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Tsai CH, Chen YJ, Yu CJ, Tzeng SR, Wu IC, Kuo WH, Lin MC, Chan NL, Wu KJ, Teng SC. SMYD3-Mediated H2A.Z.1 Methylation Promotes Cell Cycle and Cancer Proliferation. Cancer Res 2016; 76:6043-6053. [PMID: 27569210 DOI: 10.1158/0008-5472.can-16-0500] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 08/06/2016] [Indexed: 11/16/2022]
Abstract
SMYD3 methyltransferase is nearly undetectable in normal human tissues but highly expressed in several cancers, including breast cancer, although its contributions to pathogenesis in this setting are unclear. Here we report that histone H2A.Z.1 is a substrate of SMYD3 that supports malignancy. SMYD3-mediated dimethylation of H2A.Z.1 at lysine 101 (H2A.Z.1K101me2) increased stability by preventing binding to the removal chaperone ANP32E and facilitating its interaction with histone H3. Moreover, a microarray analysis identified cyclin A1 as a target coregulated by SMYD3 and H2A.Z.1K101me2. The colocalization of SMYD3 and H2A.Z.1K101me2 at the promoter of cyclin A1 activated its expression and G1-S progression. Enforced expression of cyclin A1 in cells containing mutant H2A.Z.1 rescued tumor formation in a mouse model. Our findings suggest that SMYD3-mediated H2A.Z.1K101 dimethylation activates cyclin A1 expression and contributes to driving the proliferation of breast cancer cells. Cancer Res; 76(20); 6043-53. ©2016 AACR.
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Affiliation(s)
- Cheng-Hui Tsai
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yun-Ju Chen
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chia-Jung Yu
- Department of Cell and Molecular Biology, Chang Gung University, Tao-Yuan, Taiwan. Department of Thoracic Medicine, Chang Gung Memorial Hospital, Linkou, Tao-Yuan, Taiwan
| | - Shiou-Ru Tzeng
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - I-Chen Wu
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Hung Kuo
- Department of Surgery, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ming-Chieh Lin
- Department of Pathology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Nei-Li Chan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Kou-Juey Wu
- Research Center for Tumor Medical Science, Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Shu-Chun Teng
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan.
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52
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Choi K, Kim J, Müller SY, Oh M, Underwood C, Henderson I, Lee I. Regulation of MicroRNA-Mediated Developmental Changes by the SWR1 Chromatin Remodeling Complex. PLANT PHYSIOLOGY 2016; 171:1128-43. [PMID: 27208270 PMCID: PMC4902616 DOI: 10.1104/pp.16.00332] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 04/11/2016] [Indexed: 05/04/2023]
Abstract
The ATP-dependent SWR1 chromatin remodeling complex (SWR1-C) exchanges the histone H2A-H2B dimer with the H2A.Z-H2B dimer, producing variant nucleosomes. Arabidopsis thaliana SWR1-C contributes to the active transcription of many genes, but also to the repression of genes that respond to environmental and developmental stimuli. Unlike other higher eukaryotic H2A.Z deposition mutants (which are embryonically lethal), Arabidopsis SWR1-C component mutants, including arp6, survive and display a pleiotropic developmental phenotype. However, the molecular mechanisms of early flowering, leaf serration, and the production of extra petals in arp6 have not been completely elucidated. We report here that SWR1-C is required for miRNA-mediated developmental control via transcriptional regulation. In the mutants of the components of SWR1-C such as arp6, sef, and pie1, miR156 and miR164 levels are reduced at the transcriptional level, which results in the accumulation of target mRNAs and associated morphological changes. Sequencing of small RNA libraries confirmed that many miRNAs including miR156 decreased in arp6, though some miRNAs increased. The arp6 mutation suppresses the accumulation of not only unprocessed primary miRNAs, but also miRNA-regulated mRNAs in miRNA processing mutants, hyl1 and serrate, which suggests that arp6 has a transcriptional effect on both miRNAs and their targets. We consistently detected that the arp6 mutant exhibits increased nucleosome occupancy at the tested MIR gene promoters, indicating that SWR1-C contributes to transcriptional activation via nucleosome dynamics. Our findings suggest that SWR1-C contributes to the fine control of plant development by generating a balance between miRNAs and target mRNAs at the transcriptional level.
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Affiliation(s)
- Kyuha Choi
- Laboratory of Plant Developmental Genetics, School of Biological Sciences, Seoul National University, Seoul, 151-742, Korea (K.C., J.K., M.O., I.L.); and Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom (K.C., S.Y.M., C.U., I.H.)
| | - Juhyun Kim
- Laboratory of Plant Developmental Genetics, School of Biological Sciences, Seoul National University, Seoul, 151-742, Korea (K.C., J.K., M.O., I.L.); and Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom (K.C., S.Y.M., C.U., I.H.)
| | - Sebastian Y Müller
- Laboratory of Plant Developmental Genetics, School of Biological Sciences, Seoul National University, Seoul, 151-742, Korea (K.C., J.K., M.O., I.L.); and Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom (K.C., S.Y.M., C.U., I.H.)
