenerating new organs after mechanical injury. The regeneration process involves genome-wide reprogramming of transcription, which usually requires dynamic changes in the chromatin landscape. We show that the histone 3 variant HISTONE THREE RELATED 15 (H3.15) plays an important role in cell fate reprogramming during plant regeneration in Arabidopsis H3.15 expression is rapidly induced upon wounding. Ectopic overexpression of H3.15 promotes cell proliferation to form a larger callus at the wound site, whereas htr15 mutation compromises callus formation. H3.15 is distinguished from other Arabidopsis histones by the absence of the lysine residue 27 that is trimethylated by the POLYCOMB REPRESSIVE COMPLEX 2 (PRC2) in constitutively expressed H3 variants. Overexpression of H3.15 promotes the removal of the transcriptional repressive mark H3K27me3 from chromatin, which results in transcriptional de-repression of downstream genes, such as WUSCHEL RELATED HOMEOBOX 11 (WOX11). Our results reveal a new mechanism for a release from PRC2-mediated gene repression through H3.15 deposition into chromatin, which is involved in reprogramming cell fate to produce pluripotent callus cells.
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Affiliation(s)
- An Yan
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Singapore
| | - Michael Borg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Zhong Chen
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Singapore
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11
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Monteonofrio L, Valente D, Rinaldo C, Soddu S. Extrachromosomal Histone H2B Contributes to the Formation of the Abscission Site for Cell Division. Cells 2019; 8:cells8111391. [PMID: 31694230 PMCID: PMC6912571 DOI: 10.3390/cells8111391] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/25/2019] [Accepted: 10/31/2019] [Indexed: 12/13/2022] Open
Abstract
Histones are constitutive components of nucleosomes and key regulators of chromatin structure. We previously observed that an extrachromosomal histone H2B (ecH2B) localizes at the intercellular bridge (ICB) connecting the two daughter cells during cytokinesis independently of DNA and RNA. Here, we show that ecH2B binds and colocalizes with CHMP4B, a key component of the ESCRT-III machinery responsible for abscission, the final step of cell division. Abscission requires the formation of an abscission site at the ICB where the ESCRT-III complex organizes into narrowing cortical helices that drive the physical separation of sibling cells. ecH2B depletion does not prevent membrane cleavage rather results in abscission delay and accumulation of abnormally long and thin ICBs. In the absence of ecH2B, CHMP4B and other components of the fission machinery, such as IST1 and Spastin, are recruited to the ICB and localize at the midbody. However, in the late stage of abscission, these fission factors fail to re-localize at the periphery of the midbody and the abscission site fails to form. These results show that extrachromosomal activity of histone H2B is required in the formation of the abscission site and the proper localization of the fission machinery.
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Affiliation(s)
- Laura Monteonofrio
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (D.V.); (C.R.)
- Correspondence: (L.M.); (S.S.); Tel.: +1-(443)-410-9571 (L.M.); +39-065266-2492 (S.S.)
| | - Davide Valente
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (D.V.); (C.R.)
| | - Cinzia Rinaldo
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (D.V.); (C.R.)
- Institutes of Molecular Biology and Pathology (IBPM), National Research Council (CNR), c/o Sapienza University, 00185 Rome, Italy
| | - Silvia Soddu
- Unit of Cellular Networks and Molecular Therapeutic Targets, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (D.V.); (C.R.)
- Correspondence: (L.M.); (S.S.); Tel.: +1-(443)-410-9571 (L.M.); +39-065266-2492 (S.S.)
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12
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Balasubramanian S, Raghunath A, Perumal E. Role of epigenetics in zebrafish development. Gene 2019; 718:144049. [DOI: 10.1016/j.gene.2019.144049] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 02/07/2023]
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13
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Shen T, Ji F, Wang Y, Lei X, Zhang D, Jiao J. Brain-specific deletion of histone variant H2A.z results in cortical neurogenesis defects and neurodevelopmental disorder. Nucleic Acids Res 2019; 46:2290-2307. [PMID: 29294103 PMCID: PMC5861433 DOI: 10.1093/nar/gkx1295] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/19/2017] [Indexed: 12/14/2022] Open
Abstract
Defects in neurogenesis alter brain circuit formations and may lead to neurodevelopmental disorders such as autism and schizophrenia. Histone H2A.z, a variant of histone H2A, plays critical roles in chromatin structure and epigenetic regulation, but its function and mechanism in brain development remain largely unknown. Here, we find that the deletion of H2A.z results in enhanced proliferation of neural progenitors but reduced neuronal differentiation. In addition, neurons in H2A.z knockout mice exhibit abnormal dendrites during brain development. Furthermore, H2A.zcKO mice exhibit serial behavioral deficits, such as decreased exploratory activity and impaired learning and memory. Mechanistically, H2A.z regulates embryonic neurogenesis by targeting Nkx2–4 through interaction with Setd2, thereby promoting H3K36me3 modification to activate the transcription of Nkx2–4. Furthermore, enforced expression of Nkx2–4 can rescue the defective neurogenesis in the H2A.z-knockdown embryonic brain. Together, our findings implicate the epigenetic regulation by H2A.z in embryonic neurogenesis and provide a framework for understanding how disruption in the H2A.z gene may contribute to neurological disorders.
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Affiliation(s)
- Tianjin Shen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fen Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanyuan Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuepei Lei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongming Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianwei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Singh R, Bassett E, Chakravarti A, Parthun MR. Replication-dependent histone isoforms: a new source of complexity in chromatin structure and function. Nucleic Acids Res 2019; 46:8665-8678. [PMID: 30165676 PMCID: PMC6158624 DOI: 10.1093/nar/gky768] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/24/2018] [Indexed: 12/11/2022] Open
Abstract
Replication-dependent histones are expressed in a cell cycle regulated manner and supply the histones necessary to support DNA replication. In mammals, the replication-dependent histones are encoded by a family of genes that are located in several clusters. In humans, these include 16 genes for histone H2A, 22 genes for histone H2B, 14 genes for histone H3, 14 genes for histone H4 and 6 genes for histone H1. While the proteins encoded by these genes are highly similar, they are not identical. For many years, these genes were thought to encode functionally equivalent histone proteins. However, several lines of evidence have emerged that suggest that the replication-dependent histone genes can have specific functions and may constitute a novel layer of chromatin regulation. This Survey and Summary reviews the literature on replication-dependent histone isoforms and discusses potential mechanisms by which the small variations in primary sequence between the isoforms can alter chromatin function. In addition, we summarize the wealth of data implicating altered regulation of histone isoform expression in cancer.
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Affiliation(s)
- Rajbir Singh
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Emily Bassett
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Arnab Chakravarti
- Department of Radiation Oncology, The Ohio State University, Columbus, OH 43210, USA
| | - Mark R Parthun
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
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15
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Zhao H, Winogradoff D, Dalal Y, Papoian GA. The Oligomerization Landscape of Histones. Biophys J 2019; 116:1845-1855. [PMID: 31005236 DOI: 10.1016/j.bpj.2019.03.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/06/2019] [Accepted: 03/14/2019] [Indexed: 12/29/2022] Open
Abstract
In eukaryotes, DNA is packaged within nucleosomes. The DNA of each nucleosome is typically centered around an octameric histone protein core: one central tetramer plus two separate dimers. Studying the assembly mechanisms of histones is essential for understanding the dynamics of entire nucleosomes and higher-order DNA packaging. Here, we investigate canonical histone assembly and that of the centromere-specific histone variant, centromere protein A (CENP-A), using molecular dynamics simulations. We quantitatively characterize their thermodynamical and dynamical features, showing that two H3/H4 dimers form a structurally floppy, weakly bound complex, the latter exhibiting large instability around the central interface manifested via a swiveling motion of two halves. This finding is consistent with the recently observed DNA handedness flipping of the tetrasome. In contrast, the variant CENP-A encodes distinctive stability to its tetramer with a rigid but twisted interface compared to the crystal structure, implying diverse structural possibilities of the histone variant. Interestingly, the observed tetramer dynamics alter significantly and appear to reach a new balance when H2A/H2B dimers are present. Furthermore, we found that the preferred structure for the (CENP-A/H4)2 tetramer is incongruent with the octameric structure, explaining many of the unusual dynamical behaviors of the CENP-A nucleosome. In all, these data reveal key mechanistic insights and structural details for the assembly of canonical and variant histone tetramers and octamers, providing theoretical quantifications and physical interpretations for longstanding and recent experimental observations. Based on these findings, we propose different chaperone-assisted binding and nucleosome assembly mechanisms for the canonical and CENP-A histone oligomers.
