151
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Hassan HE, Keita JA, Narayan L, Brady SM, Frederick R, Carlson S, C Glass K, Natesan S, Buttolph T, Fandy TE. The combination of dimethoxycurcumin with DNA methylation inhibitor enhances gene re-expression of promoter-methylated genes and antagonizes their cytotoxic effect. Epigenetics 2016; 11:740-749. [PMID: 27588609 DOI: 10.1080/15592294.2016.1226452] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Curcumin and its analogs exhibited antileukemic activity either as single agent or in combination therapy. Dimethoxycurcumin (DMC) is a more metabolically stable curcumin analog that was shown to induce the expression of promoter-methylated genes without reversing DNA methylation. Accordingly, co-treatment with DMC and DNA methyltransferase (DNMT) inhibitors could hypothetically enhance the re-expression of promoter-methylated tumor suppressor genes. In this study, we investigated the cytotoxic effects and epigenetic changes associated with the combination of DMC and the DNMT inhibitor decitabine (DAC) in primary leukemia samples and cell lines. The combination demonstrated antagonistic cytotoxic effects and was minimally cytotoxic to primary leukemia cells. The combination did not affect the metabolic stability of DMC. Although the combination enhanced the downregulation of nuclear DNMT proteins, the hypomethylating activity of the combination was not increased significantly compared to DAC alone. On the other hand, the combination significantly increased H3K27 acetylation (H3K27Ac) compared to the single agents near the promoter region of promoter-methylated genes. Furthermore, sequential chromatin immunoprecipitation (ChIP) and DNA pyrosequencing of the chromatin-enriched H3K27Ac did not show any significant decrease in DNA methylation compared to other regions. Consequently, the enhanced induction of promoter-methylated genes by the combination compared to DAC alone is mediated by a mechanism that involves increased histone acetylation and not through potentiation of the DNA hypomethylating activity of DAC. Collectively, our results provide the mechanistic basis for further characterization of this combination in leukemia animal models and early phase clinical trials.
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Affiliation(s)
- Hazem E Hassan
- a Department of Pharmaceutical Sciences , University of Maryland , Baltimore , MD , USA.,b Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy , Helwan University , Cairo , Egypt
| | - Jean-Arnaud Keita
- c Department of Pharmaceutical Sciences , Albany College of Pharmacy (Vermont Campus) , Colchester , VT , USA
| | - Lawrence Narayan
- c Department of Pharmaceutical Sciences , Albany College of Pharmacy (Vermont Campus) , Colchester , VT , USA
| | - Sean M Brady
- c Department of Pharmaceutical Sciences , Albany College of Pharmacy (Vermont Campus) , Colchester , VT , USA
| | - Richard Frederick
- c Department of Pharmaceutical Sciences , Albany College of Pharmacy (Vermont Campus) , Colchester , VT , USA
| | - Samuel Carlson
- c Department of Pharmaceutical Sciences , Albany College of Pharmacy (Vermont Campus) , Colchester , VT , USA
| | - Karen C Glass
- c Department of Pharmaceutical Sciences , Albany College of Pharmacy (Vermont Campus) , Colchester , VT , USA
| | - Senthil Natesan
- d Department of Experimental and Systems Pharmacology , Washington State University , Spokane , WA , USA
| | - Thomm Buttolph
- e Department of Neurological Sciences , University of Vermont , Burlington , VT , USA
| | - Tamer E Fandy
- c Department of Pharmaceutical Sciences , Albany College of Pharmacy (Vermont Campus) , Colchester , VT , USA
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152
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van de Leemput J, Hess JL, Glatt SJ, Tsuang MT. Genetics of Schizophrenia: Historical Insights and Prevailing Evidence. ADVANCES IN GENETICS 2016; 96:99-141. [PMID: 27968732 DOI: 10.1016/bs.adgen.2016.08.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Schizophrenia's (SZ's) heritability and familial transmission have been known for several decades; however, despite the clear evidence for a genetic component, it has been very difficult to pinpoint specific causative genes. Even so genetic studies have taught us a lot, even in the pregenomic era, about the molecular underpinnings and disease-relevant pathways. Recurring themes emerged revealing the involvement of neurodevelopmental processes, glutamate regulation, and immune system differential activation in SZ etiology. The recent emergence of epigenetic studies aimed at shedding light on the biological mechanisms underlying SZ has provided another layer of information in the investigation of gene and environment interactions. However, this epigenetic insight also brings forth another layer of complexity to the (epi)genomic landscape such as interactions between genetic variants, epigenetic marks-including cross-talk between DNA methylation and histone modification processes-, gene expression regulation, and environmental influences. In this review, we seek to synthesize perspectives, including limitations and obstacles yet to overcome, from genetic and epigenetic literature on SZ through a qualitative review of risk factors and prevailing hypotheses. Encouraged by the findings of both genetic and epigenetic studies to date, as well as the continued development of new technologies to collect and interpret large-scale studies, we are left with a positive outlook for the future of elucidating the molecular genetic mechanisms underlying SZ and other complex neuropsychiatric disorders.
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Affiliation(s)
- J van de Leemput
- University of California, San Diego, La Jolla, CA, United States
| | - J L Hess
- SUNY Upstate Medical University, Syracuse, NY, United States
| | - S J Glatt
- SUNY Upstate Medical University, Syracuse, NY, United States
| | - M T Tsuang
- University of California, San Diego, La Jolla, CA, United States
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153
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ChIP-seq Data Processing for PcG Proteins and Associated Histone Modifications. Methods Mol Biol 2016. [PMID: 27659973 DOI: 10.1007/978-1-4939-6380-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Chromatin Immunoprecipitation followed by massively parallel DNA sequencing (ChIP-sequencing) has emerged as an essential technique to study the genome-wide location of DNA- or chromatin-associated proteins, such as the Polycomb group (PcG) proteins. After being generated by the sequencer, raw ChIP-seq sequence reads need to be processed by a data analysis pipeline. Here we describe the computational steps required to process PcG ChIP-seq data, including alignment, peak calling, and downstream analysis.
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154
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Samuelsson JK, Dumbovic G, Polo C, Moreta C, Alibés A, Ruiz-Larroya T, Giménez-Bonafé P, Alonso S, Forcales SV, Manuel P. Helicase Lymphoid-Specific Enzyme Contributes to the Maintenance of Methylation of SST1 Pericentromeric Repeats That Are Frequently Demethylated in Colon Cancer and Associate with Genomic Damage. EPIGENOMES 2016; 1. [PMID: 31867127 PMCID: PMC6924650 DOI: 10.3390/epigenomes1010002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
DNA hypomethylation at repetitive elements accounts for the genome-wide DNA hypomethylation common in cancer, including colorectal cancer (CRC). We identified a pericentromeric repeat element called SST1 frequently hypomethylated (>5% demethylation compared with matched normal tissue) in several cancers, including 28 of 128 (22%) CRCs. SST1 somatic demethylation associated with genome damage, especially in tumors with wild-type TP53. Seven percent of the 128 CRCs exhibited a higher (“severe”) level of demethylation (≥10%) that co-occurred with TP53 mutations. SST1 demethylation correlated with distinct histone marks in CRC cell lines and primary tumors: demethylated SST1 associated with high levels of the repressive histone 3 lysine 27 trimethylation (H3K27me3) mark and lower levels of histone 3 lysine 9 trimethylation (H3K9me3). Furthermore, induced demethylation of SST1 by 5-aza-dC led to increased H3K27me3 and reduced H3K9me3. Thus, in some CRCs, SST1 demethylation reflects an epigenetic reprogramming associated with changes in chromatin structure that may affect chromosomal integrity. The chromatin remodeler factor, the helicase lymphoid-specific (HELLS) enzyme, called the “epigenetic guardian of repetitive elements”, interacted with SST1 as shown by chromatin immunoprecipitation, and down-regulation of HELLS by shRNA resulted in demethylation of SST1 in vitro. Altogether these results suggest that HELLS contributes to SST1 methylation maintenance. Alterations in HELLS recruitment and function could contribute to the somatic demethylation of SST1 repeat elements undergone before and/or during CRC pathogenesis.
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Affiliation(s)
- Johanna K. Samuelsson
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
- Active Motif, 1914 Palomar Oaks Way, Suite 150, Carlsbad, CA 92008, USA
| | - Gabrijela Dumbovic
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Badalona 08916, Barcelona, Spain
| | - Cristian Polo
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Badalona 08916, Barcelona, Spain
| | - Cristina Moreta
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Badalona 08916, Barcelona, Spain
| | - Andreu Alibés
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Badalona 08916, Barcelona, Spain
| | | | - Pepita Giménez-Bonafé
- Departament de Ciències Fisiòlogiques, Facultat de Medicina i Ciències de la Salut, Campus Ciències de la Salut, Bellvitge, Universitat de Barcelona, Hospitalet del Llobregat 08916, Barcelona, Spain
| | - Sergio Alonso
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Badalona 08916, Barcelona, Spain
| | - Sonia-V. Forcales
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Badalona 08916, Barcelona, Spain
- Correspondence: (S.-V.F.); (M.P.)
| | - Perucho Manuel
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Campus Can Ruti, Badalona 08916, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
- Correspondence: (S.-V.F.); (M.P.)