| | - Mijin Oh
- Laboratory of Plant Developmental Genetics, School of Biological Sciences, Seoul National University, Seoul, 151-742, Korea (K.C., J.K., M.O., I.L.); and Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom (K.C., S.Y.M., C.U., I.H.)
| | - Charles Underwood
- Laboratory of Plant Developmental Genetics, School of Biological Sciences, Seoul National University, Seoul, 151-742, Korea (K.C., J.K., M.O., I.L.); and Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom (K.C., S.Y.M., C.U., I.H.)
| | - Ian Henderson
- Laboratory of Plant Developmental Genetics, School of Biological Sciences, Seoul National University, Seoul, 151-742, Korea (K.C., J.K., M.O., I.L.); and Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom (K.C., S.Y.M., C.U., I.H.)
| | - Ilha Lee
- Laboratory of Plant Developmental Genetics, School of Biological Sciences, Seoul National University, Seoul, 151-742, Korea (K.C., J.K., M.O., I.L.); and Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, United Kingdom (K.C., S.Y.M., C.U., I.H.)
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53
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Colino-Sanguino Y, Clark SJ, Valdes-Mora F. H2A.Z acetylation and transcription: ready, steady, go! Epigenomics 2016; 8:583-6. [PMID: 27087541 DOI: 10.2217/epi-2016-0016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Yolanda Colino-Sanguino
- Histone Variants Group, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia.,Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia.,St. Vincent's Clinical School, University of NSW, Sydney 2010, New South Wales, Australia
| | - Fatima Valdes-Mora
- Histone Variants Group, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia.,Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia.,St. Vincent's Clinical School, University of NSW, Sydney 2010, New South Wales, Australia
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Fernandez-Salas E, Wang S, Chinnaiyan AM. Role of BET proteins in castration-resistant prostate cancer. DRUG DISCOVERY TODAY. TECHNOLOGIES 2016; 19:29-38. [PMID: 27769354 DOI: 10.1016/j.ddtec.2016.07.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 06/29/2016] [Accepted: 07/03/2016] [Indexed: 06/06/2023]
Abstract
Castration resistant prostate cancer (CRPC) is a deadly disease with few therapeutic options once patients become resistant to second generation drugs targeting the AR-transcriptional program. The BET-BRD readers of chromatin are key regulators of AR-, ERG-, and c-Myc-mediated transcription in CRPC. BET-BRD inhibitors have demonstrated pre-clinical efficacy in models of CRPC and are currently being evaluated in several clinical trials. These novel drugs have the potential to transform the way we treat CRPC in the near future.
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Affiliation(s)
- Ester Fernandez-Salas
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Shaomeng Wang
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Medicinal Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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55
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Ng MK, Cheung P. A brief histone in time: understanding the combinatorial functions of histone PTMs in the nucleosome context. Biochem Cell Biol 2016. [DOI: 10.1139/bcb-2015-0031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
It has been over 50 years since Allfrey et al. proposed that histone acetylation regulates RNA synthesis, and the study of histone modifications has progressed at an extraordinary pace for the past two decades. In this review, we provide a perspective on some key events and advances in our understanding of histone modifications. We also highlight reagents and tools from past to present that facilitated progress in this research field. Using histone H3 phosphorylation as an underlying thread, we review the rationale that led to the proposal of the histone code hypothesis, as well as examples that illustrate the concepts of combinatorial histone modifications and cross-talk pathways. We further highlight the importance of investigating these mechanisms in the context of nucleosomes rather than just at the histone level and present current and developing approaches for such studies. Overall, research on histone modifications has yielded great mechanistic insights into the regulation of genomic functions, and extending these studies using nucleosomes will further elucidate the complexity of these pathways in a more physiologically relevant context.
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Affiliation(s)
- Marlee K. Ng
- Department of Biology, York University, Life Sciences Building, Rm 331A, Toronto, ON M3J 1P3, Canada
- Department of Biology, York University, Life Sciences Building, Rm 331A, Toronto, ON M3J 1P3, Canada
| | - Peter Cheung
- Department of Biology, York University, Life Sciences Building, Rm 331A, Toronto, ON M3J 1P3, Canada
- Department of Biology, York University, Life Sciences Building, Rm 331A, Toronto, ON M3J 1P3, Canada
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56
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H2A.Z.1 Monoubiquitylation Antagonizes BRD2 to Maintain Poised Chromatin in ESCs. Cell Rep 2016; 14:1142-1155. [PMID: 26804911 DOI: 10.1016/j.celrep.2015.12.100] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 10/16/2015] [Accepted: 12/22/2015] [Indexed: 12/13/2022] Open
Abstract
Histone variant H2A.Z occupies the promoters of active and poised, bivalent genes in embryonic stem cells (ESCs) to regulate developmental programs, yet how it contributes to these contrasting states is poorly understood. Here, we investigate the function of H2A.Z.1 monoubiquitylation (H2A.Z.1ub) by mutation of the PRC1 target residues (H2A.Z.1(K3R3)). We show that H2A.Z.1(K3R3) is properly incorporated at target promoters in murine ESCs (mESCs), but loss of monoubiquitylation leads to de-repression of bivalent genes, loss of Polycomb binding, and faulty lineage commitment. Using quantitative proteomics, we find that tandem bromodomain proteins, including the BET family member BRD2, are enriched in H2A.Z.1 chromatin. We further show that BRD2 is gained at de-repressed promoters in H2A.Z.1(K3R3) mESCs, whereas BRD2 inhibition restores gene silencing at these sites. Together, our study reveals an antagonistic relationship between H2A.Z.1ub and BRD2 to regulate the transcriptional balance at bivalent genes to enable proper execution of developmental programs.