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Affiliation(s)
- Haiqing Zhao
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland; Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - David Winogradoff
- Chemical Physics Program, Institute for Physical Science and Technology
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
| | - Garegin A Papoian
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland; Chemical Physics Program, Institute for Physical Science and Technology; Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland.
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16
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Nishimura M, Nozawa K, Kurumizaka H. Crystallographic analysis of the overlapping dinucleosome as a novel chromatin unit. Biophys Physicobiol 2019; 15:251-254. [PMID: 30713825 PMCID: PMC6353640 DOI: 10.2142/biophysico.15.0_251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/18/2018] [Indexed: 12/01/2022] Open
Abstract
Recent evidence has suggested that chromatin is not simply repeats of the canonical nucleosome, called the “octasome”, but may include diverse repertoires of basic structural units. During the transcription process, a nucleosome is repositioned by a chromatin remodeler and collides with a neighboring nucleosome, thus creating an unusual nucleosome substructure termed the “overlapping dinucleosome”. We previously developed a method for the large-scale preparation of the overlapping dinucleosome. This method enabled us to solve the crystal structure of the overlapping dinucleosome, which revealed an unexpected structure composed of an octameric histone core associated with a hexameric histone core lacking one H2A-H2B dimer.
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Affiliation(s)
- Masahiro Nishimura
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kayo Nozawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 162-8480, Japan
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17
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Abstract
Gametogenesis represents the most dramatic cellular differentiation pathways in both female and male flies. At the genome level, meiosis ensures that diploid germ cells become haploid gametes. At the epigenome level, extensive changes are required to turn on and shut off gene expression in a precise spatiotemporally controlled manner. Research applying conventional molecular genetics and cell biology, in combination with rapidly advancing genomic tools have helped us to investigate (1) how germ cells maintain lineage specificity throughout their adult reproductive lifetime; (2) what molecular mechanisms ensure proper oogenesis and spermatogenesis, as well as protect genome integrity of the germline; (3) how signaling pathways contribute to germline-soma communication; and (4) if such communication is important. In this chapter, we highlight recent discoveries that have improved our understanding of these questions. On the other hand, restarting a new life cycle upon fertilization is a unique challenge faced by gametes, raising questions that involve intergenerational and transgenerational epigenetic inheritance. Therefore, we also discuss new developments that link changes during gametogenesis to early embryonic development-a rapidly growing field that promises to bring more understanding to some fundamental questions regarding metazoan development.
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18
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Evidence for the implication of the histone code in building the genome structure. Biosystems 2018; 164:49-59. [DOI: 10.1016/j.biosystems.2017.11.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/13/2017] [Accepted: 11/15/2017] [Indexed: 12/13/2022]
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19
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Afzal M, Alghamdi SS, Habib Ur Rahman M, Ahmad A, Farooq T, Alam M, Khan IA, Ullah H, Nasim W, Fahad S. Current status and future possibilities of molecular genetics techniques in Brassica napus. Biotechnol Lett 2018; 40:479-492. [PMID: 29344848 DOI: 10.1007/s10529-018-2510-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 01/08/2018] [Indexed: 12/25/2022]
Abstract
As PCR methods have improved over the last 15 years, there has been an upsurge in the number of new DNA marker tools, which has allowed the generation of high-density molecular maps for all the key Brassica crop types. Biotechnology and molecular plant breeding have emerged as a significant tool for molecular understanding that led to a significant crop improvement in the Brassica napus species. Brassica napus possess a very complicated polyploidy-based genomics. The quantitative trait locus (QTL) is not sufficient to develop effective markers for trait introgression. In the coming years, the molecular marker techniques will be more effective to determine the whole genome impairing desired traits. Available genetic markers using the single-nucleotide sequence (SNP) technique and high-throughput sequencing are effective in determining the maps and genome polymorphisms amongst candidate genes and allele interactions. High-throughput sequencing and gene mapping techniques are involved in discovering new alleles and gene pairs, serving as a bridge between the gene map and genome evaluation. The decreasing cost for DNA sequencing will help in discovering full genome sequences with less resources and time. This review describes (1) the current use of integrated approaches, such as molecular marker technologies, to determine genome arrangements and interspecific outcomes combined with cost-effective genomes to increase the efficiency in prognostic breeding efforts. (2) It also focused on functional genomics, proteomics and field-based breeding practices to achieve insight into the genetics underlying both simple and complex traits in canola.
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Affiliation(s)
- Muhammad Afzal
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Salem Safer Alghamdi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Muhammad Habib Ur Rahman
- Department of Agronomy, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
- AgWeatherNet, Washington State University, Prosser, WA, USA
| | - Awais Ahmad
- Plant Physiology Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Tahir Farooq
- Department of Plant Protection, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
| | - Mukhtar Alam
- Department of Agriculture, The University of Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Imtiaz Ali Khan
- Department of Agriculture, The University of Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Hidayat Ullah
- Department of Agriculture, The University of Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Wajid Nasim
- Department of Environmental Sciences, COMSATS Institute of Information Technology (CIIT), Vehari, 61000, Pakistan
- CIHEAM-IAMM, 3191 route de Mende, 34090, Montpellier, France
- CSIRO Sustainable Ecosystem, National Research Flagship, 203 Tor St, Toowoomba, QLD, 4350, Australia
| | - Shah Fahad
- Department of Agriculture, The University of Swabi, Khyber Pakhtunkhwa, Pakistan.
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China.
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20
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Ors A, Papin C, Favier B, Roulland Y, Dalkara D, Ozturk M, Hamiche A, Dimitrov S, Padmanabhan K. Histone H3.3 regulates mitotic progression in mouse embryonic fibroblasts. Biochem Cell Biol 2017; 95:491-499. [DOI: 10.1139/bcb-2016-0190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
H3.3 is a histone variant that marks transcription start sites as well as telomeres and heterochromatic sites on the genome. The presence of H3.3 is thought to positively correlate with the transcriptional status of its target genes. Using a conditional genetic strategy against H3.3B, combined with short hairpin RNAs against H3.3A, we essentially depleted all H3.3 gene expression in mouse embryonic fibroblasts. Following nearly complete loss of H3.3 in the cells, our transcriptomic analyses show very little impact on global gene expression or on the localization of histone variant H2A.Z. Instead, fibroblasts displayed slower cell growth and an increase in cell death, coincident with large-scale chromosome misalignment in mitosis and large polylobed or micronuclei in interphase cells. Thus, we conclude that H3.3 may have an important under-explored additional role in chromosome segregation, nuclear structure, and the maintenance of genome integrity.