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155
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Zheng H, Huang B, Zhang B, Xiang Y, Du Z, Xu Q, Li Y, Wang Q, Ma J, Peng X, Xu F, Xie W. Resetting Epigenetic Memory by Reprogramming of Histone Modifications in Mammals. Mol Cell 2016; 63:1066-79. [DOI: 10.1016/j.molcel.2016.08.032] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 06/01/2016] [Accepted: 08/24/2016] [Indexed: 12/24/2022]
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156
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Tang WWC, Kobayashi T, Irie N, Dietmann S, Surani MA. Specification and epigenetic programming of the human germ line. Nat Rev Genet 2016; 17:585-600. [DOI: 10.1038/nrg.2016.88] [Citation(s) in RCA: 274] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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157
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Defining, distinguishing and detecting the contribution of heterogeneous methylation to cancer heterogeneity. Semin Cell Dev Biol 2016; 64:5-17. [PMID: 27582426 DOI: 10.1016/j.semcdb.2016.08.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 08/24/2016] [Indexed: 01/07/2023]
Abstract
DNA methylation is a fundamental means of epigenetic gene regulation that occurs in virtually all cell types. In many higher organisms, including humans, it plays vital roles in cell differentiation and homeostatic maintenance of cell phenotype. The control of DNA methylation has traditionally been attributed to a highly coordinated, linear process, whose dysregulation has been associated with numerous pathologies including cancer, where it occurs early in, and even prior to, the development of neoplastic tissues. Recent experimental evidence has demonstrated that, contrary to prevailing paradigms, methylation patterns are actually maintained through inexact, dynamic processes. These processes normally result in minor stochastic differences between cells that accumulate with age. However, various factors, including cancer itself, can lead to substantial differences in intercellular methylation patterns, viz. methylation heterogeneity. Advancements in molecular biology techniques are just now beginning to allow insight into how this heterogeneity contributes to clonal evolution and overall cancer heterogeneity. In the current review, we begin by presenting a didactic overview of how the basal bimodal methylome is established and maintained. We then provide a synopsis of some of the factors that lead to the accrual of heterogeneous methylation and how this heterogeneity may lead to gene silencing and impact the development of cancerous phenotypes. Lastly, we highlight currently available methylation assessment techniques and discuss their suitability to the study of heterogeneous methylation.
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158
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Liu H, Li S, Wang X, Zhu J, Wei Y, Wang Y, Wen Y, Wang L, Huang Y, Zhang B, Shang S, Zhang Y. DNA methylation dynamics: identification and functional annotation. Brief Funct Genomics 2016; 15:470-484. [PMID: 27515490 DOI: 10.1093/bfgp/elw029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
DNA methylation is an epigenetic modification of cytosines that undergoes dynamic changes in a temporal, spatial and cell-type-specific manner. Recent advances in technology have permitted the profiling of high-throughput methylomes in large numbers of biological samples. Various computational tools have been developed to identify and analyze DNA methylation dynamics in a variety of critical biological processes. As DNA methylation is becoming increasingly viewed as a dynamic process, the mechanisms governing DNA methylation dynamics and its roles in the transcriptional regulatory network are of great interest. It has been reported that DNA methylation dynamics plays essential roles in multiple biological processes, including development and cancer. As a functional event, the dynamics of DNA methylation have become increasingly relevant to many researchers. Here, we review state-of-the-art advances at three levels (genome-wide identification, regulatory mechanism investigation and the functional annotation) in the field of DNA methylation dynamics, as well as the future perspective of DNA methylation dynamics.
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159
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Jung J, Buisman S, de Haan G. Hematopoiesis during development, aging, and disease. Exp Hematol 2016; 44:689-95. [DOI: 10.1016/j.exphem.2016.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 11/26/2022]
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160
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Hosogane M, Funayama R, Shirota M, Nakayama K. Lack of Transcription Triggers H3K27me3 Accumulation in the Gene Body. Cell Rep 2016; 16:696-706. [PMID: 27396330 DOI: 10.1016/j.celrep.2016.06.034] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 05/07/2016] [Accepted: 06/05/2016] [Indexed: 10/21/2022] Open
Abstract
Trimethylated H3K27 (H3K27me3) is associated with transcriptional repression, and its abundance in chromatin is frequently altered in cancer. However, it has remained unclear how genomic regions modified by H3K27me3 are specified and formed. We previously showed that downregulation of transcription by oncogenic Ras signaling precedes upregulation of H3K27me3 level. Here, we show that lack of transcription as a result of deletion of the transcription start site of a gene is sufficient to increase H3K27me3 content in the gene body. We further found that histone deacetylation mediates Ras-induced gene silencing and subsequent H3K27me3 accumulation. The H3K27me3 level increased gradually after Ras activation, requiring at least 35 days to achieve saturation. Such maximal accumulation of H3K27me3 was reversed by forced induction of transcription with the dCas9-activator system. Thus, our results indicate that changes in H3K27me3 level, especially in the body of a subset of genes, are triggered by changes in transcriptional activity itself.
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Affiliation(s)
- Masaki Hosogane
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Ryo Funayama
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Matsuyuki Shirota
- Division of Interdisciplinary Medical Sciences, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Keiko Nakayama
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan.
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161
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Jin J, Lian T, Gu C, Yu K, Gao YQ, Su XD. The effects of cytosine methylation on general transcription factors. Sci Rep 2016; 6:29119. [PMID: 27385050 PMCID: PMC4935894 DOI: 10.1038/srep29119] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/15/2016] [Indexed: 12/24/2022] Open
Abstract
DNA methylation on CpG sites is the most common epigenetic modification. Recently, methylation in a non-CpG context was found to occur widely on genomic DNA. Moreover, methylation of non-CpG sites is a highly controlled process, and its level may vary during cellular development. To study non-CpG methylation effects on DNA/protein interactions, we have chosen three human transcription factors (TFs): glucocorticoid receptor (GR), brain and muscle ARNT-like 1 (BMAL1) - circadian locomotor output cycles kaput (CLOCK) and estrogen receptor (ER) with methylated or unmethylated DNA binding sequences, using single-molecule and isothermal titration calorimetry assays. The results demonstrated that these TFs interact with methylated DNA with different effects compared with their cognate DNA sequences. The effects of non-CpG methylation on transcriptional regulation were validated by cell-based luciferase assay at protein level. The mechanisms of non-CpG methylation influencing DNA-protein interactions were investigated by crystallographic analyses and molecular dynamics simulation. With BisChIP-seq assays in HEK-293T cells, we found that GR can recognize highly methylated sites within chromatin in cells. Therefore, we conclude that non-CpG methylation of DNA can provide a mechanism for regulating gene expression through directly affecting the binding of TFs.
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Affiliation(s)
- Jianshi Jin
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Tengfei Lian
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Chan Gu
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Kai Yu
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Yi Qin Gao
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Xiao-Dong Su
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
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162
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Nichol JN, Dupéré-Richer D, Ezponda T, Licht JD, Miller WH. H3K27 Methylation: A Focal Point of Epigenetic Deregulation in Cancer. Adv Cancer Res 2016; 131:59-95. [PMID: 27451124 PMCID: PMC5325795 DOI: 10.1016/bs.acr.2016.05.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Epigenetics, the modification of chromatin without changing the DNA sequence itself, determines whether a gene is expressed, and how much of a gene is expressed. Methylation of lysine 27 on histone 3 (H3K27me), a modification usually associated with gene repression, has established roles in regulating the expression of genes involved in lineage commitment and differentiation. Not surprisingly, alterations in the homeostasis of this critical mark have emerged as a recurrent theme in the pathogenesis of many cancers. Perturbations in the distribution or levels of H3K27me occur due to deregulation at all levels of the process, either by mutation in the histone itself, or changes in the activity of the writers, erasers, or readers of this mark. Additionally, as no single histone mark alone determines the overall transcriptional readiness of a chromatin region, deregulation of other chromatin marks can also have dramatic consequences. Finally, the significance of mutations altering H3K27me is highlighted by the poor clinical outcome of patients whose tumors harbor such lesions. Current therapeutic approaches targeting aberrant H3K27 methylation remain to be proven useful in the clinic. Understanding the biological consequences and gene expression pathways affected by aberrant H3K27 methylation may lead to identification of new therapeutic targets and strategies.
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Affiliation(s)
- J N Nichol
- Segal Cancer Centre and Lady Davis Institute, Jewish General Hospital, Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - D Dupéré-Richer
- Division of Hematology Oncology, The University of Florida Health Cancer Center, Gainesville, FL, United States
| | - T Ezponda
- Division of Hematology/Oncology, Centro de Investigacion Medica Aplicada (CIMA), IDISNA, Pamplona, Spain
| | - J D Licht
- Division of Hematology Oncology, The University of Florida Health Cancer Center, Gainesville, FL, United States
| | - W H Miller
- Segal Cancer Centre and Lady Davis Institute, Jewish General Hospital, Division of Experimental Medicine, McGill University, Montreal, QC, Canada.
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163
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von Meyenn F, Iurlaro M, Habibi E, Liu NQ, Salehzadeh-Yazdi A, Santos F, Petrini E, Milagre I, Yu M, Xie Z, Kroeze LI, Nesterova TB, Jansen JH, Xie H, He C, Reik W, Stunnenberg HG. Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells. Mol Cell 2016; 62:848-861. [PMID: 27237052 PMCID: PMC4914828 DOI: 10.1016/j.molcel.2016.04.025] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/04/2016] [Accepted: 04/21/2016] [Indexed: 12/20/2022]
Abstract
Global demethylation is part of a conserved program of epigenetic reprogramming to naive pluripotency. The transition from primed hypermethylated embryonic stem cells (ESCs) to naive hypomethylated ones (serum-to-2i) is a valuable model system for epigenetic reprogramming. We present a mathematical model, which accurately predicts global DNA demethylation kinetics. Experimentally, we show that the main drivers of global demethylation are neither active mechanisms (Aicda, Tdg, and Tet1-3) nor the reduction of de novo methylation. UHRF1 protein, the essential targeting factor for DNMT1, is reduced upon transition to 2i, and so is recruitment of the maintenance methylation machinery to replication foci. Concurrently, there is global loss of H3K9me2, which is needed for chromatin binding of UHRF1. These mechanisms synergistically enforce global DNA hypomethylation in a replication-coupled fashion. Our observations establish the molecular mechanism for global demethylation in naive ESCs, which has key parallels with those operating in primordial germ cells and early embryos. Impaired DNA methylation maintenance is the cause of global demethylation in naive ESCs Loss of H3K9me2 and UHRF1 lead to impaired maintenance targeting to replication foci TET enzymes are not required for global demethylation Mathematical model accurately predicts global 5mC and 5hmC during epigenetic resetting
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Affiliation(s)
| | - Mario Iurlaro
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Ehsan Habibi
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA Nijmegen, the Netherlands
| | - Ning Qing Liu
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA Nijmegen, the Netherlands
| | - Ali Salehzadeh-Yazdi
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Fátima Santos
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Edoardo Petrini
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Inês Milagre
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Miao Yu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Zhenqing Xie
- Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - Leonie I Kroeze
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Nijmegen Medical Centre and Radboudumc Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Tatyana B Nesterova
- Developmental Epigenetics Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Joop H Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Nijmegen Medical Centre and Radboudumc Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Hehuang Xie
- Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24060, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA Nijmegen, the Netherlands.
