51
|
Jang CW, Shibata Y, Starmer J, Yee D, Magnuson T. Histone H3.3 maintains genome integrity during mammalian development. Genes Dev 2015; 29:1377-92. [PMID: 26159997 PMCID: PMC4511213 DOI: 10.1101/gad.264150.115] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 06/16/2015] [Indexed: 12/19/2022]
Abstract
Histone H3.3 is a highly conserved histone H3 replacement variant in metazoans and has been implicated in many important biological processes, including cell differentiation and reprogramming. Germline and somatic mutations in H3.3 genomic incorporation pathway components or in H3.3 encoding genes have been associated with human congenital diseases and cancers, respectively. However, the role of H3.3 in mammalian development remains unclear. To address this question, we generated H3.3-null mouse models through classical genetic approaches. We found that H3.3 plays an essential role in mouse development. Complete depletion of H3.3 leads to developmental retardation and early embryonic lethality. At the cellular level, H3.3 loss triggers cell cycle suppression and cell death. Surprisingly, H3.3 depletion does not dramatically disrupt gene regulation in the developing embryo. Instead, H3.3 depletion causes dysfunction of heterochromatin structures at telomeres, centromeres, and pericentromeric regions of chromosomes, leading to mitotic defects. The resulting karyotypical abnormalities and DNA damage lead to p53 pathway activation. In summary, our results reveal that an important function of H3.3 is to support chromosomal heterochromatic structures, thus maintaining genome integrity during mammalian development.
Collapse
Affiliation(s)
- Chuan-Wei Jang
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Yoichiro Shibata
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Joshua Starmer
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Della Yee
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Terry Magnuson
- Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| |
Collapse
|
52
|
Point mutations in an epigenetic factor lead to multiple types of bone tumors: role of H3.3 histone variant in bone development and disease. BONEKEY REPORTS 2015; 4:715. [PMID: 26157578 DOI: 10.1038/bonekey.2015.84] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 04/24/2015] [Indexed: 12/27/2022]
Abstract
Coordinated post-translational modifications (PTMs) of nucleosomal histones emerge as a key mechanism of gene regulation by defining chromatin configuration. Patterns of histone modifications vary in different cells and constitute core elements of cell-specific epigenomes. Recently, in addition to canonical histone proteins produced during the S phase of cell cycle, several non-canonical histone variants have been identified and shown to express in a DNA replication-independent manner. These histone variants generate diversity in nucleosomal structures and add further complexity to mechanisms of epigenetic regulation. Cell-specific functions of histone variants remain to be determined. Several recent studies reported an association between some point mutations in the non-canonical histone H3.3 and particular types of brain and bone tumors. This suggests a possibility of differential physiological effects of histone variants in different cells and tissues, including bone. In this review, we outline the roles of histone variants and their PTMs in the epigenetic regulation of chromatin structure and discuss possible mechanisms of biological effects of the non-canonical histone mutations found in bone tumors on tumorigenesis in differentiating bone stem cells.
Collapse
|
53
|
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.