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Affiliation(s)
- Aysegul Ors
- Université de Grenoble Alpes, Institute for Advanced Biosciences, INSERM U1209/CNRS 5309, 38700 La Tronche, France
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, 06800 Ankara, Turkey
| | - Christophe Papin
- Université de Strasbourg, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), CNRS, INSERM, Equipe labélisée Ligue contre le Cancer, 1 rue Laurent Fries, B.P. 10142, 67404 Illkirch Cedex, France
| | - Bertrand Favier
- Université de Grenoble Alpes, Team GREPI, Etablissement Français du Sang, EA 7408, BP35, 38701 La Tronche, France
| | - Yohan Roulland
- Université de Grenoble Alpes, Institute for Advanced Biosciences, INSERM U1209/CNRS 5309, 38700 La Tronche, France
| | - Defne Dalkara
- Université de Grenoble Alpes, Institute for Advanced Biosciences, INSERM U1209/CNRS 5309, 38700 La Tronche, France
| | - Mehmet Ozturk
- Izmir Biomedicine and Genome Center, Faculty of Medicine, Dokuz Eylül University, Izmir, Turkey
| | - Ali Hamiche
- Université de Strasbourg, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), CNRS, INSERM, Equipe labélisée Ligue contre le Cancer, 1 rue Laurent Fries, B.P. 10142, 67404 Illkirch Cedex, France
| | - Stefan Dimitrov
- Université de Grenoble Alpes, Institute for Advanced Biosciences, INSERM U1209/CNRS 5309, 38700 La Tronche, France
| | - Kiran Padmanabhan
- Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole normale supérieur de Lyon, Université Claude Bernard Lyon 1, 46 Allée d’Italie, F-69364 Lyon, France
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21
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Zhao H, Winogradoff D, Bui M, Dalal Y, Papoian GA. Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones. J Am Chem Soc 2016; 138:13207-13218. [PMID: 27454815 PMCID: PMC7757119 DOI: 10.1021/jacs.6b05355] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Histone proteins are essential for the organization, expression, and inheritance of genetic material for eukaryotic cells. A centromere-specific H3 histone variant, centromere protein A (CENP-A), shares about 50% amino acid sequence identity with H3. CENP-A is required for packaging the centromere and for the proper separation of chromosomes during mitosis. Despite their distinct biological functions, previously reported crystal structures of the CENP-A/H4 and H3/H4 dimers reveal a high degree of similarity. In this work, we characterize the structural dynamics of CENP-A/H4 and H3/H4 dimers based on a dual-resolution approach, using both microsecond-scale explicit-solvent all-atom and coarse-grained (CG) molecular dynamics (MD) simulations. Our data show that the H4 histone is significantly more rigid compared with the H3 histone and its variant CENP-A, hence, serving as a reinforcing structural element within the histone core. We report that the CENP-A/H4 dimer is significantly more dynamic than its canonical counterpart H3/H4, and our results provide a physical explanation for this flexibility. Further, we observe that the centromere-specific chaperone Holliday Junction Recognition Protein (HJURP) stabilizes the CENP-A/H4 dimer by forming a specific electrostatic interaction network. Finally, replacing CENP-A S68 with E68 disrupts the binding interface between CENP-A and HJURP in all-atom MD simulation, and consistently, in vivo experiments demonstrate that replacing CENP-A S68 with E68 disrupts CENP-A's localization to the centromere. Based on all our results, we propose that, during the CENP-A/H4 deposition process, the chaperone HJURP protects various substructures of the dimer, serving both as a folding and binding chaperone.
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Affiliation(s)
- Haiqing Zhao
- Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - David Winogradoff
- Chemical Physics Program, University of Maryland, College Park, Maryland 20742, United States
| | - Minh Bui
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Garegin A. Papoian
- Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
- Chemical Physics Program, University of Maryland, College Park, Maryland 20742, United States
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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22
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Jiang D, Berger F. Histone variants in plant transcriptional regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:123-130. [PMID: 27412913 DOI: 10.1016/j.bbagrm.2016.07.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/18/2016] [Accepted: 07/03/2016] [Indexed: 12/28/2022]
Abstract
Chromatin based organization of eukaryotic genome plays a profound role in regulating gene transcription. Nucleosomes form the basic subunits of chromatin by packaging DNA with histone proteins, impeding the access of DNA to transcription factors and RNA polymerases. Exchange of histone variants in nucleosomes alters the properties of nucleosomes and thus modulates DNA exposure during transcriptional regulation. Growing evidence indicates the important function of histone variants in programming transcription during developmental transitions and stress response. Here we review how histone variants and their deposition machineries regulate the nucleosome stability and dynamics, and discuss the link between histone variants and transcriptional regulation in plants. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Danhua Jiang
- Gregor Mendel Institute, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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23
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Foo SA, Byrne M. Acclimatization and Adaptive Capacity of Marine Species in a Changing Ocean. ADVANCES IN MARINE BIOLOGY 2016; 74:69-116. [PMID: 27573050 DOI: 10.1016/bs.amb.2016.06.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
To persist in an ocean changing in temperature, pH and other stressors related to climate change, many marine species will likely need to acclimatize or adapt to avoid extinction. If marine populations possess adequate genetic variation in tolerance to climate change stressors, species might be able to adapt to environmental change. Marine climate change research is moving away from single life stage studies where individuals are directly placed into projected scenarios ('future shock' approach), to focus on the adaptive potential of populations in an ocean that will gradually change over coming decades. This review summarizes studies that consider the adaptive potential of marine invertebrates to climate change stressors and the methods that have been applied to this research, including quantitative genetics, laboratory selection studies and trans- and multigenerational experiments. Phenotypic plasticity is likely to contribute to population persistence providing time for genetic adaptation to occur. Transgenerational and epigenetic effects indicate that the environmental and physiological history of the parents can affect offspring performance. There is a need for long-term, multigenerational experiments to determine the influence of phenotypic plasticity, genetic variation and transgenerational effects on species' capacity to persist in a changing ocean. However, multigenerational studies are only practicable for short generation species. Consideration of multiple morphological and physiological traits, including changes in molecular processes (eg, DNA methylation) and long-term studies that facilitate acclimatization will be essential in making informed predictions of how the seascape and marine communities will be altered by climate change.
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Affiliation(s)
- S A Foo
- School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia.
| | - M Byrne
- Schools of Medical and Biological Sciences, The University of Sydney, Sydney, NSW, Australia
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24
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Rea M, Jiang T, Eleazer R, Eckstein M, Marshall AG, Fondufe-Mittendorf YN. Quantitative Mass Spectrometry Reveals Changes in Histone H2B Variants as Cells Undergo Inorganic Arsenic-Mediated Cellular Transformation. Mol Cell Proteomics 2016; 15:2411-22. [PMID: 27169413 PMCID: PMC4937513 DOI: 10.1074/mcp.m116.058412] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 05/09/2016] [Indexed: 11/06/2022] Open
Abstract
Exposure to inorganic arsenic, a ubiquitous environmental toxic metalloid, leads to carcinogenesis. However, the mechanism is unknown. Several studies have shown that inorganic arsenic exposure alters specific gene expression patterns, possibly through alterations in chromatin structure. While most studies on understanding the mechanism of chromatin-mediated gene regulation have focused on histone post-translational modifications, the role of histone variants remains largely unknown. Incorporation of histone variants alters the functional properties of chromatin. To understand the global dynamics of chromatin structure and function in arsenic-mediated carcinogenesis, analysis of the histone variants incorporated into the nucleosome and their covalent modifications is required. Here we report the first global mass spectrometric analysis of histone H2B variants as cells undergo arsenic-mediated epithelial to mesenchymal transition. We used electron capture dissociation-based top-down tandem mass spectrometry analysis validated with quantitative reverse transcription real-time polymerase chain reaction to identify changes in the expression levels of H2B variants in inorganic arsenic-mediated epithelial-mesenchymal transition. We identified changes in the expression levels of specific histone H2B variants in two cell types, which are dependent on dose and length of exposure of inorganic arsenic. In particular, we found increases in H2B variants H2B1H/1K/1C/1J/1O and H2B2E/2F, and significant decreases in H2B1N/1D/1B as cells undergo inorganic arsenic-mediated epithelial-mesenchymal transition. The analysis of these histone variants provides a first step toward an understanding of the functional significance of the diversity of histone structures, especially in inorganic arsenic-mediated gene expression and carcinogenesis.