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164
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Feichtinger J, Hernández I, Fischer C, Hanscho M, Auer N, Hackl M, Jadhav V, Baumann M, Krempl PM, Schmidl C, Farlik M, Schuster M, Merkel A, Sommer A, Heath S, Rico D, Bock C, Thallinger GG, Borth N. Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time. Biotechnol Bioeng 2016; 113:2241-53. [PMID: 27072894 PMCID: PMC5006888 DOI: 10.1002/bit.25990] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 03/15/2016] [Accepted: 04/07/2016] [Indexed: 01/03/2023]
Abstract
The most striking characteristic of CHO cells is their adaptability, which enables efficient production of proteins as well as growth under a variety of culture conditions, but also results in genomic and phenotypic instability. To investigate the relative contribution of genomic and epigenetic modifications towards phenotype evolution, comprehensive genome and epigenome data are presented for six related CHO cell lines, both in response to perturbations (different culture conditions and media as well as selection of a specific phenotype with increased transient productivity) and in steady state (prolonged time in culture under constant conditions). Clear transitions were observed in DNA‐methylation patterns upon each perturbation, while few changes occurred over time under constant conditions. Only minor DNA‐methylation changes were observed between exponential and stationary growth phase; however, throughout a batch culture the histone modification pattern underwent continuous adaptation. Variation in genome sequence between the six cell lines on the level of SNPs, InDels, and structural variants is high, both upon perturbation and under constant conditions over time. The here presented comprehensive resource may open the door to improved control and manipulation of gene expression during industrial bioprocesses based on epigenetic mechanisms. Biotechnol. Bioeng. 2016;113: 2241–2253. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Julia Feichtinger
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria.,Graz University of Technology, Graz, Austria
| | - Inmaculada Hernández
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Christoph Fischer
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria.,Graz University of Technology, Graz, Austria
| | - Michael Hanscho
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Norbert Auer
- University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, 1190, Austria
| | - Matthias Hackl
- University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, 1190, Austria
| | - Vaibhav Jadhav
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Martina Baumann
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Peter M Krempl
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria.,Graz University of Technology, Graz, Austria
| | - Christian Schmidl
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | | | - Andreas Sommer
- Research Institute of Molecular Pathology, Vienna, Austria
| | - Simon Heath
- Center for Genomic Regulation (CRG), Barcelona, Spain
| | - Daniel Rico
- Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Gerhard G Thallinger
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria.,Graz University of Technology, Graz, Austria
| | - Nicole Borth
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria. .,University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, 1190, Austria.
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165
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Crampton M, Sripathi VR, Hossain K, Kalavacharla V. Analyses of Methylomes Derived from Meso-American Common Bean (Phaseolus vulgaris L.) Using MeDIP-Seq and Whole Genome Sodium Bisulfite-Sequencing. FRONTIERS IN PLANT SCIENCE 2016; 7:447. [PMID: 27199997 PMCID: PMC4845718 DOI: 10.3389/fpls.2016.00447] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/22/2016] [Indexed: 05/25/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is economically important for its high protein, fiber, and micronutrient contents, with a relatively small genome size of ∼587 Mb. Common bean is genetically diverse with two major gene pools, Meso-American and Andean. The phenotypic variability within common bean is partly attributed to the genetic diversity and epigenetic changes that are largely influenced by environmental factors. It is well established that an important epigenetic regulator of gene expression is DNA methylation. Here, we present results generated from two high-throughput sequencing technologies, methylated DNA immunoprecipitation-sequencing (MeDIP-seq) and whole genome bisulfite-sequencing (BS-Seq). Our analyses revealed that this Meso-American common bean displays similar methylation patterns as other previously published plant methylomes, with CG ∼50%, CHG ∼30%, and CHH ∼2.7% methylation, however, these differ from the common bean reference methylome of Andean origin. We identified higher CG methylation levels in both promoter and genic regions than CHG and CHH contexts. Moreover, we found relatively higher CG methylation levels in genes than in promoters. Conversely, the CHG and CHH methylation levels were highest in promoters than in genes. This is the first genome-wide DNA methylation profiling study in a Meso-American common bean cultivar ("Sierra") using NGS approaches. Our long-term goal is to generate genome-wide epigenomic maps in common bean focusing on chromatin accessibility, histone modifications, and DNA methylation.
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Affiliation(s)
- Mollee Crampton
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, DoverDE, USA
| | | | - Khwaja Hossain
- Division of Science and Mathematics, Mayville State University, MayvilleND, USA
| | - Venu Kalavacharla
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, DoverDE, USA
- Center for Integrated Biological and Environmental Research, Delaware State University, DoverDE, USA
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166
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Moreno-Romero J, Jiang H, Santos-González J, Köhler C. Parental epigenetic asymmetry of PRC2-mediated histone modifications in the Arabidopsis endosperm. EMBO J 2016; 35:1298-311. [PMID: 27113256 DOI: 10.15252/embj.201593534] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/17/2016] [Indexed: 12/11/2022] Open
Abstract
Parental genomes in the endosperm are marked by differential DNA methylation and are therefore epigenetically distinct. This epigenetic asymmetry is established in the gametes and maintained after fertilization by unknown mechanisms. In this manuscript, we have addressed the key question whether parentally inherited differential DNA methylation affects de novo targeting of chromatin modifiers in the early endosperm. Our data reveal that polycomb-mediated H3 lysine 27 trimethylation (H3K27me3) is preferentially localized to regions that are targeted by the DNA glycosylase DEMETER (DME), mechanistically linking DNA hypomethylation to imprinted gene expression. Our data furthermore suggest an absence of de novo DNA methylation in the early endosperm, providing an explanation how DME-mediated hypomethylation of the maternal genome is maintained after fertilization. Lastly, we show that paternal-specific H3K27me3-marked regions are located at pericentromeric regions, suggesting that H3K27me3 and DNA methylation are not necessarily exclusive marks at pericentromeric regions in the endosperm.
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Affiliation(s)
- Jordi Moreno-Romero
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, Sweden
| | - Hua Jiang
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala, Sweden
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167
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Bell JSK, Kagey JD, Barwick BG, Dwivedi B, McCabe MT, Kowalski J, Vertino PM. Factors affecting the persistence of drug-induced reprogramming of the cancer methylome. Epigenetics 2016; 11:273-87. [PMID: 27082926 DOI: 10.1080/15592294.2016.1158364] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aberrant DNA methylation is a critical feature of cancer. Epigenetic therapy seeks to reverse these changes to restore normal gene expression. DNA demethylating agents, including 5-aza-2'-deoxycytidine (DAC), are currently used to treat certain leukemias, and can sensitize solid tumors to chemotherapy and immunotherapy. However, it has been difficult to pin the clinical efficacy of these agents to specific demethylation events, and the factors that contribute to the durability of response remain largely unknown. Here we examined the genome-wide kinetics of DAC-induced DNA demethylation and subsequent remethylation after drug withdrawal in breast cancer cells. We find that CpGs differ in both their susceptibility to demethylation and propensity for remethylation after drug removal. DAC-induced demethylation was most apparent at CpGs with higher initial methylation levels and further from CpG islands. Once demethylated, such sites exhibited varied remethylation potentials. The most rapidly remethylating CpGs regained >75% of their starting methylation within a month of drug withdrawal. These sites had higher pretreatment methylation levels, were enriched in gene bodies, marked by H3K36me3, and tended to be methylated in normal breast cells. In contrast, a more resistant class of CpG sites failed to regain even 20% of their initial methylation after 3 months. These sites had lower pretreatment methylation levels, were within or near CpG islands, marked by H3K79me2 or H3K4me2/3, and were overrepresented in sites that become aberrantly hypermethylated in breast cancers. Thus, whereas DAC-induced demethylation affects both endogenous and aberrantly methylated sites, tumor-specific hypermethylation is more slowly regained, even as normal methylation promptly recovers. Taken together, these data suggest that the durability of DAC response is linked to its selective ability to stably reset at least a portion of the cancer methylome.
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Affiliation(s)
- Joshua S K Bell
- a Graduate Program in Genetics and Molecular Biology , Emory University , Atlanta , GA , USA
| | - Jacob D Kagey
- a Graduate Program in Genetics and Molecular Biology , Emory University , Atlanta , GA , USA
| | - Benjamin G Barwick
- a Graduate Program in Genetics and Molecular Biology , Emory University , Atlanta , GA , USA
| | - Bhakti Dwivedi
- b Winship Cancer Institute , Emory University , Atlanta , GA , USA
| | - Michael T McCabe
- c Department of Radiation Oncology , Emory University , Atlanta , GA , USA
| | - Jeanne Kowalski
- b Winship Cancer Institute , Emory University , Atlanta , GA , USA.,d Department of Biostatistics and Bioinformatics , Emory University , Atlanta , GA , USA
| | - Paula M Vertino
- b Winship Cancer Institute , Emory University , Atlanta , GA , USA.,c Department of Radiation Oncology , Emory University , Atlanta , GA , USA
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168
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Graham B, Marcais A, Dharmalingam G, Carroll T, Kanellopoulou C, Graumann J, Nesterova TB, Bermange A, Brazauskas P, Xella B, Kriaucionis S, Higgs DR, Brockdorff N, Mann M, Fisher AG, Merkenschlager M. MicroRNAs of the miR-290-295 Family Maintain Bivalency in Mouse Embryonic Stem Cells. Stem Cell Reports 2016; 6:635-642. [PMID: 27150236 PMCID: PMC4939759 DOI: 10.1016/j.stemcr.2016.03.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 03/19/2016] [Accepted: 03/21/2016] [Indexed: 11/03/2022] Open
Abstract
Numerous developmentally regulated genes in mouse embryonic stem cells (ESCs) are marked by both active (H3K4me3)- and polycomb group (PcG)-mediated repressive (H3K27me3) histone modifications. This bivalent state is thought to be important for transcriptional poising, but the mechanisms that regulate bivalent genes and the bivalent state remain incompletely understood. Examining the contribution of microRNAs (miRNAs) to the regulation of bivalent genes, we found that the miRNA biogenesis enzyme DICER was required for the binding of the PRC2 core components EZH2 and SUZ12, and for the presence of the PRC2-mediated histone modification H3K27me3 at many bivalent genes. Genes that lost bivalency were preferentially upregulated at the mRNA and protein levels. Finally, reconstituting Dicer-deficient ESCs with ESC miRNAs restored bivalent gene repression and PRC2 binding at formerly bivalent genes. Therefore, miRNAs regulate bivalent genes and the bivalent state itself.