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57
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Wang L, Wolgemuth DJ. BET Protein BRDT Complexes With HDAC1, PRMT5, and TRIM28 and Functions in Transcriptional Repression During Spermatogenesis. J Cell Biochem 2015; 117:1429-38. [PMID: 26565999 DOI: 10.1002/jcb.25433] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 11/10/2015] [Indexed: 02/01/2023]
Abstract
The expression of BRDT, a member of the BET sub-family of double bromodomain-containing proteins, is restricted to the male germ line, specifically to pachytene-diplotene spermatocytes and early spermatids. We previously showed that loss of the first bromodomain of BRDT by targeted mutagenesis (Brdt(ΔBD1) ) resulted in sterility and abnormalities in spermiogenesis, but little is known about BRDT's function at the molecular level. As part of studies designed to identify BRDT-interacting proteins we stably introduced a FLAG-tagged BRDT cDNA into 293T cells, which do not normally express BRDT. Affinity-purification of FLAG-tagged BRDT complexes indicated that BRDT has novel interactions with the histone deacetylase HDAC1, the arginine-specific histone methyltransferase 5 PRMT5, and the Tripartite motif-containing 28 protein TRIM28. Immunofluorescent microscopy revealed that BRDT co-localized with each of these proteins in round spermatids and co-immunoprecipitation of testicular extracts showed that these proteins interact with BRDT. Furthermore, they bind the promoter of H1t, a putative target of BRDT-containing complexes. This binding of H1t was lost in mice expressing the Brdt(ΔBD1) mutant protein and concomitantly, H1t expression was elevated in round spermatids. Our study reveals a role for BRDT-containing complexes in the repression of gene expression in vivo that correlates with dramatic effects on chromatin remodeling and the progression of spermiogenesis.
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Affiliation(s)
- Li Wang
- Department of Genetics and Development, New York, New York, 10032
| | - Debra J Wolgemuth
- Department of Genetics and Development, New York, New York, 10032.,Department of Obstetrics and Gynecology, New York, New York, 10032.,Institute of Human Nutrition, New York, New York, 10032.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, 10032
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58
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Gallagher SJ, Tiffen JC, Hersey P. Histone Modifications, Modifiers and Readers in Melanoma Resistance to Targeted and Immune Therapy. Cancers (Basel) 2015; 7:1959-82. [PMID: 26426052 PMCID: PMC4695870 DOI: 10.3390/cancers7040870] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/17/2015] [Accepted: 09/18/2015] [Indexed: 02/06/2023] Open
Abstract
The treatment of melanoma has been revolutionized by new therapies targeting MAPK signaling or the immune system. Unfortunately these therapies are hindered by either primary resistance or the development of acquired resistance. Resistance mechanisms involving somatic mutations in genes associated with resistance have been identified in some cases of melanoma, however, the cause of resistance remains largely unexplained in other cases. The importance of epigenetic factors targeting histones and histone modifiers in driving the behavior of melanoma is only starting to be unraveled and provides significant opportunity to combat the problems of therapy resistance. There is also an increasing ability to target these epigenetic changes with new drugs that inhibit these modifications to either prevent or overcome resistance to both MAPK inhibitors and immunotherapy. This review focuses on changes in histones, histone reader proteins and histone positioning, which can mediate resistance to new therapeutics and that can be targeted for future therapies.
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Affiliation(s)
- Stuart J Gallagher
- Melanoma Immunology and Oncology Group, Centenary Institute, University of Sydney, Camperdown 2050, Australia.
- Melanoma Institute Australia, Crow's Nest 2065, Sydney, Australia.
| | - Jessamy C Tiffen
- Melanoma Immunology and Oncology Group, Centenary Institute, University of Sydney, Camperdown 2050, Australia.
- Melanoma Institute Australia, Crow's Nest 2065, Sydney, Australia.
| | - Peter Hersey
- Melanoma Immunology and Oncology Group, Centenary Institute, University of Sydney, Camperdown 2050, Australia.
- Melanoma Institute Australia, Crow's Nest 2065, Sydney, Australia.
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59
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Jung M, Gelato KA, Fernández-Montalván A, Siegel S, Haendler B. Targeting BET bromodomains for cancer treatment. Epigenomics 2015; 7:487-501. [PMID: 26077433 DOI: 10.2217/epi.14.91] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The bromodomain and extraterminal (BET) subfamily of bromodomain-containing proteins has emerged in the last few years as an exciting, novel target group. BRD4, the best studied BET protein, is implicated in a number of hematological and solid tumors. This is linked to its role in modulating transcription elongation of essential genes involved in cell cycle and apoptosis such as c-Myc and BCL2. Potent BET inhibitors with promising antitumor efficacy in a number of preclinical cancer models have been identified in recent years. This led to clinical studies focusing mostly on the treatment of leukemia and lymphoma, and first encouraging signs of efficacy have already been reported. Here we discuss the biology of BRD4, its known interaction partners and implication in different tumor types. Further, we summarize the current knowledge on BET bromodomain inhibitors.