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Affiliation(s)
- Matthew Rea
- From the ‡Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536
| | - Tingting Jiang
- §Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Rebekah Eleazer
- From the ‡Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536
| | - Meredith Eckstein
- From the ‡Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536
| | - Alan G Marshall
- §Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306; ¶Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310
| | - Yvonne N Fondufe-Mittendorf
- From the ‡Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536;
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25
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Yildirim O, Kingston RE. Molecular Dissection of Chromatin Maturation via Click Chemistry. ACTA ACUST UNITED AC 2016; 114:21.33.1-21.33.11. [PMID: 27038388 DOI: 10.1002/0471142727.mb2133s114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
DNA synthesis and chromatin assembly are the two most critical processes of eukaryotic cell division. It is well known that their coordination is tightly regulated. Although the interplay between DNA and its higher-order chromatin state is integral for many processes, including cell survival and genome stability, little is known about the re-establishment of chromatin structure during the cell cycle. Moreover, the extent to which the fidelity of the newly synthesized chromatin plays a role in the maintenance of cellular identity is still under debate. Here, we present a novel approach to purify nascent chromatin from the replication fork. In this protocol, we take advantage of click chemistry, a method that allows efficient conjugation of azide-containing biotin molecules to ethynyl-labeled nucleic acids. Using this approach, we selectively enrich biotin-nucleic acid conjugates via streptavidin affinity purification to pull down and assess chromatin states as well as chromatin-bound complexes from newly replicated DNA fragments.
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Affiliation(s)
- Ozlem Yildirim
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
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Yasueda Y, Tamura T, Hamachi I. Nucleus-selective Chemical Proteomics Using Hoechst-tagged Reactive Molecules. CHEM LETT 2016. [DOI: 10.1246/cl.151083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yuki Yasueda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency
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Urahama T, Harada A, Maehara K, Horikoshi N, Sato K, Sato Y, Shiraishi K, Sugino N, Osakabe A, Tachiwana H, Kagawa W, Kimura H, Ohkawa Y, Kurumizaka H. Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis. Epigenetics Chromatin 2016; 9:2. [PMID: 26779285 PMCID: PMC4714512 DOI: 10.1186/s13072-016-0051-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 01/05/2016] [Indexed: 11/19/2022] Open
Abstract
Background Human histone H3.5 is a non-allelic H3 variant evolutionally derived from H3.3. The H3.5 mRNA is highly expressed in human testis. However, the function of H3.5 has remained poorly understood. Results We found that the H3.5 nucleosome is less stable than the H3.3 nucleosome. The crystal structure of the H3.5 nucleosome showed that the H3.5-specific Leu103 residue, which corresponds to the H3.3 Phe104 residue, reduces the hydrophobic interaction with histone H4. Mutational analyses revealed that the H3.5-specific Leu103 residue is responsible for the instability of the H3.5 nucleosome, both in vitro and in living cells. The H3.5 protein was present in human seminiferous tubules, but little to none was found in mature sperm. A chromatin immunoprecipitation coupled with sequencing analysis revealed that H3.5 accumulated around transcription start sites (TSSs) in testicular cells. Conclusions We performed comprehensive studies of H3.5, and found the instability of the H3.5 nucleosome and the accumulation of H3.5 protein around TSSs in human testis. The unstable H3.5 nucleosome may function in the chromatin dynamics around the TSSs, during spermatogenesis.
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Affiliation(s)
- Takashi Urahama
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582 Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582 Japan
| | - Naoki Horikoshi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan
| | - Koichi Sato
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan
| | - Yuko Sato
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Koji Shiraishi
- Faculty of Medicine and Health Sciences, Yamaguchi University, 1-1-1 Minami-Kogushi, Ube, 755-8505 Japan
| | - Norihiro Sugino
- Faculty of Medicine and Health Sciences, Yamaguchi University, 1-1-1 Minami-Kogushi, Ube, 755-8505 Japan
| | - Akihisa Osakabe
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan
| | - Hiroaki Tachiwana
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan
| | - Wataru Kagawa
- Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-8506 Japan
| | - Hiroshi Kimura
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582 Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan
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28
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Gomez D, Swiatlowska P, Owens GK. Epigenetic Control of Smooth Muscle Cell Identity and Lineage Memory. Arterioscler Thromb Vasc Biol 2015; 35:2508-16. [PMID: 26449751 PMCID: PMC4662608 DOI: 10.1161/atvbaha.115.305044] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/23/2015] [Indexed: 12/31/2022]
Abstract
Vascular smooth muscle cells (SMCs), like all cells, acquire a cell-specific epigenetic signature during development that includes acquisition of a unique repertoire of histone and DNA modifications. These changes are postulated to induce an open chromatin state (referred to as euchromatin) on the repertoire of genes that are expressed in differentiated SMC, including SMC-selective marker genes like Acta2 and Myh11, as well as housekeeping genes expressed by most cell types. In contrast, genes that are silenced in differentiated SMC acquire modifications associated with a closed chromatin state (ie, heterochromatin) and transcriptional silencing. Herein, we review mechanisms that regulate epigenetic control of the differentiated state of SMC. In addition, we identify some of the major limitations in the field and future challenges, including development of innovative new tools and approaches, for performing single-cell epigenetic assays and locus-selective editing of the epigenome that will allow direct studies of the functional role of specific epigenetic controls during development, injury repair, and disease, including major cardiovascular diseases, such as atherosclerosis, hypertension, and microvascular disease, associated with diabetes mellitus.
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MESH Headings
- Animals
- Cardiovascular Diseases/genetics
- Cardiovascular Diseases/metabolism
- Cardiovascular Diseases/pathology
- Cardiovascular Diseases/physiopathology
- Cell Differentiation/genetics
- Cell Lineage/drug effects
- Chromatin Assembly and Disassembly
- Embryonic Stem Cells/metabolism
- Embryonic Stem Cells/pathology
- Epigenesis, Genetic
- Epigenomics/methods
- Gene Expression Regulation, Developmental
- Genetic Markers
- Humans
- Muscle Development/genetics
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Muscle, Smooth, Vascular/physiopathology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Phenotype
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Affiliation(s)
- Delphine Gomez
- From the Department of Molecular Physiology and Biological Physics (D.G., G.K.O.), and Robert M. Berne Cardiovascular Research Center (P.S.), University of Virginia School of Medicine, Charlottesville
| | - Pamela Swiatlowska
- From the Department of Molecular Physiology and Biological Physics (D.G., G.K.O.), and Robert M. Berne Cardiovascular Research Center (P.S.), University of Virginia School of Medicine, Charlottesville
| | - Gary K Owens
- From the Department of Molecular Physiology and Biological Physics (D.G., G.K.O.), and Robert M. Berne Cardiovascular Research Center (P.S.), University of Virginia School of Medicine, Charlottesville.
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Abstract
Eukaryotic replication disrupts each nucleosome as the fork passes, followed by re-assembly of disrupted nucleosomes and incorporation of newly synthesized histones into nucleosomes in the daughter genomes. In this review, we examine this process of replication-coupled nucleosome assembly to understand how characteristic steady state nucleosome landscapes are attained. Recent studies have begun to elucidate mechanisms involved in histone transfer during replication and maturation of the nucleosome landscape after disruption by replication. A fuller understanding of replication-coupled nucleosome assembly will be needed to explain how epigenetic information is replicated at every cell division.
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Affiliation(s)
- Srinivas Ramachandran
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Corresponding author. E-mail:
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30
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Abstract
Histone variants are an important part of the histone contribution to chromatin epigenetics. In this review, we describe how the known structural differences of these variants from their canonical histone counterparts impart a chromatin signature ultimately responsible for their epigenetic contribution. In terms of the core histones, H2A histone variants are major players while H3 variant CenH3, with a controversial role in the nucleosome conformation, remains the genuine epigenetic histone variant. Linker histone variants (histone H1 family) haven’t often been studied for their role in epigenetics. However, the micro-heterogeneity of the somatic canonical forms of linker histones appears to play an important role in maintaining the cell-differentiated states, while the cell cycle independent linker histone variants are involved in development. A picture starts to emerge in which histone H2A variants, in addition to their individual specific contributions to the nucleosome structure and dynamics, globally impair the accessibility of linker histones to defined chromatin locations and may have important consequences for determining different states of chromatin metabolism.
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Affiliation(s)
- Manjinder S Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W-3P6, Canada.
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W-3P6, Canada.