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Affiliation(s)
- Bryony Graham
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK; Epigenetics Section, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK; MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Antoine Marcais
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK; Epigenetics Section, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Gopuraja Dharmalingam
- Epigenetics Section, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Thomas Carroll
- Epigenetics Section, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Chryssa Kanellopoulou
- Laboratory of Immunology, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Johannes Graumann
- Department of Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, 82152 Martinsried, Germany
| | | | - Anna Bermange
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK; Epigenetics Section, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Pijus Brazauskas
- Ludwig Institute for Cancer Research, University of Oxford, Nuffield Department of Clinical Medicine, Oxford OX3 7DQ, UK
| | - Barbara Xella
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Skirmantas Kriaucionis
- Ludwig Institute for Cancer Research, University of Oxford, Nuffield Department of Clinical Medicine, Oxford OX3 7DQ, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Neil Brockdorff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, 82152 Martinsried, Germany
| | - Amanda G Fisher
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK; Epigenetics Section, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK; Epigenetics Section, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK.
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169
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Abstract
Hundreds of distinct chemical modifications to DNA and histone amino acids have been described. Regulation exerted by these so-called epigenetic marks is vital to normal development, stability of cell identity through mitosis, and nongenetic transmission of traits between generations through meiosis. Loss of this regulation contributes to many diseases. Evidence indicates epigenetic marks function in combinations, whereby a given modification has distinct effects on local genome control, depending on which additional modifications are locally present. This review summarizes emerging methods for assessing combinatorial epigenomic states, as well as challenges and opportunities for their refinement.
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Affiliation(s)
- Paul D. Soloway
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, United States
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170
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Abstract
Differentiating somatic cells are progressively restricted to specialized functions during ontogeny, but they can be experimentally directed to form other cell types, including those with complete embryonic potential. Early nuclear reprogramming methods, such as somatic cell nuclear transfer (SCNT) and cell fusion, posed significant technical hurdles to precise dissection of the regulatory programmes governing cell identity. However, the discovery of reprogramming by ectopic expression of a defined set of transcription factors, known as direct reprogramming, provided a tractable platform to uncover molecular characteristics of cellular specification and differentiation, cell type stability and pluripotency. We discuss the control and maintenance of cellular identity during developmental transitions as they have been studied using direct reprogramming, with an emphasis on transcriptional and epigenetic regulation.
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171
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Kress C, Montillet G, Jean C, Fuet A, Pain B. Chicken embryonic stem cells and primordial germ cells display different heterochromatic histone marks than their mammalian counterparts. Epigenetics Chromatin 2016; 9:5. [PMID: 26865862 PMCID: PMC4748481 DOI: 10.1186/s13072-016-0056-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/27/2016] [Indexed: 12/17/2022] Open
Abstract
Background Chromatin epigenetics participate in control of gene expression during metazoan development. DNA methylation and post-translational modifications (PTMs) of histones have been extensively characterised in cell types present in, or derived from, mouse embryos. In embryonic stem cells (ESCs) derived from blastocysts, factors involved in deposition of epigenetic marks regulate properties related to self-renewal and pluripotency. In the germ lineage, changes in histone PTMs and DNA demethylation occur during formation of the primordial germ cells (PGCs) to reset the epigenome of the future gametes. Trimethylation of histone H3 on lysine 27 (H3K27me3) by Polycomb group proteins is involved in several epigenome-remodelling steps, but it remains unclear whether these epigenetic features are conserved in non-mammalian vertebrates. To investigate this question, we compared the abundance and nuclear distribution of the main histone PTMs, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in chicken ESCs, PGCs and blastodermal cells (BCs) with differentiated chicken ESCs and embryonic fibroblasts. In addition, we analysed the expression of chromatin modifier genes to better understand the establishment and dynamics of chromatin epigenetic profiles. Results The nuclear distributions of most PTMs and 5hmC in chicken stem cells were similar to what has been described for mammalian cells. However, unlike mouse pericentric heterochromatin (PCH), chicken ESC PCH contained high levels of trimethylated histone H3 on lysine 27 (H3K27me3). In differentiated chicken cells, PCH was less enriched in H3K27me3 relative to chromatin overall. In PGCs, the H3K27me3 global level was greatly reduced, whereas the H3K9me3 level was elevated. Most chromatin modifier genes known in mammals were expressed in chicken ESCs, PGCs and BCs. Genes presumably involved in de novo DNA methylation were very highly expressed. DNMT3B and HELLS/SMARCA6 were highly expressed in chicken ESCs, PGCs and BCs compared to differentiated chicken ESCs and embryonic fibroblasts, and DNMT3A was strongly expressed in ESCs, differentiated ESCs and BCs. Conclusions Chicken ESCs and PGCs differ from their mammalian counterparts with respect to H3K27 methylation. High enrichment of H3K27me3 at PCH is specific to pluripotent cells in chicken. Our results demonstrate that the dynamics in chromatin constitution described during mouse development is not universal to all vertebrate species. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0056-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Clémence Kress
- Inserm, U1208, INRA, USC1361, Stem Cell and Brain Research Institute, 18 avenue du Doyen Lépine, 69500 Bron, France ; Université de Lyon, Université Lyon 1, Lyon, France
| | - Guillaume Montillet
- Inserm, U1208, INRA, USC1361, Stem Cell and Brain Research Institute, 18 avenue du Doyen Lépine, 69500 Bron, France ; Université de Lyon, Université Lyon 1, Lyon, France
| | - Christian Jean
- Inserm, U1208, INRA, USC1361, Stem Cell and Brain Research Institute, 18 avenue du Doyen Lépine, 69500 Bron, France ; Université de Lyon, Université Lyon 1, Lyon, France
| | - Aurélie Fuet
- Inserm, U1208, INRA, USC1361, Stem Cell and Brain Research Institute, 18 avenue du Doyen Lépine, 69500 Bron, France ; Université de Lyon, Université Lyon 1, Lyon, France
| | - Bertrand Pain
- Inserm, U1208, INRA, USC1361, Stem Cell and Brain Research Institute, 18 avenue du Doyen Lépine, 69500 Bron, France ; Université de Lyon, Université Lyon 1, Lyon, France
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172
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Walter M, Teissandier A, Pérez-Palacios R, Bourc'his D. An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells. eLife 2016; 5. [PMID: 26814573 PMCID: PMC4769179 DOI: 10.7554/elife.11418] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 01/27/2016] [Indexed: 12/11/2022] Open
Abstract
DNA methylation is extensively remodeled during mammalian gametogenesis and embryogenesis. Most transposons become hypomethylated, raising the question of their regulation in the absence of DNA methylation. To reproduce a rapid and extensive demethylation, we subjected mouse ES cells to chemically defined hypomethylating culture conditions. Surprisingly, we observed two phases of transposon regulation. After an initial burst of de-repression, various transposon families were efficiently re-silenced. This was accompanied by a reconfiguration of the repressive chromatin landscape: while H3K9me3 was stable, H3K9me2 globally disappeared and H3K27me3 accumulated at transposons. Interestingly, we observed that H3K9me3 and H3K27me3 occupy different transposon families or different territories within the same family, defining three functional categories of adaptive chromatin responses to DNA methylation loss. Our work highlights that H3K9me3 and, most importantly, polycomb-mediated H3K27me3 chromatin pathways can secure the control of a large spectrum of transposons in periods of intense DNA methylation change, ensuring longstanding genome stability.
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Affiliation(s)
- Marius Walter
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France.,Paris Science Lettres Research University, .,UMR3215, CNRS, Paris, France.,U934, Inserm, Paris, France
| | - Aurélie Teissandier
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France.,UMR3215, CNRS, Paris, France.,U934, Inserm, Paris, France.,Paris Science Lettres Research University, .,Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Paris, France.,Mines Paris Tech, Paris, France.,U900, Inserm, Paris, France
| | - Raquel Pérez-Palacios
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France.,UMR3215, CNRS, Paris, France.,U934, Inserm, Paris, France.,Paris Science Lettres Research University,
| | - Déborah Bourc'his
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France.,UMR3215, CNRS, Paris, France.,U934, Inserm, Paris, France.,Paris Science Lettres Research University,
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173
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Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:343-430. [DOI: 10.1007/978-3-319-43624-1_15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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174
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Embryonic transcription is controlled by maternally defined chromatin state. Nat Commun 2015; 6:10148. [PMID: 26679111 PMCID: PMC4703837 DOI: 10.1038/ncomms10148] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 11/10/2015] [Indexed: 12/02/2022] Open
Abstract
Histone-modifying enzymes are required for cell identity and lineage commitment, however little is known about the regulatory origins of the epigenome during embryonic development. Here we generate a comprehensive set of epigenome reference maps, which we use to determine the extent to which maternal factors shape chromatin state in Xenopus embryos. Using α-amanitin to inhibit zygotic transcription, we find that the majority of H3K4me3- and H3K27me3-enriched regions form a maternally defined epigenetic regulatory space with an underlying logic of hypomethylated islands. This maternal regulatory space extends to a substantial proportion of neurula stage-activated promoters. In contrast, p300 recruitment to distal regulatory regions requires embryonic transcription at most loci. The results show that H3K4me3 and H3K27me3 are part of a regulatory space that exerts an extended maternal control well into post-gastrulation development, and highlight the combinatorial action of maternal and zygotic factors through proximal and distal regulatory sequences. Histone modifying enzymes are required for cell differentiation and lineage commitment during embryonic development. By a comprehensive set of epigenome reference maps of Xenopus embryos, the authors show that H3K4me3 and H3K27me3 exert an extended maternal control well into post-gastrulation development.