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Affiliation(s)
- Marie Jung
- Global Drug Discovery, Bayer Pharma AG, D-13353 Berlin, Germany.,Institute of Chemistry & Biochemistry, Free University, D-14195 Berlin, Germany
| | - Kathy A Gelato
- Global Drug Discovery, Bayer Pharma AG, D-13353 Berlin, Germany
| | | | - Stephan Siegel
- Global Drug Discovery, Bayer Pharma AG, D-13353 Berlin, Germany
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60
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Vardabasso C, Gaspar-Maia A, Hasson D, Pünzeler S, Valle-Garcia D, Straub T, Keilhauer EC, Strub T, Dong J, Panda T, Chung CY, Yao JL, Singh R, Segura MF, Fontanals-Cirera B, Verma A, Mann M, Hernando E, Hake SB, Bernstein E. Histone Variant H2A.Z.2 Mediates Proliferation and Drug Sensitivity of Malignant Melanoma. Mol Cell 2015; 59:75-88. [PMID: 26051178 DOI: 10.1016/j.molcel.2015.05.009] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 03/24/2015] [Accepted: 04/30/2015] [Indexed: 01/19/2023]
Abstract
Histone variants are emerging as key regulatory molecules in cancer. We report a unique role for the H2A.Z isoform H2A.Z.2 as a driver of malignant melanoma. H2A.Z.2 is highly expressed in metastatic melanoma, correlates with decreased patient survival, and is required for cellular proliferation. Our integrated genomic analyses reveal that H2A.Z.2 controls the transcriptional output of E2F target genes in melanoma cells. These genes are highly expressed and display a distinct signature of H2A.Z occupancy. We identify BRD2 as an H2A.Z-interacting protein, levels of which are also elevated in melanoma. We further demonstrate that H2A.Z.2-regulated genes are bound by BRD2 and E2F1 in an H2A.Z.2-dependent manner. Importantly, H2A.Z.2 deficiency sensitizes melanoma cells to chemotherapy and targeted therapies. Collectively, our findings implicate H2A.Z.2 as a mediator of cell proliferation and drug sensitivity in malignant melanoma, holding translational potential for novel therapeutic strategies.
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Affiliation(s)
- Chiara Vardabasso
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexandre Gaspar-Maia
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dan Hasson
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sebastian Pünzeler
- Center for Integrated Protein Science Munich and Department of Molecular Biology, Adolf-Butenandt Institute, Ludwig-Maximilians University, 80336 Munich, Germany
| | - David Valle-Garcia
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Molecular Genetics Department, Institute for Cellular Physiology, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Tobias Straub
- Center for Integrated Protein Science Munich and Department of Molecular Biology, Adolf-Butenandt Institute, Ludwig-Maximilians University, 80336 Munich, Germany
| | - Eva C Keilhauer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Thomas Strub
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joanna Dong
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Taniya Panda
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chi-Yeh Chung
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan L Yao
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rajendra Singh
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miguel F Segura
- Department of Pathology and Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY 10016, USA
| | - Barbara Fontanals-Cirera
- Department of Pathology and Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY 10016, USA
| | - Amit Verma
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Eva Hernando
- Department of Pathology and Interdisciplinary Melanoma Cooperative Group, New York University Langone Medical Center, New York, NY 10016, USA
| | - Sandra B Hake
- Center for Integrated Protein Science Munich and Department of Molecular Biology, Adolf-Butenandt Institute, Ludwig-Maximilians University, 80336 Munich, Germany.
| | - Emily Bernstein
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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61
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Abstract
Histone variant exchange is a novel epigenetic regulator of cognition. We speculate that H2A.Z, a variant of canonical histone H2A, exerts unique effects on transcription during distinct stages of memory formation, ultimately acting to maintain memory of previous transcriptional states and poise genes for re-activation. Hippocampus-dependent memory formation is initiated by transient expression of memory-related genes, which support the storage of recently acquired memories. Soon after, memories undergo systems consolidation, which transfers memories from the hippocampus to the cortex for long-term storage, and requires ongoing re-activation of memory-related genes. We speculate that learning-induced H2A.Z eviction from nucleosomes initially contributes to stimulus-induced transcriptional induction needed for the initial process of memory consolidation. During systems consolidation, we speculate that delayed incorporation of H2A.Z into nucleosomes of memory-related genes in the cortex is needed to poise genes for rapid re-activation, thus supporting the long-term process of memory stabilization.