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31
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Kawashima T, Lorković ZJ, Nishihama R, Ishizaki K, Axelsson E, Yelagandula R, Kohchi T, Berger F. Diversification of histone H2A variants during plant evolution. TRENDS IN PLANT SCIENCE 2015; 20:419-25. [PMID: 25983206 DOI: 10.1016/j.tplants.2015.04.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/11/2015] [Accepted: 04/13/2015] [Indexed: 05/19/2023]
Abstract
Among eukaryotes, the four core histones show an extremely high conservation of their structure and form nucleosomes that compact, protect, and regulate access to genetic information. Nevertheless, in multicellular eukaryotes the two families, histone H2A and histone H3, have diversified significantly in key residues. We present a phylogenetic analysis across the green plant lineage that reveals an early diversification of the H2A family in unicellular green algae and remarkable expansions of H2A variants in flowering plants. We define motifs and domains that differentiate plant H2A proteins into distinct variant classes. In non-flowering land plants, we identify a new class of H2A variants and propose their possible role in the emergence of the H2A.W variant class in flowering plants.
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Affiliation(s)
- Tomokazu Kawashima
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Zdravko J Lorković
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | | | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Ramesh Yelagandula
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Frederic Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Dr. Bohrgasse 3, 1030 Vienna, Austria.
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32
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Borg M, Berger F. Chromatin remodelling during male gametophyte development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:177-188. [PMID: 25892182 DOI: 10.1111/tpj.12856] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/10/2015] [Accepted: 04/14/2015] [Indexed: 05/28/2023]
Abstract
The plant life cycle alternates between a diploid sporophytic phase and haploid gametophytic phase, with the latter giving rise to the gametes. Male gametophyte development encompasses two mitotic divisions that results in a simple three-celled structure knows as the pollen grain, in which two sperm cells are encased within a larger vegetative cell. Both cell types exhibit a very different type of chromatin organization - highly condensed in sperm cell nuclei and highly diffuse in the vegetative cell. Distinct classes of histone variants have dynamic and differential expression in the two cell lineages of the male gametophyte. Here we review how the dynamics of histone variants are linked to reprogramming of chromatin activities in the male gametophyte, compaction of the sperm cell genome and zygotic transitions post-fertilization.
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Affiliation(s)
- Michael Borg
- Gregor Mendel Institute, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030, Vienna, Austria
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33
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Saade E, Pirozhkova I, Aimbetov R, Lipinski M, Ogryzko V. Molecular turnover, the H3.3 dilemma and organismal aging (hypothesis). Aging Cell 2015; 14:322-33. [PMID: 25720734 PMCID: PMC4406661 DOI: 10.1111/acel.12332] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2015] [Indexed: 12/22/2022] Open
Abstract
The H3.3 histone variant has been a subject of increasing interest in the field of chromatin studies due to its two distinguishing features. First, its incorporation into chromatin is replication independent unlike the replication-coupled deposition of its canonical counterparts H3.1/2. Second, H3.3 has been consistently associated with an active state of chromatin. In accordance, this histone variant should be expected to be causally involved in the regulation of gene expression, or more generally, its incorporation should have downstream consequences for the structure and function of chromatin. This, however, leads to an apparent paradox: In cells that slowly replicate in the organism, H3.3 will accumulate with time, opening the way to aberrant effects on heterochromatin. Here, we review the indications that H3.3 is expected both to be incorporated in the heterochromatin of slowly replicating cells and to retain its functional downstream effects. Implications for organismal aging are discussed.
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Affiliation(s)
- Evelyne Saade
- Faculty of Public Health Lebanese University LU Beirut Lebanon
| | - Iryna Pirozhkova
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
| | - Rakhan Aimbetov
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
| | - Marc Lipinski
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
| | - Vasily Ogryzko
- Institute Gustave Roussy University Paris SUD 114, rue Edouard Vaillant Villejuif 94805France
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34
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Molden RC, Bhanu NV, LeRoy G, Arnaudo AM, Garcia BA. Multi-faceted quantitative proteomics analysis of histone H2B isoforms and their modifications. Epigenetics Chromatin 2015; 8:15. [PMID: 25922622 PMCID: PMC4411797 DOI: 10.1186/s13072-015-0006-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 03/25/2015] [Indexed: 01/01/2023] Open
Abstract
Background Histone isoforms and their post-translational modifications (PTMs) play an important role in the control of many chromatin-related processes including transcription and DNA damage. Variants of histones H2A and H3 have been studied in depth and have been found to have distinct functions. Although 13 somatic histone H2B isoforms have been identified by various biochemical and mass spectrometric (MS) approaches, the distinct roles of these isoforms within human cells are as yet unknown. Here, we have developed quantitative MS techniques to characterize isoform-specific H2B expression across the cell cycle, in differentiated myogenic cells, and in different cancer cell lines to illuminate potential functional roles. Results Using the MS strategies that we developed, we identified differences in H2B isoform levels between different cancer cell types, suggesting cancer or tissue-specific H2B isoform regulation. In particular, we found large variations in the levels of isoforms H2B1B and H2B1M across the panel of cell lines. We also found that, while individual H2B isoforms do not differ in their acetylation levels, trends in the acetylation on all H2B isoforms correlated with acetylation on other histone family members in the cancer cell line panel. We also used the MS strategies to study H2B protein expression across the cell cycle and determined that H2B isoforms that are alternatively spliced to carry a polyadenylation signal rather than the standard histone downstream element are expressed independently of the cell cycle. However, the level of protein produced from the polyadenylated transcripts does not contribute significantly to the total pool of H2B isoforms translated across the cell cycle or in non-cycling myogenic cells. Conclusions Our results show that H2B isoforms are expressed at varying levels in different cells, suggesting isoform-specific, and possibly cell-type-specific, H2B gene regulation. The bottom-up mass spectrometry technique we developed for H2B quantification is compatible with the current standard histone H3 and H4 bottom-up ‘one-pot’ analysis platform so that H2B isoforms and their modifications can be studied in future experiments at the same time as histone H3 and H4 modifications. Therefore, we have expanded the histone landscape that can be interrogated in future experiments. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0006-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rosalynn C Molden
- Department of Chemistry, Princeton University, Princeton, NJ 08544 USA
| | - Natarajan V Bhanu
- Department of Biochemistry and Biophysics, Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Room 9-124, 3400 Civic Center Blvd., Bldg. 421, Philadelphia, PA 19104 USA
| | - Gary LeRoy
- Department of Chemistry, Princeton University, Princeton, NJ 08544 USA
| | - Anna M Arnaudo
- Department of Chemistry, Princeton University, Princeton, NJ 08544 USA ; Department of Biochemistry and Biophysics, Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Room 9-124, 3400 Civic Center Blvd., Bldg. 421, Philadelphia, PA 19104 USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Room 9-124, 3400 Civic Center Blvd., Bldg. 421, Philadelphia, PA 19104 USA
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35
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Abstract
Genetic and epigenetic changes are at the root of all cancers. The epigenetic component involves alterations of the post-synthetic modifications of DNA (methylation) and histones (histone posttranslational modifications, PTMs) as well as of those of their molecular "writers," "readers," and "erasers." Noncoding RNAs (ncRNA) can also play a role. Here, we focus on the involvement of histone alterations in cancer, in particular that of the histone variant H2A.Z in the etiology of prostate cancer. The structural mechanisms putatively responsible for the contribution of H2A.Z to oncogenic gene expression programs are first described, followed by what is currently known about the involvement of this histone variant in the regulation of androgen receptor regulated gene expression. The implications of this and their relevance to oncogene deregulation in different stages of prostate cancer, including the progression toward androgen independence, are discussed. This review underscores the increasing awareness of the epigenetic contribution of histone variants to oncogenic progression.