Collapse
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
| |
Collapse
|
54
|
Voon HPJ, Hughes JR, Rode C, De La Rosa-Velázquez IA, Jenuwein T, Feil R, Higgs DR, Gibbons RJ. ATRX Plays a Key Role in Maintaining Silencing at Interstitial Heterochromatic Loci and Imprinted Genes. Cell Rep 2015; 11:405-18. [PMID: 25865896 PMCID: PMC4410944 DOI: 10.1016/j.celrep.2015.03.036] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 01/30/2015] [Accepted: 03/14/2015] [Indexed: 11/27/2022] Open
Abstract
Histone H3.3 is a replication-independent histone variant, which replaces histones that are turned over throughout the entire cell cycle. H3.3 deposition at euchromatin is dependent on HIRA, whereas ATRX/Daxx deposits H3.3 at pericentric heterochromatin and telomeres. The role of H3.3 at heterochromatic regions is unknown, but mutations in the ATRX/Daxx/H3.3 pathway are linked to aberrant telomere lengthening in certain cancers. In this study, we show that ATRX-dependent deposition of H3.3 is not limited to pericentric heterochromatin and telomeres but also occurs at heterochromatic sites throughout the genome. Notably, ATRX/H3.3 specifically localizes to silenced imprinted alleles in mouse ESCs. ATRX KO cells failed to deposit H3.3 at these sites, leading to loss of the H3K9me3 heterochromatin modification, loss of repression, and aberrant allelic expression. We propose a model whereby ATRX-dependent deposition of H3.3 into heterochromatin is normally required to maintain the memory of silencing at imprinted loci. ATRX deposits H3.3 at heterochromatin throughout the genome ATRX and H3.3 preferentially bind the methylated allele of imprinted DMRs H3.3 deposition at imprinted DMRs is dependent on ATRX Loss of ATRX/H3.3 leads to loss of H3K9me3 modification at imprinted DMRs
Collapse
Affiliation(s)
- Hsiao P J Voon
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Christina Rode
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | - Thomas Jenuwein
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS), 34293 Montpellier, France
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Richard J Gibbons
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| |
Collapse
|
55
|
Tang MCW, Jacobs SA, Mattiske DM, Soh YM, Graham AN, Tran A, Lim SL, Hudson DF, Kalitsis P, O’Bryan MK, Wong LH, Mann JR. Contribution of the two genes encoding histone variant h3.3 to viability and fertility in mice. PLoS Genet 2015; 11:e1004964. [PMID: 25675407 PMCID: PMC4335506 DOI: 10.1371/journal.pgen.1004964] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 12/22/2014] [Indexed: 12/29/2022] Open
Abstract
Histones package DNA and regulate epigenetic states. For the latter, probably the most important histone is H3. Mammals have three near-identical H3 isoforms: canonical H3.1 and H3.2, and the replication-independent variant H3.3. This variant can accumulate in slowly dividing somatic cells, replacing canonical H3. Some replication-independent histones, through their ability to incorporate outside S-phase, are functionally important in the very slowly dividing mammalian germ line. Much remains to be learned of H3.3 functions in germ cell development. Histone H3.3 presents a unique genetic paradigm in that two conventional intron-containing genes encode the identical protein. Here, we present a comprehensive analysis of the developmental effects of null mutations in each of these genes. H3f3a mutants were viable to adulthood. Females were fertile, while males were subfertile with dysmorphic spermatozoa. H3f3b mutants were growth-deficient, dying at birth. H3f3b heterozygotes were also growth-deficient, with males being sterile because of arrest of round spermatids. This sterility was not accompanied by abnormalities in sex chromosome inactivation in meiosis I. Conditional ablation of H3f3b at the beginning of folliculogenesis resulted in zygote cleavage failure, establishing H3f3b as a maternal-effect gene, and revealing a requirement for H3.3 in the first mitosis. Simultaneous ablation of H3f3a and H3f3b in folliculogenesis resulted in early primary oocyte death, demonstrating a crucial role for H3.3 in oogenesis. These findings reveal a heavy reliance on H3.3 for growth, gametogenesis, and fertilization, identifying developmental processes that are particularly susceptible to H3.3 deficiency. They also reveal partial redundancy in function of H3f3a and H3f3b, with the latter gene being generally the most important.