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175
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Lin HY, Hung SK, Lee MS, Chiou WY, Huang TT, Tseng CE, Shih LY, Lin RI, Lin JMJ, Lai YH, Chang CB, Hsu FC, Chen LC, Tsai SJ, Su YC, Li SC, Lai HC, Hsu WL, Liu DW, Tai CK, Wu SF, Chan MWY. DNA methylome analysis identifies epigenetic silencing of FHIT as a determining factor for radiosensitivity in oral cancer: an outcome-predicting and treatment-implicating study. Oncotarget 2015; 6:915-34. [PMID: 25460508 PMCID: PMC4359265 DOI: 10.18632/oncotarget.2821] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 11/24/2014] [Indexed: 12/17/2022] Open
Abstract
Radioresistance is still an emerging problem for radiotherapy of oral cancer. Aberrant epigenetic alterations play an important role in cancer development, yet the role of such alterations in radioresistance of oral cancer is not fully explored. Using a methylation microarray, we identified promoter hypermethylation of FHIT (fragile histidine triad) in radioresistant OML1-R cells, established from hypo-fractionated irradiation of parental OML1 radiosensitive oral cancer cells. Further analysis confirmed that transcriptional repression of FHIT was due to promoter hypermethylation, H3K27me3 and overexpression of methyltransferase EZH2 in OML1-R cells. Epigenetic interventions or depletion of EZH2 restored FHIT expression. Ectopic expression of FHIT inhibited tumor growth in both in vitro and in vivo models, while also resensitizing radioresistant cancer cells to irradiation, by restoring Chk2 phosphorylation and G2/M arrest. Clinically, promoter hypermethylation of FHIT inversely correlated with its expression and independently predicted both locoregional control and overall survival in 40 match-paired oral cancer patient samples. Further in vivo therapeutic experiments confirmed that inhibition of DNA methylation significantly resensitized radioresistant oral cancer cell xenograft tumors. These results show that epigenetic silencing of FHIT contributes partially to radioresistance and predicts clinical outcomes in irradiated oral cancer. The radiosensitizing effect of epigenetic interventions warrants further clinical investigation.
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Affiliation(s)
- Hon-Yi Lin
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC
| | - Shih-Kai Hung
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Moon-Sing Lee
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Wen-Yen Chiou
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Tze-Ta Huang
- Department of Oral and Maxillofacial Surgery, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC.,Institute of Oral Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Chih-En Tseng
- Department of Anatomic Pathology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Liang-Yu Shih
- Department of Anatomic Pathology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Ru-Inn Lin
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC.,Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC
| | - Jora M J Lin
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC.,Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC
| | - Yi-Hui Lai
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC.,Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC
| | - Chia-Bin Chang
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC.,Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC
| | - Feng-Chun Hsu
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC
| | - Liang-Cheng Chen
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC
| | - Shiang-Jiun Tsai
- Department of Radiation Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC
| | - Yu-Chieh Su
- Department of Hematology-Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Szu-Chi Li
- Department of Hematology-Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Hung-Chih Lai
- Department of Hematology-Oncology, Buddhist Dalin Tzu Chi General Hospital, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Wen-Lin Hsu
- Department of Radiation Oncology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Dai-Wei Liu
- Department of Radiation Oncology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan, ROC.,School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Chien-Kuo Tai
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC.,Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC
| | - Shu-Fen Wu
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC.,Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC
| | - Michael W Y Chan
- Institute of Molecular Biology, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC.Department of Life Science, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC.Human Epigenomics Center, National Chung Cheng University, Min-Hsiung, Chia-Yi, Taiwan, ROC
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176
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Chen PB, Chen HV, Acharya D, Rando OJ, Fazzio TG. R loops regulate promoter-proximal chromatin architecture and cellular differentiation. Nat Struct Mol Biol 2015; 22:999-1007. [PMID: 26551076 PMCID: PMC4677832 DOI: 10.1038/nsmb.3122] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 10/09/2015] [Indexed: 12/11/2022]
Abstract
Numerous chromatin-remodeling factors are regulated by interactions with RNA, although the contexts and functions of RNA binding are poorly understood. Here we show that R-loops, RNA:DNA hybrids consisting of nascent transcripts hybridized to template DNA, modulate the binding of two key chromatin regulatory complexes, Tip60–p400 and polycomb repressive complex 2 (PRC2) in mouse embryonic stem cells (ESCs). Like PRC2, the Tip60–p400 histone acetyltransferase complex binds to nascent transcripts, but unlike PRC2, transcription promotes chromatin binding by Tip60–p400. Interestingly, we observed higher Tip60–p400 and lower PRC2 levels at genes marked by promoter-proximal R-loops. Furthermore, disruption of R-loops broadly reduced Tip60–p400 and increased PRC2 occupancy genome-wide. Consistent with these alterations, ESCs with reduced R-loops exhibited impaired differentiation. These results show that R-loops act both positively and negatively to modulate the recruitment of key pluripotency regulators.
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Affiliation(s)
- Poshen B Chen
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Hsiuyi V Chen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Diwash Acharya
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Thomas G Fazzio
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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177
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Wu HC, Lin YC, Liu CH, Chung HC, Wang YT, Lin YW, Ma HI, Tu PH, Lawler SE, Chen RH. USP11 regulates PML stability to control Notch-induced malignancy in brain tumours. Nat Commun 2015; 5:3214. [PMID: 24487962 PMCID: PMC5645609 DOI: 10.1038/ncomms4214] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 01/07/2014] [Indexed: 01/31/2023] Open
Abstract
The promyelocytic leukaemia (PML) protein controls multiple tumour suppressive functions and is downregulated in diverse types of human cancers through incompletely characterized post-translational mechanisms. Here we identify USP11 as a PML regulator by RNAi screening. USP11 deubiquitinates and stabilizes PML, thereby counteracting the functions of PML ubiquitin ligases RNF4 and the KLHL20-Cul3 (Cullin 3)-Roc1 complex. We find that USP11 is transcriptionally repressed through a Notch/Hey1-dependent mechanism, leading to PML destabilization. In human glioma, Hey1 upregulation correlates with USP11 and PML downregulation and with high-grade malignancy. The Notch/Hey1-induced downregulation of USP11 and PML not only confers multiple malignant characteristics of aggressive glioma, including proliferation, invasiveness and tumour growth in an orthotopic mouse model, but also potentiates self-renewal, tumour-forming capacity and therapeutic resistance of patient-derived glioma-initiating cells. Our study uncovers a PML degradation mechanism through Notch/Hey1-induced repression of the PML deubiquitinase USP11 and suggests an important role for this pathway in brain tumour pathogenesis.
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Affiliation(s)
- Hsin-Chieh Wu
- 1] Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan [2] Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Ching Lin
- 1] Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan [2] Institute of Biochemical Sciences, National Taiwan University, Taipei 100, Taiwan
| | - Cheng-Hsin Liu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | | | - Ya-Ting Wang
- 1] Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan [2] Institute of Biochemical Sciences, National Taiwan University, Taipei 100, Taiwan
| | - Ya-Wen Lin
- 1] Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan [2] Department of Microbiology and Immunology, National Defense Medical Center, Taipei 114, Taiwan
| | - Hsin-I Ma
- 1] Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan [2] Department of Neurological Surgery, Tri-service General Hospital, Taipei 114, Taiwan
| | - Pang-Hsien Tu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Sean E Lawler
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ruey-Hwa Chen
- 1] Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan [2] Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan [3] Institute of Biochemical Sciences, National Taiwan University, Taipei 100, Taiwan
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178
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179
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Abstract
Colorectal cancer stem cells (CSCs) were initially considered to be a subset of undifferentiated tumor cells with well-defined phenotypic and molecular markers. However, emerging evidence indicates instead that colorectal CSCs are heterogeneous subsets of tumor cells that are continuously reshaped by the dynamic interactions between genetic, epigenetic, and immune factors in the tumor microenvironment. Thus, the colorectal CSC phenotypes and responsiveness to therapy may not only be a tumor cell-intrinsic feature, but also depend on tumor-extrinsic microenvironmental factors. Furthermore, emerging evidence also implicates colorectal CSCs in potential immune evasion. Therefore, understanding how colorectal CSC-intrinsic mechanisms cooperate with the extrinsic microenvironmental factors to dynamically shape colorectal CSC resistance to chemotherapy and immunotherapy holds great promise for development of targeted CSC therapies of advanced human CRC.
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180
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The quest for mammalian Polycomb response elements: are we there yet? Chromosoma 2015; 125:471-96. [PMID: 26453572 PMCID: PMC4901126 DOI: 10.1007/s00412-015-0539-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 08/31/2015] [Accepted: 09/02/2015] [Indexed: 12/12/2022]
Abstract
A long-standing mystery in the field of Polycomb and Trithorax regulation is how these proteins, which are highly conserved between flies and mammals, can regulate several hundred equally highly conserved target genes, but recognise these targets via cis-regulatory elements that appear to show no conservation in their DNA sequence. These elements, termed Polycomb/Trithorax response elements (PRE/TREs or PREs), are relatively well characterised in flies, but their mammalian counterparts have proved to be extremely difficult to identify. Recent progress in this endeavour has generated a wealth of data and raised several intriguing questions. Here, we ask why and to what extent mammalian PREs are so different to those of the fly. We review recent advances, evaluate current models and identify open questions in the quest for mammalian PREs.