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Affiliation(s)
- Iva B Zovkic
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Brandon J Walters
- Department of Neuroscience and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
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62
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Law C, Cheung P. Expression of Non-acetylatable H2A.Z in Myoblast Cells Blocks Myoblast Differentiation through Disruption of MyoD Expression. J Biol Chem 2015; 290:13234-49. [PMID: 25839232 DOI: 10.1074/jbc.m114.595462] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Indexed: 11/06/2022] Open
Abstract
H2A.Z is a histone H2A variant that is essential for viability in Tetrahymena and Drosophila and also during embryonic development of mice. Although implicated in diverse cellular processes, including transcriptional regulation, chromosome segregation, and heterochromatin formation, its essential function in cells remains unknown. Cellular differentiation is part of the developmental process of multicellular organisms. To elucidate the roles of H2A.Z and H2A.Z acetylation in cellular differentiation, we examined the effects of expressing wild type (WT) or a non-acetylatable form of H2A.Z in the growth and differentiation of the myoblast C2C12 cell line. Ectopic expression of wild type or mutant H2A.Z resulted in distinct phenotypes in the differentiation of the C2C12 cells and the formation of myotubes. Most strikingly, expression of the H2A.Z non-acetylatable mutant (H2A.Z-Ac-mut) resulted in a complete block of myoblast differentiation. We determined that this phenotype is caused by a loss of MyoD expression in the Ac-mut-expressing cells prior to and after induction of differentiation. Moreover, chromatin accessibility assays showed that the promoter region of MyoD is less accessible in the differentiation-defective cells. Altogether, these new findings show that expression of the Ac-mut form of H2A.Z resulted in a dominant phenotype that blocked differentiation due to chromatin changes at the MyoD promoter.
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Affiliation(s)
- Cindy Law
- From the Department of Medical Biophysics, University of Toronto, Ontario M5G 1L7, Canada and
| | - Peter Cheung
- From the Department of Medical Biophysics, University of Toronto, Ontario M5G 1L7, Canada and the Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
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63
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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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64
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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65
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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]
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66
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Histone exchange, chromatin structure and the regulation of transcription. Nat Rev Mol Cell Biol 2015; 16:178-89. [DOI: 10.1038/nrm3941] [Citation(s) in RCA: 650] [Impact Index Per Article: 72.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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67
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Sun R, Wu Y, Wang Y, Zang K, Wei H, Wang F, Yu M. DNA methylation regulates bromodomain-containing protein 2 expression during adipocyte differentiation. Mol Cell Biochem 2015; 402:23-31. [DOI: 10.1007/s11010-014-2310-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/20/2014] [Indexed: 01/24/2023]
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68
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Subramanian* V, Fields* PA, Boyer LA. H2A.Z: a molecular rheostat for transcriptional control. F1000PRIME REPORTS 2015; 7:01. [PMID: 25705384 PMCID: PMC4311278 DOI: 10.12703/p7-01] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The replacement of nucleosomal H2A with the histone variant H2A.Z is critical for regulating DNA-mediated processes across eukaryotes and for early development of multicellular organisms. How this variant performs these seemingly diverse roles has remained largely enigmatic. Here, we discuss recent mechanistic insights that have begun to reveal how H2A.Z functions as a molecular rheostat for gene control. We focus on specific examples in metazoans as a model for understanding how H2A.Z integrates information from histone post-translational modifications, other histone variants, and transcription factors (TFs) to regulate proper induction of gene expression programs in response to cellular cues. Finally, we propose a general model of how H2A.Z incorporation regulates chromatin states in diverse processes.
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69
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Wyce A, Degenhardt Y, Bai Y, Le B, Korenchuk S, Crouthame MC, McHugh CF, Vessella R, Creasy CL, Tummino PJ, Barbash O. Inhibition of BET bromodomain proteins as a therapeutic approach in prostate cancer. Oncotarget 2014; 4:2419-29. [PMID: 24293458 PMCID: PMC3926837 DOI: 10.18632/oncotarget.1572] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BET (bromodomain and extra-terminal) proteins regulate gene expression through their ability to bind to acetylated chromatin and subsequently activate RNA PolII-driven transcriptional elongation. Small molecule BET inhibitors prevent binding of BET proteins to acetylated histones and inhibit transcriptional activation of BET target genes. BET inhibitors attenuate cell growth and survival in several hematologic cancer models, partially through the down-regulation of the critical oncogene, MYC. We hypothesized that BET inhibitors will regulate MYC expression in solid tumors that frequently over-express MYC. Here we describe the effects of the highly specific BET inhibitor, I-BET762, on MYC expression in prostate cancer models. I-BET762 potently reduced MYC expression in prostate cancer cell lines and a patient-derived tumor model with subsequent inhibition of cell growth and reduction of tumor burden in vivo. Our data suggests that I-BET762 effects are partially driven by MYC down-regulation and underlines the critical importance of additional mechanisms of I-BET762 induced phenotypes.