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Affiliation(s)
- Deanna Dryhurst
- Department of Biochemistry and Microbiology, University of Victoria, Petch building, 258a, Victoria, British Columbia Canada V8W 3P6
- ImmunoPrecise Antibodies Ltd., 3204-4464 Markham St., Victoria, British Columbia Canada V8Z 7X8
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Petch building, 258a, Victoria, British Columbia Canada V8W 3P6
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Landgrave-Gómez J, Mercado-Gómez O, Guevara-Guzmán R. Epigenetic mechanisms in neurological and neurodegenerative diseases. Front Cell Neurosci 2015; 9:58. [PMID: 25774124 PMCID: PMC4343006 DOI: 10.3389/fncel.2015.00058] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 02/06/2015] [Indexed: 11/13/2022] Open
Abstract
The role of epigenetic mechanisms in the function and homeostasis of the central nervous system (CNS) and its regulation in diseases is one of the most interesting processes of contemporary neuroscience. In the last decade, a growing body of literature suggests that long-term changes in gene transcription associated with CNS's regulation and neurological disorders are mediated via modulation of chromatin structure. "Epigenetics", introduced for the first time by Waddington in the early 1940s, has been traditionally referred to a variety of mechanisms that allow heritable changes in gene expression even in the absence of DNA mutation. However, new definitions acknowledge that many of these mechanisms used to perpetuate epigenetic traits in dividing cells are used by neurons to control a variety of functions dependent on gene expression. Indeed, in the recent years these mechanisms have shown their importance in the maintenance of a healthy CNS. Moreover, environmental inputs that have shown effects in CNS diseases, such as nutrition, that can modulate the concentration of a variety of metabolites such as acetyl-coenzyme A (acetyl-coA), nicotinamide adenine dinucleotide (NAD(+)) and beta hydroxybutyrate (β-HB), regulates some of these epigenetic modifications, linking in a precise way environment with gene expression. This manuscript will portray what is currently understood about the role of epigenetic mechanisms in the function and homeostasis of the CNS and their participation in a variety of neurological disorders. We will discuss how the machinery that controls these modifications plays an important role in processes involved in neurological disorders such as neurogenesis and cell growth. Moreover, we will discuss how environmental inputs modulate these modifications producing metabolic and physiological alterations that could exert beneficial effects on neurological diseases. Finally, we will highlight possible future directions in the field of epigenetics and neurological disorders.
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Affiliation(s)
- Jorge Landgrave-Gómez
- Facultad de Medicina, Departamento de Fisiología, Universidad Nacional Autónoma de MéxicoMéxico, D.F., México
| | - Octavio Mercado-Gómez
- Facultad de Medicina, Departamento de Fisiología, Universidad Nacional Autónoma de MéxicoMéxico, D.F., México
| | - Rosalinda Guevara-Guzmán
- Facultad de Medicina, Departamento de Fisiología, Universidad Nacional Autónoma de MéxicoMéxico, D.F., México
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37
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Histone variants: the artists of eukaryotic chromatin. SCIENCE CHINA-LIFE SCIENCES 2015; 58:232-9. [DOI: 10.1007/s11427-015-4817-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 01/23/2015] [Indexed: 10/24/2022]
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38
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Kraushaar DC, Jin W, Maunakea A, Abraham B, Ha M, Zhao K. Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3. Genome Biol 2014; 14:R121. [PMID: 24176123 PMCID: PMC3983652 DOI: 10.1186/gb-2013-14-10-r121] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/31/2013] [Indexed: 11/16/2022] Open
Abstract
Background Nucleosomes are present throughout the genome and must be dynamically regulated to accommodate binding of transcription factors and RNA polymerase machineries by various mechanisms. Despite the development of protocols and techniques that have enabled us to map nucleosome occupancy genome-wide, the dynamic properties of nucleosomes remain poorly understood, particularly in mammalian cells. The histone variant H3.3 is incorporated into chromatin independently of DNA replication and requires displacement of existing nucleosomes for its deposition. Here, we measure H3.3 turnover at high resolution in the mammalian genome in order to present a genome-wide characterization of replication-independent H3.3-nucleosome dynamics. Results We developed a system to study the DNA replication-independent turnover of nucleosomes containing the histone variant H3.3 in mammalian cells. By measuring the genome-wide incorporation of H3.3 at different time points following epitope-tagged H3.3 expression, we find three categories of H3.3-nucleosome turnover in vivo: rapid turnover, intermediate turnover and, specifically at telomeres, slow turnover. Our data indicate that H3.3-containing nucleosomes at enhancers and promoters undergo rapid turnover that is associated with active histone modification marks including H3K4me1, H3K4me3, H3K9ac, H3K27ac and the histone variant H2A.Z. The rate of turnover is negatively correlated with H3K27me3 at regulatory regions and with H3K36me3 at gene bodies. Conclusions We have established a reliable approach to measure turnover rates of H3.3-containing nucleosomes on a genome-wide level in mammalian cells. Our results suggest that distinct mechanisms control the dynamics of H3.3 incorporation at functionally different genomic regions.
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Lewis CR, Olive MF. Early-life stress interactions with the epigenome: potential mechanisms driving vulnerability toward psychiatric illness. Behav Pharmacol 2014; 25:341-51. [PMID: 25003947 PMCID: PMC4119485 DOI: 10.1097/fbp.0000000000000057] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Throughout the 20th century a body of literature concerning the long-lasting effects of the early environment was produced. Adverse experiences in early life, or early-life stress (ELS), is associated with a higher risk of developing various psychiatric illnesses. The mechanisms driving the complex interplay between ELS and adult phenotype has baffled many investigators for decades. Over the last decade, the new field of neuroepigenetics has emerged as one possible mechanism by which ELS can have far-reaching effects on adult phenotype, behavior, and risk for psychiatric illness. Here we review two commonly investigated epigenetic mechanisms, histone modifications and DNA methylation, and the emerging field of neuroepigenetics as they relate to ELS. We discuss the current animal literature demonstrating ELS-induced epigenetic modulation of gene expression that results in altered adult phenotypes. We also briefly discuss other areas in which neuroepigenetics has emerged as a potential mechanism underlying environmental and genetic interactions.
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Affiliation(s)
- Candace Renee Lewis
- Arizona State University, Tempe, AZ, 930 S McAllister Ave, Tempe, AZ 85281, , Phone: (602) 680 – 8786
| | - Michael Foster Olive
- Arizona State University, Tempe, AZ, 930 S McAllister Ave, Tempe, AZ 85281, , Phone: (480) 727-9557
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Cossetti C, Lugini L, Astrologo L, Saggio I, Fais S, Spadafora C. Soma-to-germline transmission of RNA in mice xenografted with human tumour cells: possible transport by exosomes. PLoS One 2014; 9:e101629. [PMID: 24992257 PMCID: PMC4081593 DOI: 10.1371/journal.pone.0101629] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 06/10/2014] [Indexed: 12/21/2022] Open
Abstract
Mendelian laws provide the universal founding paradigm for the mechanism of genetic inheritance through which characters are segregated and assorted. In recent years, however, parallel with the rapid growth of epigenetic studies, cases of inheritance deviating from Mendelian patterns have emerged. Growing studies underscore phenotypic variations and increased risk of pathologies that are transgenerationally inherited in a non-Mendelian fashion in the absence of any classically identifiable mutation or predisposing genetic lesion in the genome of individuals who develop the disease. Non-Mendelian inheritance is most often transmitted through the germline in consequence of primary events occurring in somatic cells, implying soma-to-germline transmission of information. While studies of sperm cells suggest that epigenetic variations can potentially underlie phenotypic alterations across generations, no instance of transmission of DNA- or RNA-mediated information from somatic to germ cells has been reported as yet. To address these issues, we have now generated a mouse model xenografted with human melanoma cells stably expressing EGFP-encoding plasmid. We find that EGFP RNA is released from the xenografted human cells into the bloodstream and eventually in spermatozoa of the mice. Tumor-released EGFP RNA is associated with an extracellular fraction processed for exosome purification and expressing exosomal markers, in all steps of the process, from the xenografted cancer cells to the spermatozoa of the recipient animals, strongly suggesting that exosomes are the carriers of a flow of information from somatic cells to gametes. Together, these results indicate that somatic RNA is transferred to sperm cells, which can therefore act as the final recipients of somatic cell-derived information.