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181
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Switching between Epigenetic States at Pericentromeric Heterochromatin. Trends Genet 2015; 31:661-672. [PMID: 26431676 DOI: 10.1016/j.tig.2015.09.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/21/2015] [Accepted: 09/04/2015] [Indexed: 02/05/2023]
Abstract
Pericentromeric DNA represents a large fraction of the mammalian genome that is usually assembled into heterochromatin. Recent advances have revealed that the composition of pericentromeric heterochromatin is surprisingly dynamic. Indeed, high levels of histone H3 trimethylation on lysine 9 (H3K9me3) and DNA methylation normally characterize the repressive environment of this region. However, in specific tissues and in cancer cells, Polycomb proteins can occupy pericentromeric heterochromatin and act as a molecular sink for transcriptional regulators. Restoring heterochromatin methylation marks could, thus, be an important way to bring back normal gene expression programs in disease. Here, I discuss the potential mechanisms by which Polycomb complexes are recruited to pericentromeric DNA.
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182
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Maupetit-Méhouas S, Montibus B, Nury D, Tayama C, Wassef M, Kota SK, Fogli A, Cerqueira Campos F, Hata K, Feil R, Margueron R, Nakabayashi K, Court F, Arnaud P. Imprinting control regions (ICRs) are marked by mono-allelic bivalent chromatin when transcriptionally inactive. Nucleic Acids Res 2015; 44:621-35. [PMID: 26400168 PMCID: PMC4737186 DOI: 10.1093/nar/gkv960] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 09/12/2015] [Indexed: 01/10/2023] Open
Abstract
Parental allele-specific expression of imprinted genes is mediated by imprinting control regions (ICRs) that are constitutively marked by DNA methylation imprints on the maternal or paternal allele. Mono-allelic DNA methylation is strictly required for the process of imprinting and has to be faithfully maintained during the entire life-span. While the regulation of DNA methylation itself is well understood, the mechanisms whereby the opposite allele remains unmethylated are unclear. Here, we show that in the mouse, at maternally methylated ICRs, the paternal allele, which is constitutively associated with H3K4me2/3, is marked by default by H3K27me3 when these ICRs are transcriptionally inactive, leading to the formation of a bivalent chromatin signature. Our data suggest that at ICRs, chromatin bivalency has a protective role by ensuring that DNA on the paternal allele remains unmethylated and protected against spurious and unscheduled gene expression. Moreover, they provide the proof of concept that, beside pluripotent cells, chromatin bivalency is the default state of transcriptionally inactive CpG island promoters, regardless of the developmental stage, thereby contributing to protect cell identity.
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Affiliation(s)
- Stéphanie Maupetit-Méhouas
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Bertille Montibus
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - David Nury
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Michel Wassef
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Satya K Kota
- Institute of Molecular Genetics, CNRS UMR-5535 and University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Anne Fogli
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Fabiana Cerqueira Campos
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Robert Feil
- Institute of Molecular Genetics, CNRS UMR-5535 and University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Raphael Margueron
- Institut Curie, 26 Rue d'Ulm, 75005 Paris, France; INSERM U934, 26 Rue d'Ulm, 75005 Paris, France; CNRS UMR3215, 26 Rue d'Ulm, 75005 Paris, France
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Franck Court
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
| | - Philippe Arnaud
- CNRS, UMR6293, F-63001 Clermont-Ferrand, France Inserm, U1103, 63001 Clermont-Ferrand, France Université Clermont Auvergne, Laboratoire GReD, BP 10448, 63000 Clermont-Ferrand, France
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183
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Das PP, Hendrix DA, Apostolou E, Buchner AH, Canver MC, Beyaz S, Ljuboja D, Kuintzle R, Kim W, Karnik R, Shao Z, Xie H, Xu J, De Los Angeles A, Zhang Y, Choe J, Jun DLJ, Shen X, Gregory RI, Daley GQ, Meissner A, Kellis M, Hochedlinger K, Kim J, Orkin SH. PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells. Cell Rep 2015; 12:1456-70. [PMID: 26299972 PMCID: PMC5384103 DOI: 10.1016/j.celrep.2015.07.053] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 07/19/2015] [Accepted: 07/27/2015] [Indexed: 01/08/2023] Open
Abstract
Polycomb Repressive Complex 2 (PRC2) function and DNA methylation (DNAme) are typically correlated with gene repression. Here, we show that PRC2 is required to maintain expression of maternal microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) from the Gtl2-Rian-Mirg locus, which is essential for full pluripotency of iPSCs. In the absence of PRC2, the entire locus becomes transcriptionally repressed due to gain of DNAme at the intergenic differentially methylated regions (IG-DMRs). Furthermore, we demonstrate that the IG-DMR serves as an enhancer of the maternal Gtl2-Rian-Mirg locus. Further analysis reveals that PRC2 interacts physically with Dnmt3 methyltransferases and reduces recruitment to and subsequent DNAme at the IG-DMR, thereby allowing for proper expression of the maternal Gtl2-Rian-Mirg locus. Our observations are consistent with a mechanism through which PRC2 counteracts the action of Dnmt3 methyltransferases at an imprinted locus required for full pluripotency.
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Affiliation(s)
- Partha Pratim Das
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute (HHMI), Boston, MA 02115, USA
| | - David A Hendrix
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Biochemistry and Biophysics, School of Electrical Engineering and Computer Science, Oregon State University, 2011 Ag and Life Science Building, Corvallis, OR 97331-7305, USA
| | - Effie Apostolou
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Medical School, 7 Divinity Avenue, Cambridge, MA 02138, USA; Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Boston, MA 02114, USA
| | - Alice H Buchner
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Molecular Biology Program, International Max Planck Research School, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Matthew C Canver
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Semir Beyaz
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Damir Ljuboja
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Rachael Kuintzle
- Department of Biochemistry and Biophysics, School of Electrical Engineering and Computer Science, Oregon State University, 2011 Ag and Life Science Building, Corvallis, OR 97331-7305, USA
| | - Woojin Kim
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Rahul Karnik
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Medical School, 7 Divinity Avenue, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Zhen Shao
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Huafeng Xie
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jian Xu
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Alejandro De Los Angeles
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yingying Zhang
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Medical School, 7 Divinity Avenue, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Junho Choe
- Stem Cell Program, Department of Biological Chemistry and Molecular Pharmacology and Department of Pediatrics, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Don Leong Jia Jun
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; School of Chemical and Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Singapore
| | - Xiaohua Shen
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Richard I Gregory
- Stem Cell Program, Department of Biological Chemistry and Molecular Pharmacology and Department of Pediatrics, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - George Q Daley
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute (HHMI), Boston, MA 02115, USA
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Medical School, 7 Divinity Avenue, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Konrad Hochedlinger
- Howard Hughes Medical Institute (HHMI), Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Medical School, 7 Divinity Avenue, Cambridge, MA 02138, USA; Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Boston, MA 02114, USA
| | - Jonghwan Kim
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute (HHMI), Boston, MA 02115, USA.
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184
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Implications of epigenetics in tissue engineering. Tissue Eng Regen Med 2015. [DOI: 10.1007/s13770-014-0419-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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185
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Get to Understand More from Single-Cells: Current Studies of Microfluidic-Based Techniques for Single-Cell Analysis. Int J Mol Sci 2015. [PMID: 26213918 PMCID: PMC4581168 DOI: 10.3390/ijms160816763] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
This review describes the microfluidic techniques developed for the analysis of a single cell. The characteristics of microfluidic (e.g., little sample amount required, high-throughput performance) make this tool suitable to answer and to solve biological questions of interest about a single cell. This review aims to introduce microfluidic related techniques for the isolation, trapping and manipulation of a single cell. The major approaches for detection in single-cell analysis are introduced; the applications of single-cell analysis are then summarized. The review concludes with discussions of the future directions and opportunities of microfluidic systems applied in analysis of a single cell.
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186
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Genome-wide epigenetic cross-talk between DNA methylation and H3K27me3 in zebrafish embryos. GENOMICS DATA 2015; 6:7-9. [PMID: 26697317 PMCID: PMC4664660 DOI: 10.1016/j.gdata.2015.07.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 07/17/2015] [Indexed: 01/08/2023]
Abstract
DNA methylation and histone modifications are epigenetic marks implicated in the complex regulation of vertebrate embryogenesis. The cross-talk between DNA methylation and Polycomb-dependent H3K27me3 histone mark has been reported in a number of organisms [1], [2], [3], [4], [5], [6], [7] and both marks are known to be required for proper developmental progression. Here we provide genome-wide DNA methylation (MethylCap-seq) and H3K27me3 (ChIP-seq) maps for three stages (dome, 24 hpf and 48 hpf) of zebrafish (Danio rerio) embryogenesis, as well as all analytical and methodological details associated with the generation of this dataset. We observe a strong antagonism between the two epigenetic marks present in CpG islands and their compatibility throughout the bulk of the genome, as previously reported in mammalian ESC lines (Brinkman et al., 2012). Next generation sequencing data linked to this project have been deposited in the Gene Expression Omnibus (GEO) database under accession numbers GSE35050 and GSE70847.
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187
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Abstract
Liao et al. (2015) recently reported on the effects of disrupting DNA methyltransferase activity in human embryonic stem cells (hESCs). This work highlights key differences between mammalian ESC models upon the loss of these essential proteins and provides comprehensive base resolution methylome maps of DNMT targets during human development.
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188
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Mozgova I, Köhler C, Hennig L. Keeping the gate closed: functions of the polycomb repressive complex PRC2 in development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:121-32. [PMID: 25762111 DOI: 10.1111/tpj.12828] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/09/2015] [Accepted: 03/10/2015] [Indexed: 05/08/2023]
Abstract
Plant ontogeny relies on the correct timing and sequence of transitions between individual developmental phases. These are specified by gene expression patterns that are established by the balanced action of activators and repressors. Polycomb repressive complexes (PRCs) represent an evolutionarily conserved system of epigenetic gene repression that governs the establishment and maintenance of cell, tissue and organ identity, contributing to the correct execution of the developmental programs. PRC2 is a four-subunit histone methyltransferase complex that catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3), which contributes to the change of chromatin structure and long-lasting gene repression. Here, we review the composition and molecular function of the different known PRC2 complexes in plants, and focus on the role of PRC2 in mediating the establishment of different developmental phases and transitions between them.