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Affiliation(s)
- Anastasia Wyce
- Cancer Epigenetics DPU, Oncology R and D GlaxoSmithKline, Collegeville, PA, USA
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70
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Raychaudhuri N, Thamotharan S, Srinivasan M, Mahmood S, Patel MS, Devaskar SU. Postnatal exposure to a high-carbohydrate diet interferes epigenetically with thyroid hormone receptor induction of the adult male rat skeletal muscle glucose transporter isoform 4 expression. J Nutr Biochem 2014; 25:1066-76. [PMID: 25086780 DOI: 10.1016/j.jnutbio.2014.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 05/09/2014] [Accepted: 05/18/2014] [Indexed: 12/19/2022]
Abstract
Early life nutritional intervention causes adult-onset insulin resistance and obesity in rats. Thyroid hormone receptor (TR), in turn, transcriptionally enhances skeletal muscle Glut4 expression. We tested the hypothesis that reduced circulating thyroid-stimulating hormone and T4 concentrations encountered in postnatal (PN4-PN24) high-carbohydrate (HC) milk formula-fed versus the mother-fed controls (MF) would epigenetically interfere with TR induction of adult (100 days) male rat skeletal muscle Glut4 expression, thereby providing a molecular mechanism mediating insulin resistance. We observed increased DNA methylation of the CpG island with enhanced recruitment of Dnmt3a, Dnmt3b and MeCP2 in the glut4 promoter region along with reduced acetylation of histone (H)2A.Z and H4 particularly at the H4.lysine (K)16 residue, which was predominantly mediated by histone deacetylase 4 (HDAC4). This was followed by enhanced recruitment of heterochromatin protein 1β to the glut4 promoter with increased Suv39H1 methylase concentrations. These changes reduced TR binding of the T3 response element of the glut4 gene (TREs; -473 to -450 bp) detected qualitatively in vivo (electromobility shift assay) and quantified ex vivo (chromatin immunoprecipitation). In addition, the recruitment of steroid receptor coactivator and CREB-binding protein to the glut4 promoter-protein complex was reduced. Co-immunoprecipitation experiments confirmed the interaction between TR and CBP to be reduced and HDAC4 to be enhanced in HC versus MF groups. These molecular changes were associated with diminished skeletal muscle Glut4 mRNA and protein concentrations. We conclude that early postnatal exposure to HC diet epigenetically reduced TR induction of adult male skeletal muscle Glut4 expression, uncovering novel molecular mechanisms contributing to adult insulin resistance and obesity.
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Affiliation(s)
- Nupur Raychaudhuri
- Department of Pediatrics, Division of Neonatology & Developmental Biology, Neonatal Research Center, David Geffen School of Medicine UCLA, Los Angeles, CA 90095-1752, USA
| | - Shanthie Thamotharan
- Department of Pediatrics, Division of Neonatology & Developmental Biology, Neonatal Research Center, David Geffen School of Medicine UCLA, Los Angeles, CA 90095-1752, USA
| | - Malathi Srinivasan
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - Saleh Mahmood
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - Mulchand S Patel
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - Sherin U Devaskar
- Department of Pediatrics, Division of Neonatology & Developmental Biology, Neonatal Research Center, David Geffen School of Medicine UCLA, Los Angeles, CA 90095-1752, USA.
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71
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Gallenkamp D, Gelato KA, Haendler B, Weinmann H. Bromodomains and their pharmacological inhibitors. ChemMedChem 2014; 9:438-64. [PMID: 24497428 DOI: 10.1002/cmdc.201300434] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/23/2013] [Indexed: 12/15/2022]
Abstract
Over 60 bromodomains belonging to proteins with very different functions have been identified in humans. Several of them interact with acetylated lysine residues, leading to the recruitment and stabilization of protein complexes. The bromodomain and extra-terminal domain (BET) proteins contain tandem bromodomains which bind to acetylated histones and are thereby implicated in a number of DNA-centered processes, including the regulation of gene expression. The recent identification of inhibitors of BET and non-BET bromodomains is one of the few examples in which effective blockade of a protein-protein interaction can be achieved with a small molecule. This has led to major strides in the understanding of the function of bromodomain-containing proteins and their involvement in diseases such as cancer and inflammation. Indeed, BET bromodomain inhibitors are now being clinically evaluated for the treatment of hematological tumors and have also been tested in clinical trials for the relatively rare BRD-NUT midline carcinoma. This review gives an overview of the newest developments in the field, with a focus on the biology of selected bromodomain proteins on the one hand, and on reported pharmacological inhibitors on the other, including recent examples from the patent literature.
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72
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Sevilla A, Binda O. Post-translational modifications of the histone variant H2AZ. Stem Cell Res 2014; 12:289-95. [PMID: 24316985 PMCID: PMC4671304 DOI: 10.1016/j.scr.2013.11.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 10/17/2013] [Accepted: 11/06/2013] [Indexed: 01/09/2023] Open
Affiliation(s)
- Ana Sevilla
- The New York Stem Cell Foundation Laboratory, New York, NY, 10032, USA
| | - Olivier Binda
- Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom.