Collapse
Affiliation(s)
- Michelle C. W. Tang
- Department of Zoology, The University of Melbourne, Melbourne, Victoria, Australia
- Genetics Theme, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Shelley A. Jacobs
- Genetics Theme, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Deidre M. Mattiske
- Genetics Theme, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Yu May Soh
- Genetics Theme, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Alison N. Graham
- Genetics Theme, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - An Tran
- Genetics Theme, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Shu Ly Lim
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
| | - Damien F. Hudson
- Genetics Theme, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Paul Kalitsis
- Genetics Theme, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Moira K. O’Bryan
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia
| | - Lee H. Wong
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
| | - Jeffrey R. Mann
- Genetics Theme, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- * E-mail:
| |
Collapse
|
56
|
Chemical “Diversity” of Chromatin Through Histone Variants and Histone Modifications. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s40610-015-0005-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
57
|
Abstract
The building block of chromatin is nucleosome, which consists of 146 base pairs of DNA wrapped around a histone octamer composed of two copies of histone H2A, H2B, H3, and H4. Significantly, the somatic missense mutations of the histone H3 variant, H3.3, are associated with childhood and young-adult tumors, such as pediatric high-grade astrocytomas, as well as chondroblastoma and giant-cell tumors of the bone. The mechanisms by which these histone mutations cause cancer are by and large unclear. Interestingly, two recent studies identified BS69/ZMYND11, which was proposed to be a candidate tumor suppressor, as a specific reader for a modified form of H3.3 (H3.3K36me3). Importantly, some H3.3 cancer mutations are predicted to abrogate the H3.3K36me3/BS69 interaction, suggesting that this interaction may play an important role in tumor suppression. These new findings also raise the question of whether H3.3 cancer mutations may lead to the disruption and/or gain of interactions of additional cellular factors that contribute to tumorigenesis.
Collapse
|
58
|
Filipescu D, Müller S, Almouzni G. Histone H3 Variants and Their Chaperones During Development and Disease: Contributing to Epigenetic Control. Annu Rev Cell Dev Biol 2014; 30:615-46. [DOI: 10.1146/annurev-cellbio-100913-013311] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dan Filipescu
- Institut Curie, Centre de Recherche, Paris, F-75248 France; , ,
| | | | | |
Collapse
|
59
|
Seridi L, Ryu T, Ravasi T. Dynamic epigenetic control of highly conserved noncoding elements. PLoS One 2014; 9:e109326. [PMID: 25289637 PMCID: PMC4188601 DOI: 10.1371/journal.pone.0109326] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 09/11/2014] [Indexed: 11/19/2022] Open
Abstract
Background Many noncoding genomic loci have remained constant over long evolutionary periods, suggesting that they are exposed to strong selective pressures. The molecular functions of these elements have been partially elucidated, but the fundamental reason for their extreme conservation is still unknown. Results To gain new insights into the extreme selection of highly conserved noncoding elements (HCNEs), we used a systematic analysis of multi-omic data to study the epigenetic regulation of such elements during the development of Drosophila melanogaster. At the sequence level, HCNEs are GC-rich and have a characteristic oligomeric composition. They have higher levels of stable nucleosome occupancy than their flanking regions, and lower levels of mononucleosomes and H3.3, suggesting that these regions reside in compact chromatin. Furthermore, these regions showed remarkable modulations in histone modification and the expression levels of adjacent genes during development. Although HCNEs are primarily initiated late in replication, about 10% were related to early replication origins. Finally, HCNEs showed strong enrichment within lamina-associated domains. Conclusion HCNEs have distinct and protective sequence properties, undergo dynamic epigenetic regulation, and appear to be associated with the structural components of the chromatin, replication origins, and nuclear matrix. These observations indicate that such elements are likely to have essential cellular functions, and offer insights into their epigenetic properties.
Collapse
Affiliation(s)
- Loqmane Seridi
- Division of Biological and Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Taewoo Ryu
- Division of Biological and Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- * E-mail: (T. Ryu); (T. Ravasi)
| | - Timothy Ravasi
- Division of Biological and Environmental Sciences & Engineering, Division of Applied Mathematics and Computer Sciences, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
- Department of Medicine, Division of Genetics, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (T. Ryu); (T. Ravasi)
| |
Collapse
|
60
|
Wen D, Noh KM, Goldberg AD, Allis CD, Rosenwaks Z, Rafii S, Banaszynski LA. Genome editing a mouse locus encoding a variant histone, H3.3B, to report on its expression in live animals. Genesis 2014; 52:959-66. [PMID: 25262655 DOI: 10.1002/dvg.22827] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/23/2014] [Accepted: 09/24/2014] [Indexed: 12/28/2022]
Abstract
Chromatin remodeling via incorporation of histone variants plays a key role in the regulation of embryonic development. The histone variant H3.3 has been associated with a number of early events including formation of the paternal pronucleus upon fertilization. The small number of amino acid differences between H3.3 and its canonical counterparts (H3.1 and H3.2) has limited studies of the developmental significance of H3.3 deposition into chromatin due to difficulties in distinguishing the H3 isoforms. To this end, we used zinc-finger nuclease (ZFN) mediated gene editing to introduce a small C-terminal hemagglutinin (HA) tag to the endogenous H3.3B locus in mouse embryonic stem cells (ESCs), along with an internal ribosome entry site (IRES) and a separately translated fluorescent reporter of expression. This system will allow detection of expression driven by the reporter in cells, animals, and embryos, and will facilitate investigation of differential roles of paternal and maternal H3.3 protein during embryogenesis that would not be possible using variant-specific antibodies. Further, the ability to monitor endogenous H3.3 protein in various cell lineages will enhance our understanding of the dynamics of this histone variant over the course of development.