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Affiliation(s)
- Iva Mozgova
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007, Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007, Uppsala, Sweden
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189
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Graffmann N, Brands J, Görgens A, Vitoriano da Conceição Castro S, Santourlidis S, Reckert A, Michele I, Ritz-Timme S, Fischer JC, Adjaye J, Kögler G, Giebel B, Uhrberg M. Age-Related Increase of EED Expression in Early Hematopoietic Progenitor Cells is Associated with Global Increase of the Histone Modification H3K27me3. Stem Cells Dev 2015; 24:2018-31. [PMID: 25961873 DOI: 10.1089/scd.2014.0435] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Human hematopoietic stem and progenitor cells (HSPCs) from umbilical cord blood exhibit higher differentiation potential and repopulation capacity compared to adult HSPCs. The molecular basis for these functional differences is currently unknown. Upon screening for epigenetic effector genes being differentially expressed in neonatal and adult HSPC subpopulations, the Polycomb Repressive Complex 2 (PRC2) member EED was identified. Even though EED is expressed at comparable amounts in neonatal and adult multipotent HSPCs, early adult lineage committed progenitors of the lymphomyeloid (LM) and erythromyeloid lineages expressed higher EED amounts than neonatal HPCs. We demonstrate that EED overexpression directly leads to higher H3K27me3 levels, a repressive histone modification that is mediated by the PRC2 complex. Quantitative analysis of H3K27me3 levels by FPLC-based ELISA revealed elevated levels in primary blood cells from adults. Besides quantitative changes, gene ontology analysis of the genome-wide H3K27me3 distribution revealed qualitative changes in adult HSPCs with elevated levels in genes associated with nonhematopoietic development pathways. In contrast, H3K4me3 which labels active chromatin was enriched on hematopoietic genes. In vitro differentiation of EED-transfected neonatal HSPCs revealed aberrant expression of the myelopoietic marker CD14, suggesting that EED affects the lymphoid versus myeloid decision processes within the lymphomyeloid lineage. This is in line with LM progenitors having the most pronounced differences in EED expression. Highlighting the dynamic roles of epigenetic modifications in human hematopoiesis, the present data demonstrate shifts in the PRC2-associated histone modification H3K27me3 from birth to adulthood.
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Affiliation(s)
- Nina Graffmann
- 1 Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany .,2 Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - Jens Brands
- 2 Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - André Görgens
- 3 Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen , Essen, Germany
| | - Symone Vitoriano da Conceição Castro
- 3 Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen , Essen, Germany .,4 CAPES Foundation, Ministry of Education of Brazil , Brasília, Brazil
| | - Simeon Santourlidis
- 2 Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - Alexandra Reckert
- 5 Institute of Forensic Medicine, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - Inga Michele
- 5 Institute of Forensic Medicine, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - Stefanie Ritz-Timme
- 5 Institute of Forensic Medicine, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - Johannes C Fischer
- 2 Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - James Adjaye
- 1 Institute for Stem Cell Research and Regenerative Medicine, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - Gesine Kögler
- 2 Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
| | - Bernd Giebel
- 3 Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen , Essen, Germany
| | - Markus Uhrberg
- 2 Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Düsseldorf , Medical Faculty, Düsseldorf, Germany
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190
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Whole-genome fingerprint of the DNA methylome during human B cell differentiation. Nat Genet 2015; 47:746-56. [PMID: 26053498 DOI: 10.1038/ng.3291] [Citation(s) in RCA: 230] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 04/03/2015] [Indexed: 02/06/2023]
Abstract
We analyzed the DNA methylome of ten subpopulations spanning the entire B cell differentiation program by whole-genome bisulfite sequencing and high-density microarrays. We observed that non-CpG methylation disappeared upon B cell commitment, whereas CpG methylation changed extensively during B cell maturation, showing an accumulative pattern and affecting around 30% of all measured CpG sites. Early differentiation stages mainly displayed enhancer demethylation, which was associated with upregulation of key B cell transcription factors and affected multiple genes involved in B cell biology. Late differentiation stages, in contrast, showed extensive demethylation of heterochromatin and methylation gain at Polycomb-repressed areas, and genes with apparent functional impact in B cells were not affected. This signature, which has previously been linked to aging and cancer, was particularly widespread in mature cells with an extended lifespan. Comparing B cell neoplasms with their normal counterparts, we determined that they frequently acquire methylation changes in regions already undergoing dynamic methylation during normal B cell differentiation.
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191
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Abstract
Stem cell decline is an important cellular driver of aging-associated pathophysiology in multiple tissues. Epigenetic regulation is central to establishing and maintaining stem cell function, and emerging evidence indicates that epigenetic dysregulation contributes to the altered potential of stem cells during aging. Unlike terminally differentiated cells, the impact of epigenetic dysregulation in stem cells is propagated beyond self; alterations can be heritably transmitted to differentiated progeny, in addition to being perpetuated and amplified within the stem cell pool through self-renewal divisions. This Review focuses on recent studies examining epigenetic regulation of tissue-specific stem cells in homeostasis, aging, and aging-related disease.
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Affiliation(s)
- Isabel Beerman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA.
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192
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Wu T, Liu Y, Wen D, Tseng Z, Tahmasian M, Zhong M, Rafii S, Stadtfeld M, Hochedlinger K, Xiao A. Histone variant H2A.X deposition pattern serves as a functional epigenetic mark for distinguishing the developmental potentials of iPSCs. Cell Stem Cell 2015; 15:281-294. [PMID: 25192463 DOI: 10.1016/j.stem.2014.06.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 04/27/2014] [Accepted: 06/05/2014] [Indexed: 01/05/2023]
Abstract
For future application of induced pluripotent stem cell (iPSC) technology, the ability to assess the overall quality of iPSC clones will be an important issue. Here we show that the histone variant H2A.X is a functional marker that can distinguish the developmental potentials of mouse iPSC lines. We found that H2A.X is specifically targeted to and negatively regulates extraembryonic lineage gene expression in embryonic stem cells (ESCs) and prevents trophectoderm lineage differentiation. ESC-specific H2A.X deposition patterns are faithfully recapitulated in iPSCs that support the development of "all-iPS" animals via tetraploid complementation, the most stringent test available of iPSC quality. In contrast, iPSCs that fail to support all-iPS embryonic development show aberrant H2A.X deposition, upregulation of extraembryonic lineage genes, and a predisposition to extraembryonic differentiation. Thus, our work has highlighted an epigenetic mechanism for maintaining cell lineage commitment in ESCs and iPSCs that can be used to distinguish the quality of iPSC lines.
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Affiliation(s)
- Tao Wu
- Yale Stem Cell Center and Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yifei Liu
- Yale Stem Cell Center and Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Duancheng Wen
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Zito Tseng
- Yale Stem Cell Center and Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Martik Tahmasian
- Yale Stem Cell Center and Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mei Zhong
- Yale Stem Cell Center and Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shahin Rafii
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Matthias Stadtfeld
- Massachusetts General Hospital Cancer Center, Howard Hughes Medical Institute and Department of Stem Cell and Regenerative Medicine, Harvard University, Boston, MA 02114, USA
| | - Konrad Hochedlinger
- Massachusetts General Hospital Cancer Center, Howard Hughes Medical Institute and Department of Stem Cell and Regenerative Medicine, Harvard University, Boston, MA 02114, USA
| | - Andrew Xiao
- Yale Stem Cell Center and Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA.
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193
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van Kruijsbergen I, Hontelez S, Veenstra GJC. Recruiting polycomb to chromatin. Int J Biochem Cell Biol 2015; 67:177-87. [PMID: 25982201 DOI: 10.1016/j.biocel.2015.05.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/04/2015] [Accepted: 05/05/2015] [Indexed: 10/23/2022]
Abstract
Polycomb group (PcG) proteins are key regulators in establishing a transcriptional repressive state. Polycomb Repressive Complex 2 (PRC2), one of the two major PcG protein complexes, is essential for proper differentiation and maintenance of cellular identity. Multiple factors are involved in recruiting PRC2 to its genomic targets. In this review, we will discuss the role of DNA sequence, transcription factors, pre-existing histone modifications, and RNA in guiding PRC2 towards specific genomic loci. The DNA sequence itself influences the DNA methylation state, which is an important determinant of PRC2 recruitment. Other histone modifications are also important for PRC2 binding as PRC2 can respond to different cellular states via crosstalk between histone modifications. Additionally, PRC2 might be able to sense the transcriptional status of genes by binding to nascent RNA, which could also guide the complex to chromatin. In this review, we will discuss how all these molecular aspects define a local chromatin state which controls accurate, cell-type-specific epigenetic silencing by PRC2. This article is part of a Directed Issue entitled: Epigenetics dynamics in development and disease.
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Affiliation(s)
- Ila van Kruijsbergen
- Radboud University Nijmegen, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen 6500 HB, The Netherlands
| | - Saartje Hontelez
- Radboud University Nijmegen, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen 6500 HB, The Netherlands
| | - Gert Jan C Veenstra
- Radboud University Nijmegen, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen 6500 HB, The Netherlands.