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Affiliation(s)
| | - Luana Lugini
- Unit of Antitumor Drugs, Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Letizia Astrologo
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University, Rome, Italy
| | - Isabella Saggio
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University, Rome, Italy
| | - Stefano Fais
- Unit of Antitumor Drugs, Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy
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41
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Rothbart SB, Strahl BD. Interpreting the language of histone and DNA modifications. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:627-43. [PMID: 24631868 DOI: 10.1016/j.bbagrm.2014.03.001] [Citation(s) in RCA: 467] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 02/14/2014] [Accepted: 03/04/2014] [Indexed: 01/10/2023]
Abstract
A major mechanism regulating the accessibility and function of eukaryotic genomes are the covalent modifications to DNA and histone proteins that dependably package our genetic information inside the nucleus of every cell. Formally postulated over a decade ago, it is becoming increasingly clear that post-translational modifications (PTMs) on histones act singly and in combination to form a language or 'code' that is read by specialized proteins to facilitate downstream functions in chromatin. Underappreciated at the time was the level of complexity harbored both within histone PTMs and their combinations, as well as within the proteins that read and interpret the language. In addition to histone PTMs, newly-identified DNA modifications that can recruit specific effector proteins have raised further awareness that histone PTMs operate within a broader language of epigenetic modifications to orchestrate the dynamic functions associated with chromatin. Here, we highlight key recent advances in our understanding of the epigenetic language encompassing histone and DNA modifications and foreshadow challenges that lie ahead as we continue our quest to decipher the fundamental mechanisms of chromatin regulation. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Scott B Rothbart
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brian D Strahl
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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42
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Mao Z, Pan L, Wang W, Sun J, Shan S, Dong Q, Liang X, Dai L, Ding X, Chen S, Zhang Z, Zhu B, Zhou Z. Anp32e, a higher eukaryotic histone chaperone directs preferential recognition for H2A.Z. Cell Res 2014; 24:389-99. [PMID: 24613878 PMCID: PMC3975505 DOI: 10.1038/cr.2014.30] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 01/22/2014] [Accepted: 01/25/2014] [Indexed: 12/17/2022] Open
Abstract
H2A.Z is a highly conserved histone variant in all species. The chromatin deposition of H2A.Z is specifically catalyzed by the yeast chromatin remodeling complex SWR1 and its mammalian counterpart SRCAP. However, the mechanism by which H2A.Z is preferentially recognized by non-histone proteins remains elusive. Here we identified Anp32e, a novel higher eukaryote-specific histone chaperone for H2A.Z. Anp32e preferentially associates with H2A.Z-H2B dimers rather than H2A-H2B dimers in vitro and in vivo and dissociates non-nucleosomal aggregates formed by DNA and H2A-H2B. We determined the crystal structure of the Anp32e chaperone domain (186-232) in complex with the H2A.Z-H2B dimer. In this structure, the region containing Anp32e residues 214-224, which is absent in other Anp32 family proteins, specifically interacts with the extended H2A.Z αC helix, which exhibits an unexpected conformational change. Genome-wide profiling of Anp32e revealed a remarkable co-occupancy between Anp32e and H2A.Z. Cells overexpressing Anp32e displayed a strong global H2A.Z loss at the +1 nucleosomes, whereas cells depleted of Anp32e displayed a moderate global H2A.Z increase at the +1 nucleosomes. This suggests that Anp32e may help to resolve the non-nucleosomal H2A.Z aggregates and also facilitate the removal of H2A.Z at the +1 nucleosomes, and the latter may help RNA polymerase II to pass the first nucleosomal barrier.
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Affiliation(s)
- Zhuo Mao
- 1] Graduate Program, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China [2] National Institute of Biological Sciences, Beijing 102206, China
| | - Lu Pan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Weixiang Wang
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Jian Sun
- National Institute of Biological Sciences, Beijing 102206, China
| | - Shan Shan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xiaoping Liang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Linchang Dai
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaojun Ding
- National Institute of Biological Sciences, Beijing 102206, China
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | - Zhuqiang Zhang
- 1] National Institute of Biological Sciences, Beijing 102206, China [2] National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhu
- 1] Graduate Program, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China [2] National Institute of Biological Sciences, Beijing 102206, China [3] National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zheng Zhou
- 1] National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China [2] Center for Age-related Diseases, Peking University Health Science Center, Beijing 100191, China
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43
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Histone variants and epigenetic inheritance. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1819:222-229. [PMID: 24459724 DOI: 10.1016/j.bbagrm.2011.06.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nucleosome particles, which are composed of core histones and DNA, are the basic unit of eukaryotic chromatin. Histone modifications and histone composition determine the structure and function of the chromatin; this genome packaging, often referred to as "epigenetic information", provides additional information beyond the underlying genomic sequence. The epigenetic information must be transmitted from mother cells to daughter cells during mitotic division to maintain the cell lineage identity and proper gene expression. However, the mechanisms responsible for mitotic epigenetic inheritance remain largely unknown. In this review, we focus on recent studies regarding histone variants and discuss the assembly pathways that may contribute to epigenetic inheritance. This article is part of a Special Issue entitled: Histone chaperones and Chromatin assembly.
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44
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Asymmetric distribution of histones during Drosophila male germline stem cell asymmetric divisions. Chromosome Res 2014; 21:255-69. [PMID: 23681658 DOI: 10.1007/s10577-013-9356-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
It has long been known that epigenetic changes are inheritable. However, except for DNA methylation, little is known about the molecular mechanisms of epigenetic inheritance. Many types of stem cells undergo asymmetric cell divisions to generate self-renewed stem cells and daughter cells committed for differentiation. Still, whether and how stem cells retain their epigenetic memory remain questions to be elucidated. During the asymmetric division of Drosophila male germline stem cell (GSC), our recent studies revealed that the preexisting histone 3 (H3) are selectively segregated to the GSC, whereas newly synthesized H3 deposited during DNA replication are enriched in the differentiating daughter cell. We propose a two-step model to explain this asymmetric histone distribution. First, prior to mitosis, preexisting histones and newly synthesized histones are differentially distributed at two sets of sister chromatids. Next, during mitosis, the set of sister chromatids that mainly consist of preexisting histones are segregated to GSCs, while the other set of sister chromatids enriched with newly synthesized histones are partitioned to the daughter cell committed for differentiation. In this review, we apply current knowledge about epigenetic inheritance and asymmetric cell division to inform our discussion of potential molecular mechanisms and the cellular basis underlying this asymmetric histone distribution pattern. We will also discuss whether this phenomenon contributes to the maintenance of stem cell identity and resetting chromatin structure in the other daughter cell for differentiation.
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45
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Sandoval J, Peiró-Chova L, Pallardó FV, García-Giménez JL. Epigenetic biomarkers in laboratory diagnostics: emerging approaches and opportunities. Expert Rev Mol Diagn 2013; 13:457-71. [PMID: 23782253 DOI: 10.1586/erm.13.37] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetics has emerged as a new and promising field in recent years. Lifestyle, stress, drugs, physiopathological situations and pharmacological interventions have a great impact on the epigenetic code of the cells by altering the methylome, miRNA expression and the covalent histone modifications. Since there exists a need to find new biomarkers and improve diagnosis for several diseases, the research on epigenetic biomarkers for molecular diagnostics encourages the translation of this field from the bench to clinical practice. In this context, deciphering intricate epigenetic modifications involved in several molecular processes is a challenge that will be solved in the near future. In this review, the authors present an overview of the high-throughput technologies and laboratory techniques available for epigenetic studies, and also discuss which of them are more reliable to be used in a clinical diagnostic laboratory. In addition, the authors describe the most promising epigenetic biomarkers in lung, colorectal and prostate cancer, in which most advances have been achieved. Finally, the authors describe epigenetic biomarkers in some rare diseases; these rare syndromes are paradigms for a specific impaired molecular pathway, thus providing valuable information on the discovery of new epigenetic biomarkers.