Collapse
Affiliation(s)
- Duancheng Wen
- Ansary Stem Cell Institute and Department of Medicine, Weill Cornell Medical College, New York, New York; Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medical College, New York, New York
| | | | | | | | | | | | | |
Collapse
|
61
|
Histone H3.3 is required to maintain replication fork progression after UV damage. Curr Biol 2014; 24:2195-2201. [PMID: 25201682 PMCID: PMC4175177 DOI: 10.1016/j.cub.2014.07.077] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/11/2014] [Accepted: 07/30/2014] [Indexed: 11/22/2022]
Abstract
Unlike histone H3, which is present only in S phase, the variant histone H3.3 is expressed throughout the cell cycle [1] and is incorporated into chromatin independent of replication [2]. Recently, H3.3 has been implicated in the cellular response to ultraviolet (UV) light [3]. Here, we show that chicken DT40 cells completely lacking H3.3 are hypersensitive to UV light, a defect that epistasis analysis suggests may result from less-effective nucleotide excision repair. Unexpectedly, H3.3-deficient cells also exhibit a substantial defect in maintaining replication fork progression on UV-damaged DNA, which is independent of nucleotide excision repair, demonstrating a clear requirement for H3.3 during S phase. Both the UV hypersensitivity and replication fork slowing are reversed by expression of H3.3 and require the specific residues in the α2 helix that are responsible for H3.3 binding its dedicated chaperones. However, expression of an H3.3 mutant in which serine 31 is replaced with alanine, the equivalent residue in H3.2, restores normal fork progression but not UV resistance, suggesting that H3.3[S31A] may be incorporated at UV-damaged forks but is unable to help cells tolerate UV lesions. Similar behavior was observed with expression of H3.3 carrying mutations at K27 and G34, which have been reported in pediatric brain cancers. We speculate that incorporation of H3.3 during replication may mark sites of lesion bypass and, possibly through an as-yet-unidentified function of the N-terminal tail, facilitate subsequent processing of the damage. We report a vertebrate cell line completely lacking the histone variant H3.3 H3.3-deficient cells are hypersensitive to DNA damage A supply of H3.3 is required to maintain fork progression after UV damage This S phase role requires the distinct chaperone-binding patch of H3.3
Collapse
|
62
|
Deb M, Kar S, Sengupta D, Shilpi A, Parbin S, Rath SK, Londhe VA, Patra SK. Chromatin dynamics: H3K4 methylation and H3 variant replacement during development and in cancer. Cell Mol Life Sci 2014; 71:3439-63. [PMID: 24676717 PMCID: PMC11113154 DOI: 10.1007/s00018-014-1605-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 02/11/2014] [Accepted: 03/06/2014] [Indexed: 12/11/2022]
Abstract
The dynamic nature of chromatin and its myriad modifications play a crucial role in gene regulation (expression and repression) during development, cellular survival, homeostasis, ageing, and apoptosis/death. Histone 3 lysine 4 methylation (H3K4 methylation) catalyzed by H3K4 specific histone methyltransferases is one of the more critical chromatin modifications that is generally associated with gene activation. Additionally, the deposition of H3 variant(s) in conjunction with H3K4 methylation generates an intricately reliable epigenetic regulatory circuit that guides transcriptional activity in normal development and homeostasis. Consequently, alterations in this epigenetic circuit may trigger disease development. The mechanistic relationship between H3 variant deposition and H3K4 methylation during normal development has remained foggy. However, recent investigations in the field of chromatin dynamics in various model organisms, tumors, cancer tissues, and cell lines cultured without and with therapeutic agents, as well as from model reconstituted chromatins reveal that there may be different subsets of chromatin assemblage with specific patterns of histone replacement executing similar functions. In this light, we attempt to explain the intricate control system that maintains chromatin structure and dynamics during normal development as well as during tumor development and cancer progression in this review. Our focus is to highlight the contribution of H3K4 methylation-histone variant crosstalk in regulating chromatin architecture and subsequently its function.