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73
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Nguyen V, Ranjan A, Stengel F, Wei D, Aebersold R, Wu C, Leschziner A. Molecular architecture of the ATP-dependent chromatin-remodeling complex SWR1. Cell 2013; 154:1220-31. [PMID: 24034246 PMCID: PMC3776929 DOI: 10.1016/j.cell.2013.08.018] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 06/24/2013] [Accepted: 08/09/2013] [Indexed: 11/19/2022]
Abstract
The ATP-dependent chromatin-remodeling complex SWR1 exchanges a variant histone H2A.Z/H2B dimer for a canonical H2A/H2B dimer at nucleosomes flanking histone-depleted regions, such as promoters. This localization of H2A.Z is conserved throughout eukaryotes. SWR1 is a 1 megadalton complex containing 14 different polypeptides, including the AAA+ ATPases Rvb1 and Rvb2. Using electron microscopy, we obtained the three-dimensional structure of SWR1 and mapped its major functional components. Our data show that SWR1 contains a single heterohexameric Rvb1/Rvb2 ring that, together with the catalytic subunit Swr1, brackets two independently assembled multisubunit modules. We also show that SWR1 undergoes a large conformational change upon engaging a limited region of the nucleosome core particle. Our work suggests an important structural role for the Rvbs and a distinct substrate-handling mode by SWR1, thereby providing a structural framework for understanding the complex dimer-exchange reaction.
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Affiliation(s)
- Vu Q. Nguyen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Anand Ranjan
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Florian Stengel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8092, Switzerland
| | - Debbie Wei
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8092, Switzerland
- Faculty of Science, University of Zurich, Zurich 8057, Switzerland
| | - Carl Wu
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
- HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
| | - Andres E. Leschziner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Corresponding author
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74
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Kim K, Punj V, Choi J, Heo K, Kim JM, Laird PW, An W. Gene dysregulation by histone variant H2A.Z in bladder cancer. Epigenetics Chromatin 2013; 6:34. [PMID: 24279307 PMCID: PMC3853418 DOI: 10.1186/1756-8935-6-34] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/27/2013] [Indexed: 12/20/2022] Open
Abstract
Background The incorporation of histone variants into nucleosomes is one of the main strategies that the cell uses to regulate the structure and function of chromatin. Histone H2A.Z is an evolutionarily conserved histone H2A variant that is preferentially localized within nucleosomes at the transcriptional start site (TSS). H2A.Z reorganizes the local chromatin structure and recruits the transcriptional machinery for gene activation. High expression of H2A.Z has been reported in several types of cancers and is causally linked to genomic instability and tumorigenesis. However, it is not entirely clear how H2A.Z overexpression in cancer cells establishes aberrant chromatin states and promotes gene expression. Results Through integration of genome-wide H2A.Z ChIP-seq data with microarray data, we demonstrate that H2A.Z is enriched around the TSS of cell cycle regulatory genes in bladder cancer cells, and this enrichment is correlated with the elevated expression of cancer-promoting genes. RNAi-mediated knockdown of H2A.Z in the cancer cells causes transcriptional suppression of multiple cell cycle regulatory genes with a distinct decrease in cell proliferation. H2A.Z nucleosomes around the TSS have higher levels of H3K4me2/me3, which coincides with the recruitment of two chromatin factors, WDR5 and BPTF. The observed recruitment is functional, as the active states of H2A.Z target genes are largely erased by suppressing the expression of WDR5 or BPTF, effects resembling H2A.Z knockdown. Conclusions We conclude that H2A.Z is overexpressed in bladder cancer cells and contributes to cancer-related transcription pathways. We also provide evidence in support of the engagement of H3K4me2/me3 and WDR5/BPTF in H2A.Z-induced cancer pathogenesis. Further studies are warranted to understand how H2A.Z overexpression contributes to the recruitment of the full repertoire of transcription machinery to target genes in bladder cancer cells.
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75
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Lalonde ME, Avvakumov N, Glass KC, Joncas FH, Saksouk N, Holliday M, Paquet E, Yan K, Tong Q, Klein BJ, Tan S, Yang XJ, Kutateladze TG, Côté J. Exchange of associated factors directs a switch in HBO1 acetyltransferase histone tail specificity. Genes Dev 2013; 27:2009-24. [PMID: 24065767 PMCID: PMC3792477 DOI: 10.1101/gad.223396.113] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 08/23/2013] [Indexed: 12/13/2022]
Abstract
Histone acetyltransferases (HATs) assemble into multisubunit complexes in order to target distinct lysine residues on nucleosomal histones. Here, we characterize native HAT complexes assembled by the BRPF family of scaffold proteins. Their plant homeodomain (PHD)-Zn knuckle-PHD domain is essential for binding chromatin and is restricted to unmethylated H3K4, a specificity that is reversed by the associated ING subunit. Native BRPF1 complexes can contain either MOZ/MORF or HBO1 as catalytic acetyltransferase subunit. Interestingly, while the previously reported HBO1 complexes containing JADE scaffold proteins target histone H4, the HBO1-BRPF1 complex acetylates only H3 in chromatin. We mapped a small region to the N terminus of scaffold proteins responsible for histone tail selection on chromatin. Thus, alternate choice of subunits associated with HBO1 can switch its specificity between H4 and H3 tails. These results uncover a crucial new role for associated proteins within HAT complexes, previously thought to be intrinsic to the catalytic subunit.