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Affiliation(s)
- Juan Sandoval
- Epigenetics and Cancer Biology, Institut d'Investigació Biomèdica de Bellvitge IDIBELL, Barcelona, Spain
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46
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Kadyrova LY, Rodriges Blanko E, Kadyrov FA. Human CAF-1-dependent nucleosome assembly in a defined system. Cell Cycle 2013; 12:3286-97. [PMID: 24036545 PMCID: PMC3885639 DOI: 10.4161/cc.26310] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Replication-coupled nucleosome assembly is a critical step in packaging newly synthesized DNA into chromatin. Previous studies have defined the importance of the histone chaperones CAF-1 and ASF1A, the replicative clamp PCNA, and the clamp loader RFC for the assembly of nucleosomes during DNA replication. Despite significant progress in the field, replication-coupled nucleosome assembly is not well understood. One of the complications in elucidating the mechanisms of replication-coupled nucleosome assembly is the lack of a defined system that faithfully recapitulates this important biological process in vitro. We describe here a defined system that assembles nucleosomal arrays in a manner dependent on the presence of CAF-1, ASF1A-H3-H4, H2A-H2B, PCNA, RFC, NAP1L1, ATP, and strand breaks. The loss of CAF-1 p48 subunit causes a strong defect in packaging DNA into nucleosomes by this system. We also show that the defined system forms nucleosomes on nascent DNA synthesized by the replicative polymerase δ. Thus, the developed system reproduces several key features of replication-coupled nucleosome assembly.
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Affiliation(s)
- Lyudmila Y Kadyrova
- Department of Biochemistry and Molecular Biology; Southern Illinois University School of Medicine; Carbondale, IL USA
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47
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Singh R, Mortazavi A, Telu KH, Nagarajan P, Lucas DM, Thomas-Ahner JM, Clinton SK, Byrd JC, Freitas MA, Parthun MR. Increasing the complexity of chromatin: functionally distinct roles for replication-dependent histone H2A isoforms in cell proliferation and carcinogenesis. Nucleic Acids Res 2013; 41:9284-95. [PMID: 23956221 PMCID: PMC3814372 DOI: 10.1093/nar/gkt736] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Replication-dependent histones are encoded by multigene families found in several large clusters in the human genome and are thought to be functionally redundant. However, the abundance of specific replication-dependent isoforms of histone H2A is altered in patients with chronic lymphocytic leukemia. Similar changes in the abundance of H2A isoforms are also associated with the proliferation and tumorigenicity of bladder cancer cells. To determine whether these H2A isoforms can perform distinct functions, expression of several H2A isoforms was reduced by siRNA knockdown. Reduced expression of the HIST1H2AC locus leads to increased rates of cell proliferation and tumorigenicity. We also observe that regulation of replication-dependent histone H2A expression can occur on a gene-specific level. Specific replication-dependent histone H2A genes are either up- or downregulated in chronic lymphocytic leukemia tumor tissue samples. In addition, discreet elements are identified in the 5′ untranslated region of the HIST1H2AC locus that confer translational repression. Taken together, these results indicate that replication-dependent histone isoforms can possess distinct cellular functions and that regulation of these isoforms may play a role in carcinogenesis.
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Affiliation(s)
- Rajbir Singh
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA
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48
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Yu Y, Deng Y, Reed SH, Millar CB, Waters R. Histone variant Htz1 promotes histone H3 acetylation to enhance nucleotide excision repair in Htz1 nucleosomes. Nucleic Acids Res 2013; 41:9006-19. [PMID: 23925126 PMCID: PMC3799447 DOI: 10.1093/nar/gkt688] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Nucleotide excision repair (NER) is critical for maintaining genome integrity. How chromatin dynamics are regulated to facilitate this process in chromatin is still under exploration. We show here that a histone H2A variant, Htz1 (H2A.Z), in nucleosomes has a positive function in promoting efficient NER in yeast. Htz1 inherently enhances the occupancy of the histone acetyltransferase Gcn5 on chromatin to promote histone H3 acetylation after UV irradiation. Consequently, this results in an increased binding of a NER protein, Rad14, to damaged DNA. Cells without Htz1 show increased UV sensitivity and defective removal of UV-induced DNA damage in the Htz1-bearing nucleosomes at the repressed MFA2 promoter, but not in the HMRa locus where Htz1 is normally absent. Thus, the effect of Htz1 on NER is specifically relevant to its presence in chromatin within a damaged region. The chromatin accessibility to micrococcal nuclease in the MFA2 promoter is unaffected by HTZ1 deletion. Acetylation on previously identified lysines of Htz1 plays little role in NER or cell survival after UV. In summary, we have identified a novel aspect of chromatin that regulates efficient NER, and we provide a model for how Htz1 influences NER in Htz1 nucleosomes.
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Affiliation(s)
- Yachuan Yu
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK and Faculty of Life Sciences, Michael Smith Building, University of Manchester, Manchester M13 9PT, UK
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49
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Jaeger S, Fernandez B, Ferrier P. Epigenetic aspects of lymphocyte antigen receptor gene rearrangement or 'when stochasticity completes randomness'. Immunology 2013; 139:141-50. [PMID: 23278765 DOI: 10.1111/imm.12057] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 01/05/2023] Open
Abstract
To perform their specific functional role, B and T lymphocytes, cells of the adaptive immune system of jawed vertebrates, need to express one (and, preferably, only one) form of antigen receptor, i.e. the immunoglobulin or T-cell receptor (TCR), respectively. This end goal depends initially on a series of DNA cis-rearrangement events between randomly chosen units from separate clusters of V, D (at some immunoglobulin and TCR loci) and J gene segments, a biomolecular process collectively referred to as V(D)J recombination. V(D)J recombination takes place in immature T and B cells and relies on the so-called RAG nuclease, a site-specific DNA cleavage apparatus that corresponds to the lymphoid-specific moiety of the VDJ recombinase. At the genome level, this recombinase's mission presents substantial biochemical challenges. These relate to the huge distance between (some of) the gene segments that it eventually rearranges and the need to achieve cell-lineage-restricted and developmentally ordered routines with at times, mono-allelic versus bi-allelic discrimination. The entire process must be completed without any recombination errors, instigators of chromosome instability, translocation and, potentially, tumorigenesis. As expected, such a precisely choreographed and yet potentially risky process demands sophisticated controls; epigenetics demonstrates what is possible when calling upon its many facets. In this vignette, we will recall the evidence that almost from the start appeared to link the two topics, V(D)J recombination and epigenetics, before reviewing the latest advances in our knowledge of this joint venture.
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Affiliation(s)
- Sébastien Jaeger
- Centre d'Immunologie de Marseille-Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (Inserm) U1104, Centre National de la Recherche Scientifique (CNRS)UMR7280, Aix-Marseille University UM2, Marseille, France
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50
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Huang C, Xu M, Zhu B. Epigenetic inheritance mediated by histone lysine methylation: maintaining transcriptional states without the precise restoration of marks? Philos Trans R Soc Lond B Biol Sci 2013; 368:20110332. [PMID: 23166395 DOI: 10.1098/rstb.2011.0332] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
'Epigenetics' has been defined as the study of 'mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence'. Chromatin modifications are major carriers of epigenetic information that both reflect and affect the transcriptional states of underlying genes. Several histone modifications are key players that are responsible for classical epigenetic phenomena. However, the mechanisms by which cells pass their histone modifications to daughter cells through mitotic division remain to be unveiled. Here, we review recent progress in the field and conclude that epigenetic modifications are not precisely maintained at a near-mononucleosome level of precision. We also suggest that transcription repression may be maintained by a buffer system that can tolerate a certain degree of fluctuation in repressive histone modification levels. This buffer system protects the repressed genes from potential improper derepression triggered by chromatin modification-level fluctuation resulting from cellular events, such as the cell-cycle-dependent dilution of the chromatin modifications and local responses to environmental cues.
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Affiliation(s)
- Chang Huang
- College of Biological Sciences, China Agricultural University, Beijing 100094, Republic of China
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