Collapse
Affiliation(s)
- Moonmoon Deb
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Swayamsiddha Kar
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Dipta Sengupta
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Arunima Shilpi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Sabnam Parbin
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Sandip K. Rath
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| | - Vedang A. Londhe
- Division of Neonatology and Developmental Biology, Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095-1752 USA
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008 India
| |
Collapse
|
63
|
Yuen BTK, Bush KM, Barrilleaux BL, Cotterman R, Knoepfler PS. Histone H3.3 regulates dynamic chromatin states during spermatogenesis. Development 2014; 141:3483-94. [PMID: 25142466 DOI: 10.1242/dev.106450] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The histone variant H3.3 is involved in diverse biological processes, including development, transcriptional memory and transcriptional reprogramming, as well as diseases, including most notably malignant brain tumors. Recently, we developed a knockout mouse model for the H3f3b gene, one of two genes encoding H3.3. Here, we show that targeted disruption of H3f3b results in a number of phenotypic abnormalities, including a reduction in H3.3 histone levels, leading to male infertility, as well as abnormal sperm and testes morphology. Additionally, null germ cell populations at specific stages in spermatogenesis, in particular spermatocytes and spermatogonia, exhibited increased rates of apoptosis. Disruption of H3f3b also altered histone post-translational modifications and gene expression in the testes, with the most prominent changes occurring at genes involved in spermatogenesis. Finally, H3f3b null testes also exhibited abnormal germ cell chromatin reorganization and reduced protamine incorporation. Taken together, our studies indicate a major role for H3.3 in spermatogenesis through regulation of chromatin dynamics.
Collapse
Affiliation(s)
- Benjamin T K Yuen
- Department of Cell Biology and Human Anatomy, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Genome Center, University of California Davis School of Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA
| | - Kelly M Bush
- Department of Cell Biology and Human Anatomy, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Genome Center, University of California Davis School of Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA
| | - Bonnie L Barrilleaux
- Department of Cell Biology and Human Anatomy, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Genome Center, University of California Davis School of Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA
| | - Rebecca Cotterman
- Department of Cell Biology and Human Anatomy, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Genome Center, University of California Davis School of Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA
| | - Paul S Knoepfler
- Department of Cell Biology and Human Anatomy, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Genome Center, University of California Davis School of Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, CA 95817, USA
| |
Collapse
|
64
|
Wegner M, Neddermann D, Piorunska-Stolzmann M, Jagodzinski PP. Role of epigenetic mechanisms in the development of chronic complications of diabetes. Diabetes Res Clin Pract 2014; 105:164-75. [PMID: 24814876 DOI: 10.1016/j.diabres.2014.03.019] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 03/13/2014] [Accepted: 03/22/2014] [Indexed: 12/24/2022]
Abstract
There is growing evidence that epigenetic regulation of gene expression including post-translational histone modifications (PTHMs), DNA methylation and microRNA (miRNA)-regulation of mRNA translation could play a crucial role in the development of chronic, diabetic complications. Hyperglycemia can induce an abnormal action of PTHMs and DNA methyltransferases as well as alter the levels of numerous miRNAs in endothelial cells, vascular smooth muscle cells, cardiomyocytes, retina, and renal cells. These epigenetic abnormalities result in changes in the expression of numerous genes contributing to effects such as development of chronic inflammation, impaired clearance of reactive oxygen species (ROS), endothelial cell dysfunction and/or the accumulation of extracellular matrix in the kidney, which causing the development of retinopathy, nephropathy or cardiomyopathy. Some epigenetic modifications, for example PTHMs and DNA methylation, become irreversible over time. Therefore, these processes have gained much attention in explaining the long-lasting detrimental consequences of hyperglycaemia causing the development of chronic complications even after improved glycaemic control is achieved. Our review suggests that the treatment of chronic complications should focus on erasing metabolic memory by targeting chromatin modification enzymes and by restoring miRNA levels.