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Affiliation(s)
- Marie-Eve Lalonde
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, Québec G1R 2J6, Canada
| | - Nikita Avvakumov
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, Québec G1R 2J6, Canada
| | | | - France-Hélène Joncas
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, Québec G1R 2J6, Canada
| | - Nehmé Saksouk
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, Québec G1R 2J6, Canada
| | - Michael Holliday
- Molecular Biology Program, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Eric Paquet
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, Québec G1R 2J6, Canada
| | - Kezhi Yan
- The Rosalind and Morris Goodman Cancer Research Center, Department of Biochemistry, McGill University, Montreal, Québec H3A 1A1, Canada
| | | | | | - Song Tan
- Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania University, University Park, Pennsylvania 16802, USA
| | - Xiang-Jiao Yang
- The Rosalind and Morris Goodman Cancer Research Center, Department of Biochemistry, McGill University, Montreal, Québec H3A 1A1, Canada
- Department of Medicine, McGill University Health Center, Montreal, Québec H3A 1A1, Canada
| | - Tatiana G. Kutateladze
- Department of Pharmacology
- Molecular Biology Program, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Jacques Côté
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, Québec G1R 2J6, Canada
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Subramanian V, Mazumder A, Surface LE, Butty VL, Fields PA, Alwan A, Torrey L, Thai KK, Levine SS, Bathe M, Boyer LA. H2A.Z acidic patch couples chromatin dynamics to regulation of gene expression programs during ESC differentiation. PLoS Genet 2013; 9:e1003725. [PMID: 23990805 PMCID: PMC3749939 DOI: 10.1371/journal.pgen.1003725] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 07/01/2013] [Indexed: 12/20/2022] Open
Abstract
The histone H2A variant H2A.Z is essential for embryonic development and for proper control of developmental gene expression programs in embryonic stem cells (ESCs). Divergent regions of amino acid sequence of H2A.Z likely determine its functional specialization compared to core histone H2A. For example, H2A.Z contains three divergent residues in the essential C-terminal acidic patch that reside on the surface of the histone octamer as an uninterrupted acidic patch domain; however, we know little about how these residues contribute to chromatin structure and function. Here, we show that the divergent amino acids Gly92, Asp97, and Ser98 in the H2A.Z C-terminal acidic patch (H2A.Z(AP3)) are critical for lineage commitment during ESC differentiation. H2A.Z is enriched at most H3K4me3 promoters in ESCs including poised, bivalent promoters that harbor both activating and repressive marks, H3K4me3 and H3K27me3 respectively. We found that while H2A.Z(AP3) interacted with its deposition complex and displayed a highly similar distribution pattern compared to wild-type H2A.Z, its enrichment levels were reduced at target promoters. Further analysis revealed that H2A.Z(AP3) was less tightly associated with chromatin, suggesting that the mutant is more dynamic. Notably, bivalent genes in H2A.Z(AP3) ESCs displayed significant changes in expression compared to active genes. Moreover, bivalent genes in H2A.Z(AP3) ESCs gained H3.3, a variant associated with higher nucleosome turnover, compared to wild-type H2A.Z. We next performed single cell imaging to measure H2A.Z dynamics. We found that H2A.Z(AP3) displayed higher mobility in chromatin compared to wild-type H2A.Z by fluorescent recovery after photobleaching (FRAP). Moreover, ESCs treated with the transcriptional inhibitor flavopiridol resulted in a decrease in the H2A.Z(AP3) mobile fraction and an increase in its occupancy at target genes indicating that the mutant can be properly incorporated into chromatin. Collectively, our work suggests that the divergent residues in the H2A.Z acidic patch comprise a unique domain that couples control of chromatin dynamics to the regulation of developmental gene expression patterns during lineage commitment.
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Affiliation(s)
- Vidya Subramanian
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Aprotim Mazumder
- Laboratory for Computational Biology and Biophysics, and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Lauren E. Surface
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Vincent L. Butty
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Paul A. Fields
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Allison Alwan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Lillian Torrey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Kevin K. Thai
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Stuart S. Levine
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Mark Bathe
- Laboratory for Computational Biology and Biophysics, and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Laurie A. Boyer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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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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Vardabasso C, Hasson D, Ratnakumar K, Chung CY, Duarte LF, Bernstein E. Histone variants: emerging players in cancer biology. Cell Mol Life Sci 2013; 71:379-404. [PMID: 23652611 DOI: 10.1007/s00018-013-1343-z] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 04/09/2013] [Accepted: 04/11/2013] [Indexed: 01/01/2023]
Abstract
Histone variants are key players in shaping chromatin structure, and, thus, in regulating fundamental cellular processes such as chromosome segregation and gene expression. Emerging evidence points towards a role for histone variants in contributing to tumor progression, and, recently, the first cancer-associated mutation in a histone variant-encoding gene was reported. In addition, genetic alterations of the histone chaperones that specifically regulate chromatin incorporation of histone variants are rapidly being uncovered in numerous cancers. Collectively, these findings implicate histone variants as potential drivers of cancer initiation and/or progression, and, therefore, targeting histone deposition or the chromatin remodeling machinery may be of therapeutic value. Here, we review the mammalian histone variants of the H2A and H3 families in their respective cellular functions, and their involvement in tumor biology.
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Affiliation(s)
- Chiara Vardabasso
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
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