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194
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Ansell BRE, McConville MJ, Ma'ayeh SY, Dagley MJ, Gasser RB, Svärd SG, Jex AR. Drug resistance in Giardia duodenalis. Biotechnol Adv 2015; 33:888-901. [PMID: 25922317 DOI: 10.1016/j.biotechadv.2015.04.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 04/21/2015] [Accepted: 04/21/2015] [Indexed: 02/07/2023]
Abstract
Giardia duodenalis is a microaerophilic parasite of the human gastrointestinal tract and a major contributor to diarrheal and post-infectious chronic gastrointestinal disease world-wide. Treatment of G. duodenalis infection currently relies on a small number of drug classes. Nitroheterocyclics, in particular metronidazole, have represented the front line treatment for the last 40 years. Nitroheterocyclic-resistant G. duodenalis have been isolated from patients and created in vitro, prompting considerable research into the biomolecular mechanisms of resistance. These compounds are redox-active and are believed to damage proteins and DNA after being activated by oxidoreductase enzymes in metabolically active cells. In this review, we explore the molecular phenotypes of nitroheterocyclic-resistant G. duodenalis described to date in the context of the protist's unusual glycolytic and antioxidant systems. We propose that resistance mechanisms are likely to extend well beyond currently described resistance-associated enzymes (i.e., pyruvate ferredoxin oxidoreductases and nitroreductases), to include NAD(P)H- and flavin-generating pathways, and possibly redox-sensitive epigenetic regulation. Mechanisms that allow G. duodenalis to tolerate oxidative stress may lead to resistance against both oxygen and nitroheterocyclics, with implications for clinical control. The present review highlights the potential for systems biology tools and advanced bioinformatics to further investigate the multifaceted mechanisms of nitroheterocyclic resistance in this important pathogen.
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Affiliation(s)
- Brendan R E Ansell
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Cnr Park Dr and Flemington Rd, Parkville, VIC 3010, Australia.
| | - Malcolm J McConville
- Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC 3010, Australia
| | - Showgy Y Ma'ayeh
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Michael J Dagley
- Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC 3010, Australia
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Cnr Park Dr and Flemington Rd, Parkville, VIC 3010, Australia
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Aaron R Jex
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Cnr Park Dr and Flemington Rd, Parkville, VIC 3010, Australia
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195
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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
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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.
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196
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Alvarado S, Tajerian M, Suderman M, Machnes Z, Pierfelice S, Millecamps M, Stone LS, Szyf M. An epigenetic hypothesis for the genomic memory of pain. Front Cell Neurosci 2015; 9:88. [PMID: 25852480 PMCID: PMC4371710 DOI: 10.3389/fncel.2015.00088] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 02/26/2015] [Indexed: 11/13/2022] Open
Abstract
Chronic pain is accompanied with long-term sensory, affective and cognitive disturbances. What are the mechanisms that mediate the long-term consequences of painful experiences and embed them in the genome? We hypothesize that alterations in DNA methylation, an enzymatic covalent modification of cytosine bases in DNA, serve as a "genomic" memory of pain in the adult cortex. DNA methylation is an epigenetic mechanism for long-term regulation of gene expression. Neuronal plasticity at the neuroanatomical, functional, morphological, physiological and molecular levels has been demonstrated throughout the neuroaxis in response to persistent pain, including in the adult prefrontal cortex (PFC). We have previously reported widespread changes in gene expression and DNA methylation in the PFC many months following peripheral nerve injury. In support of this hypothesis, we show here that up-regulation of a gene involved with synaptic function, Synaptotagmin II (syt2), in the PFC in a chronic pain model is associated with long-term changes in DNA methylation. The challenges of understanding the contributions of epigenetic mechanisms such as DNA methylation within the PFC to pain chronicity and their therapeutic implications are discussed.
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Affiliation(s)
- Sebastian Alvarado
- Department of Biology, Stanford University Palo Alto, CA, USA ; Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University Montréal, QC, Canada ; Sackler Program for Epigenetics and Developmental Psychobiology, McGill University Montréal, QC, Canada
| | - Maral Tajerian
- Department of Anesthesiology, Stanford University Palo Alto, CA, USA ; Integrated Program in Neuroscience, McGill University Montréal, QC, Canada ; Alan Edwards Centre for Research on Pain, McGill University Montréal, QC, Canada
| | - Matthew Suderman
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University Montréal, QC, Canada ; Sackler Program for Epigenetics and Developmental Psychobiology, McGill University Montréal, QC, Canada
| | - Ziv Machnes
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University Montréal, QC, Canada ; Sackler Program for Epigenetics and Developmental Psychobiology, McGill University Montréal, QC, Canada
| | - Stephanie Pierfelice
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University Montréal, QC, Canada ; Sackler Program for Epigenetics and Developmental Psychobiology, McGill University Montréal, QC, Canada
| | - Magali Millecamps
- Alan Edwards Centre for Research on Pain, McGill University Montréal, QC, Canada ; Faculty of Dentistry, McGill University Montréal, QC, Canada
| | - Laura S Stone
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University Montréal, QC, Canada ; Integrated Program in Neuroscience, McGill University Montréal, QC, Canada ; Alan Edwards Centre for Research on Pain, McGill University Montréal, QC, Canada ; Faculty of Dentistry, McGill University Montréal, QC, Canada ; Department of Anesthesiology, Anesthesia Research Unit, Faculty of Medicine, McGill University Montréal, QC, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University Montréal, QC, Canada ; Sackler Program for Epigenetics and Developmental Psychobiology, McGill University Montréal, QC, Canada ; Integrated Program in Neuroscience, McGill University Montréal, QC, Canada
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197
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SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation. Nat Commun 2015; 6:6569. [PMID: 25798578 PMCID: PMC4382998 DOI: 10.1038/ncomms7569] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 02/03/2015] [Indexed: 12/31/2022] Open
Abstract
Short interspersed nuclear elements (SINEs), such as Alu, spread by retrotransposition, which requires their transcripts to be copied into DNA and then inserted into new chromosomal sites. This can lead to genetic damage through insertional mutagenesis and chromosomal rearrangements between non-allelic SINEs at distinct loci. SINE DNA is heavily methylated and this was thought to suppress its accessibility and transcription, thereby protecting against retrotransposition. Here we provide several lines of evidence that methylated SINE DNA is occupied by RNA polymerase III, including the use of high-throughput bisulphite sequencing of ChIP DNA. We find that loss of DNA methylation has little effect on accessibility of SINEs to transcription machinery or their expression in vivo. In contrast, a histone methyltransferase inhibitor selectively promotes SINE expression and occupancy by RNA polymerase III. The data suggest that methylation of histones rather than DNA plays a dominant role in suppressing SINE transcription.
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198
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Genome-wide DNA methylome analysis reveals epigenetically dysregulated non-coding RNAs in human breast cancer. Sci Rep 2015; 5:8790. [PMID: 25739977 DOI: 10.1038/srep08790] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/04/2015] [Indexed: 02/01/2023] Open
Abstract
Despite growing appreciation of the importance of epigenetics in breast cancer, our understanding of epigenetic alterations of non-coding RNAs (ncRNAs) in breast cancer remains limited. Here, we explored the epigenetic patterns of ncRNAs in breast cancers using published sequencing-based methylome data, primarily focusing on the two most commonly studied ncRNA biotypes, long ncRNAs and miRNAs. We observed widely aberrant methylation in the promoters of ncRNAs, and this abnormal methylation was more frequent than that in protein-coding genes. Specifically, intergenic ncRNAs were observed to comprise a majority (51.45% of the lncRNAs and 51.57% of the miRNAs) of the aberrantly methylated ncRNA promoters. Moreover, we summarized five patterns of aberrant ncRNA promoter methylation in the context of genomic CpG islands (CGIs), in which aberrant methylation occurred not only on CGIs, but also in regions flanking CGI and in CGI-lacking promoters. Integration with transcriptional datasets enabled us to determine that the ncRNA promoter methylation events were associated with transcriptional changes. Furthermore, a panel of ncRNAs were identified as biomarkers that discriminated between disease phenotypes. Finally, the potential functions of aberrantly methylated ncRNAs were predicted, suggestiong that ncRNAs and coding genes cooperatively mediate pathway dysregulation during the development and progression of breast cancer.
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199
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Hudler P, Videtič Paska A, Komel R. Contemporary proteomic strategies for clinical epigenetic research and potential impact for the clinic. Expert Rev Proteomics 2015; 12:197-212. [PMID: 25719543 DOI: 10.1586/14789450.2015.1019479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Novel proteomic methods are revealing the intricacy of the epigenetic landscape affecting gene regulation and improving our knowledge of the pathogenesis of complex diseases. Despite the enormous amount of data regarding epigenetic modifications present in DNA and histones, deciphering their biological relevance in the context of the disease and health is currently still an ongoing process. Here, we consider the relationship between epigenetic research in tumorigenesis and the prospect of knowledge transfer to clinical use, focusing primarily on the epigenetic histone post-translational modifications, which could be used as biomarkers. We additionally focus on the use of proteomic techniques in research and evaluate their usefulness in clinical setting.
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Affiliation(s)
- Petra Hudler
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
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200
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Chromatin modifications and genomic contexts linked to dynamic DNA methylation patterns across human cell types. Sci Rep 2015; 5:8410. [PMID: 25673498 PMCID: PMC4325317 DOI: 10.1038/srep08410] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/19/2015] [Indexed: 12/29/2022] Open
Abstract
DNA methylation is related closely to sequence contexts and chromatin modifications; however, their potential differences in different genomic regions across cell types remain largely unexplored. We used publicly available genome-scale DNA methylation and histone modification profiles to study their relationships among different genomic regions in human embryonic stem cells (H1), H1-derived neuronal progenitor cultured cells (NPC), and foetal fibroblasts (IMR90) using the Random forests classifier. Histone modifications achieved high accuracy in modelling DNA methylation patterns on a genome scale in the three cell types. The inclusion of sequence features helped improve accuracy only in non-promoter regions of IMR90. Furthermore, the top six feature combinations obtained by mean decrease Gini were important indicators of different DNA methylation patterns, suggesting that H3K4me2 and H3K4me3 are important indicators that are independent of genomic regions and cell types. H3K9me3 was IMR90-specific and exhibited a genomic region-specific correlation with DNA methylation. Variations of essential chromatin modification signals may effectively discriminate changes of DNA methylation between H1 and IMR90. Genes with different co-variations of epigenetic marks exhibited genomic region-specific biological relevance. This study provides an integrated strategy to identify systematically essential epigenetic and genetic elements of genomic region-specific and cell type-specific DNA methylation patterns.
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