Collapse
Affiliation(s)
- Malgorzata Wegner
- Lipid Metabolism Laboratory, Chair of Chemistry and Clinical Biochemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznan, Poland.
| | - Daniel Neddermann
- Novartis Pharma AG, Drug Metabolism and Pharmacokinetics, Postfach, 4002 Basel, Switzerland
| | - Maria Piorunska-Stolzmann
- Department of Clinical Biochemistry and Laboratory Medicine, Chair of Chemistry and Clinical Biochemistry, Poznan University of Medical Sciences, 6 Grunwaldzka Street, 60-780 Poznan, Poland
| | - Pawel P Jagodzinski
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781 Poznan, Poland
| |
Collapse
|
65
|
Every amino acid matters: essential contributions of histone variants to mammalian development and disease. Nat Rev Genet 2014; 15:259-71. [PMID: 24614311 DOI: 10.1038/nrg3673] [Citation(s) in RCA: 241] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite a conserved role for histones as general DNA packaging agents, it is now clear that another key function of these proteins is to confer variations in chromatin structure to ensure dynamic patterns of transcriptional regulation in eukaryotes. The incorporation of histone variants is particularly important to this process. Recent knockdown and knockout studies in various cellular systems, as well as direct mutational evidence from human cancers, now suggest a crucial role for histone variant regulation in processes as diverse as differentiation and proliferation, meiosis and nuclear reprogramming. In this Review, we provide an overview of histone variants in the context of their unique functions during mammalian germ cell and embryonic development, and examine the consequences of aberrant histone variant regulation in human disease.
Collapse
|
66
|
Lacoste N, Woolfe A, Tachiwana H, Garea AV, Barth T, Cantaloube S, Kurumizaka H, Imhof A, Almouzni G. Mislocalization of the centromeric histone variant CenH3/CENP-A in human cells depends on the chaperone DAXX. Mol Cell 2014; 53:631-44. [PMID: 24530302 DOI: 10.1016/j.molcel.2014.01.018] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 10/02/2013] [Accepted: 01/07/2014] [Indexed: 01/17/2023]
Abstract
Centromeres are essential for ensuring proper chromosome segregation in eukaryotes. Their definition relies on the presence of a centromere-specific H3 histone variant CenH3, known as CENP-A in mammals. Its overexpression in aggressive cancers raises questions concerning its effect on chromatin dynamics and contribution to tumorigenesis. We find that CenH3 overexpression in human cells leads to ectopic enrichment at sites of active histone turnover involving a heterotypic tetramer containing CenH3-H4 with H3.3-H4. Ectopic localization of this particle depends on the H3.3 chaperone DAXX rather than the dedicated CenH3 chaperone HJURP. This aberrant nucleosome occludes CTCF binding and has a minor effect on gene expression. Cells overexpressing CenH3 are more tolerant of DNA damage. Both the survival advantage and CTCF occlusion in these cells are dependent on DAXX. Our findings illustrate how changes in histone variant levels can disrupt chromatin dynamics and suggests a possible mechanism for cell resistance to anticancer treatments.
Collapse
Affiliation(s)
- Nicolas Lacoste
- Institut Curie, Centre de Recherche, Paris75248, France; CNRS, UMR3664, Paris75248, France; Equipe Labellisée Ligue Contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France
| | - Adam Woolfe
- Institut Curie, Centre de Recherche, Paris75248, France; CNRS, UMR3664, Paris75248, France; Equipe Labellisée Ligue Contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France
| | - Hiroaki Tachiwana
- Institut Curie, Centre de Recherche, Paris75248, France; CNRS, UMR3664, Paris75248, France; Equipe Labellisée Ligue Contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France
| | - Ana Villar Garea
- Histone Modifications Group, Scientific Coordinator ZfP (Zentrallabor für Proteinanalytik), Adolf Butenandt Institut, University of Munich, Schillerstraße 44, 80336 Munich, Germany
| | - Teresa Barth
- Histone Modifications Group, Scientific Coordinator ZfP (Zentrallabor für Proteinanalytik), Adolf Butenandt Institut, University of Munich, Schillerstraße 44, 80336 Munich, Germany
| | - Sylvain Cantaloube
- Institut Curie, Centre de Recherche, Paris75248, France; CNRS, UMR3664, Paris75248, France; Equipe Labellisée Ligue Contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Axel Imhof
- Histone Modifications Group, Scientific Coordinator ZfP (Zentrallabor für Proteinanalytik), Adolf Butenandt Institut, University of Munich, Schillerstraße 44, 80336 Munich, Germany
| | - Geneviève Almouzni
- Institut Curie, Centre de Recherche, Paris75248, France; CNRS, UMR3664, Paris75248, France; Equipe Labellisée Ligue Contre le Cancer, UMR3664, Paris 75248, France; UPMC, UMR3664, Paris 75248, France.
| |
Collapse
|
67
|
Banaszynski LA, Wen D, Dewell S, Whitcomb SJ, Lin M, Diaz N, Elsässer SJ, Chapgier A, Goldberg AD, Canaani E, Rafii S, Zheng D, Allis CD. Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells. Cell 2013; 155:107-20. [PMID: 24074864 DOI: 10.1016/j.cell.2013.08.061] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 07/08/2013] [Accepted: 08/28/2013] [Indexed: 11/15/2022]
Abstract
Polycomb repressive complex 2 (PRC2) regulates gene expression during lineage specification through trimethylation of lysine 27 on histone H3 (H3K27me3). In Drosophila, polycomb binding sites are dynamic chromatin regions enriched with the histone variant H3.3. Here, we show that, in mouse embryonic stem cells (ESCs), H3.3 is required for proper establishment of H3K27me3 at the promoters of developmentally regulated genes. Upon H3.3 depletion, these promoters show reduced nucleosome turnover measured by deposition of de novo synthesized histones and reduced PRC2 occupancy. Further, we show H3.3-dependent interaction of PRC2 with the histone chaperone, Hira, and that Hira localization to chromatin requires H3.3. Our data demonstrate the importance of H3.3 in maintaining a chromatin landscape in ESCs that is important for proper gene regulation during differentiation. Moreover, our findings support the emerging notion that H3.3 has multiple functions in distinct genomic locations that are not always correlated with an "active" chromatin state.
Collapse
Affiliation(s)
- Laura A Banaszynski
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, New York, 10065 USA
| | - Duancheng Wen
- Howard Hughes Medical Institute, Ansary Stem Cell Institute, and Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, 10065 USA
| | - Scott Dewell
- Genomics Resource Center, The Rockefeller University, New York, New York, 10065 USA
| | - Sarah J Whitcomb
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, New York, 10065 USA
| | - Mingyan Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, 10461 USA
| | - Nichole Diaz
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, New York, 10065 USA
| | - Simon J Elsässer
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, New York, 10065 USA
| | - Ariane Chapgier
- Molecular Medicine Unit, Institute of Child Health, London WC1N 1EH, UK
| | - Aaron D Goldberg
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, New York, 10065 USA
| | - Eli Canaani
- The Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Isreal
| | - Shahin Rafii
- Howard Hughes Medical Institute, Ansary Stem Cell Institute, and Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, 10065 USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, 10461 USA.,Departments of Neurology and Neuroscience, Albert Einstein College of Medicine, Bronx, New York, 10461 USA
| | - C David Allis
- Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, New York, 10065 USA
| |
Collapse
|
68
|
Yuen BTK, Knoepfler PS. Histone H3.3 mutations: a variant path to cancer. Cancer Cell 2013; 24:567-74. [PMID: 24229707 PMCID: PMC3882088 DOI: 10.1016/j.ccr.2013.09.015] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 09/11/2013] [Accepted: 09/24/2013] [Indexed: 12/31/2022]
Abstract
A host of cancer types exhibit aberrant histone modifications. Recently, distinct and recurrent mutations in a specific histone variant, histone H3.3, have been implicated in a high proportion of malignant pediatric brain cancers. The presence of mutant H3.3 histone disrupts epigenetic posttranslational modifications near genes involved in cancer processes and in brain function. Here, we review possible mechanisms by which mutant H3.3 histones may act to promote tumorigenesis. Furthermore, we discuss how perturbations in normal H3.3 chromatin-related and epigenetic functions may more broadly contribute to the formation of human cancers.
Collapse
Affiliation(s)
- Benjamin T K Yuen
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, 4303 Tupper Hall, Davis, CA 95616, USA; Genome Center, University of California Davis School of Medicine, 451 Health Sciences Drive, Davis, CA 95616, USA; Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, 2425 Stockton Boulevard, Sacramento, CA 95817, USA
| | | |
Collapse
|
69
|
Catania S, Allshire RC. Anarchic centromeres: deciphering order from apparent chaos. Curr Opin Cell Biol 2013; 26:41-50. [PMID: 24529245 PMCID: PMC3978670 DOI: 10.1016/j.ceb.2013.09.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/20/2013] [Accepted: 09/24/2013] [Indexed: 12/16/2022]
Abstract
Specialised chromatin in which canonical histone H3 is replaced by CENP-A, an H3 related protein, is a signature of active centromeres and provides the foundation for kinetochore assembly. The location of centromeres is not fixed since centromeres can be inactivated and new centromeres can arise at novel locations independently of specific DNA sequence elements. Therefore, the establishment and maintenance of CENP-A chromatin and kinetochores provide an exquisite example of genuine epigenetic regulation. The composition of CENP-A nucleosomes is contentious but several studies suggest that, like regular H3 particles, they are octamers. Recent analyses have provided insight into how CENP-A is recognised and propagated, identified roles for post-translational modifications and dissected how CENP-A recruits other centromere proteins to mediate kinetochore assembly.
Collapse
Affiliation(s)
- Sandra Catania
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, 6.34 Swann Building, Mayfield Road, Edinburgh EH9 3JR, Scotland, UK
| | - Robin C Allshire
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, 6.34 Swann Building, Mayfield Road, Edinburgh EH9 3JR, Scotland, UK.
| |
Collapse
|
70
|
Salomoni P. The PML-Interacting Protein DAXX: Histone Loading Gets into the Picture. Front Oncol 2013; 3:152. [PMID: 23760585 PMCID: PMC3675705 DOI: 10.3389/fonc.2013.00152] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 05/24/2013] [Indexed: 12/23/2022] Open
Abstract
The promyelocytic leukemia (PML) protein has been implicated in regulation of multiple key cellular functions, from transcription to calcium homeostasis. PML pleiotropic role is in part related to its ability to localize to both the nucleus and cytoplasm. In the nucleus, PML is known to regulate gene transcription, a role linked to its ability to associate with transcription factors as well as chromatin-remodelers. A new twist came from the discovery that the PML-interacting protein death-associated protein 6 (DAXX) acts as chaperone for the histone H3.3 variant. H3.3 is found enriched at active genes, centromeric heterochromatin, and telomeres, and has been proposed to act as important carrier of epigenetic information. Our recent work has implicated DAXX in regulation of H3.3 loading and transcription in the central nervous system (CNS). Remarkably, driver mutations in H3.3 and/or its loading machinery have been identified in brain cancer, thus suggesting a role for altered H3.3 function/deposition in CNS tumorigenesis. Aberrant H3.3 deposition may also play a role in leukemia pathogenesis, given DAXX role in PML-RARα-driven transformation and the identification of a DAXX missense mutation in acute myeloid leukemia. This review aims to critically discuss the existing literature and propose new avenues for investigation.
Collapse
Affiliation(s)
- Paolo Salomoni
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute , University College London, London , UK
| |
Collapse
|