51
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Chakraborty A, Viswanathan P. Methylation-Demethylation Dynamics: Implications of Changes in Acute Kidney Injury. Anal Cell Pathol (Amst) 2018; 2018:8764384. [PMID: 30073137 PMCID: PMC6057397 DOI: 10.1155/2018/8764384] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/05/2018] [Accepted: 06/14/2018] [Indexed: 02/05/2023] Open
Abstract
Over the years, the epigenetic landscape has grown increasingly complex. Until recently, methylation of DNA and histones was considered one of the most important epigenetic modifications. However, with the discovery of enzymes involved in the demethylation process, several exciting prospects have emerged that focus on the dynamic regulation of methylation and its crucial role in development and disease. An interplay of the methylation-demethylation machinery controls the process of gene expression. Since acute kidney injury (AKI), a major risk factor for chronic kidney disease and death, is characterised by aberrant expression of genes, understanding the dynamics of methylation and demethylation will provide new insights into the intricacies of the disease. Research on epigenetics in AKI has only made its mark in the recent years but has provided compelling evidence that implicates the involvement of methylation and demethylation changes in its pathophysiology. In this review, we explore the role of methylation and demethylation machinery in cellular epigenetic control and further discuss the contribution of methylomic changes and histone modifications to the pathophysiology of AKI.
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Affiliation(s)
- Anubhav Chakraborty
- Renal Research Lab, Centre for Bio-Medical Research, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India
| | - Pragasam Viswanathan
- Renal Research Lab, Centre for Bio-Medical Research, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India
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52
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McCullough LD, Mirza MA, Xu Y, Bentivegna K, Steffens EB, Ritzel R, Liu F. Stroke sensitivity in the aged: sex chromosome complement vs. gonadal hormones. Aging (Albany NY) 2017; 8:1432-41. [PMID: 27405096 PMCID: PMC4993340 DOI: 10.18632/aging.100997] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/22/2016] [Indexed: 11/25/2022]
Abstract
Stroke is a sexually dimorphic disease. Elderly women not only have higher stroke incidence than age-matched men, but also have poorer recovery and higher morbidity and mortality after stroke. In older, post-menopausal women, gonadal hormone levels are similar to that of men. This suggests that tissue damage and functional outcomes are influenced by biologic sex (XX vs. XY) rather than the hormonal milieu at older ages. We employed the Four Core Genotype (FCG) mouse model to study the contribution of sex chromosome complement and gonadal hormones to stroke sensitivity in aged mice in which the testis determining gene (Sry) is removed from the Y chromosome, allowing for the generation of XX males and XY females. XXF, XXM, XYF, XYM and XYwt aged mice were subjected to middle cerebral artery occlusion (MCAO). XXF and XXM mice had significantly larger infarct volumes than XYF and XYM cohorts respectively. There was no significant difference in hormone levels among aged FCG mice. XXF/XXM mice also had more robust microglial activation and higher serum levels of pro-inflammatory cytokines than XYF/XYM cohort respectively. We concluded that the sex chromosome complement contributes to ischemic sensitivity in aged animals and leads to sex differences in innate immune responses.
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Affiliation(s)
- Louise D McCullough
- Department of Neurology, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Mehwish A Mirza
- Department of Neuroscience, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Yan Xu
- Department of Neurology, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Kathryn Bentivegna
- Department of Neuroscience, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Eleanor B Steffens
- Department of Neuroscience, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Rodney Ritzel
- Department of Neuroscience, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Fudong Liu
- Department of Neurology, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
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53
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Chatterjee RN. Dosage compensation and its roles in evolution of sex chromosomes and phenotypic dimorphism: lessons from Drosophila, C.elegans and mammals. THE NUCLEUS 2017. [DOI: 10.1007/s13237-017-0223-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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54
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Bai GY, Song SH, Sun RZ, Zhang ZH, Li J, Wang ZD, Liu ZH, Lei L. RNAi-mediated knockdown of Parp1 does not improve the development of female cloned mouse embryos. Oncotarget 2017; 8:69863-69873. [PMID: 29050247 PMCID: PMC5642522 DOI: 10.18632/oncotarget.19418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/20/2017] [Indexed: 12/04/2022] Open
Abstract
Somatic cell nuclear transfer is an important technique for life science research, but its efficiency is still extremely low, and most genes that are important during early development, such as X chromosome-linked genes, are not appropriately expressed during this process. Poly (ADP-ribose) polymerase (PARP) is an enzyme that transfers ADP ribose clusters to target proteins. PARP family members such as PARP1 participate in cellular signalling pathways through poly (ADP-ribosylation) (PARylation), which ultimately promotes changes in chromatin structure, gene expression, and the localization and activity of proteins that mediate signalling responses. PARP1 is associated with X chromosome inactivation (Xi). Here, we showed that abnormal Xi occurs in somatic cell nuclear transfer (NT) blastocysts, whereas in female blastocysts derived from cumulus cell nuclear transfer, both X chromosomes were inactive. Parp1 expression was higher in female NT blastocysts than that in intracytoplasmic sperm injection (ICSI) embryos but not in male NT blastocysts. After knocking down Parp1 expression, both the pre-rRNA 47S and X-inactivation-specific transcript (Xist) levels increased. Moreover, the expression of genes on the inactivated X chromosome, such as Magea6 and Msn, were also increased in the NT embryos. However, the development of Parp1si NT embryos was impaired, although total RNA sequencing showed that overall gene expression between the Parp1si NT blastocysts and the control was similar. Our findings demonstrate that increases in the expression of several genes on the X chromosome and of rRNA primary products in NT blastocysts with disrupted Parp1 expression are insufficient to rescue the impaired development of female cloned mouse embryos and could even exacerbate the associated developmental deficiencies.
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Affiliation(s)
- Guang-Yu Bai
- Department of Histology and Embryology, Harbin Medical University, Harbin, 150081, China
| | - Si-Hang Song
- Department of Histology and Embryology, Harbin Medical University, Harbin, 150081, China
| | - Rui-Zhen Sun
- Department of Histology and Embryology, Harbin Medical University, Harbin, 150081, China
| | - Zi-Hui Zhang
- Department of Histology and Embryology, Harbin Medical University, Harbin, 150081, China
| | - Jingyu Li
- Laboratory of Embryo Biotechnology, College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Zhen-Dong Wang
- Department of Histology and Embryology, Harbin Medical University, Harbin, 150081, China
| | - Zhong-Hua Liu
- Laboratory of Embryo Biotechnology, College of Life Science, Northeast Agricultural University, Harbin, 150030, China
| | - Lei Lei
- Department of Histology and Embryology, Harbin Medical University, Harbin, 150081, China
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55
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Richard G, Legeai F, Prunier-Leterme N, Bretaudeau A, Tagu D, Jaquiéry J, Le Trionnaire G. Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid. Epigenetics Chromatin 2017. [PMID: 28638443 PMCID: PMC5471693 DOI: 10.1186/s13072-017-0137-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Background Heterogametic species display a differential number of sex chromosomes resulting in imbalanced transcription levels for these chromosomes between males and females. To correct this disequilibrium, dosage compensation mechanisms involving gene expression and chromatin accessibility regulations have emerged throughout evolution. In insects, these mechanisms have been extensively characterized only in Drosophila but not in insects of agronomical importance. Aphids are indeed major pests of a wide range of crops. Their remarkable ability to switch from asexual to sexual reproduction during their life cycle largely explains the economic losses they can cause. As heterogametic insects, male aphids are X0, while females (asexual and sexual) are XX. Results Here, we analyzed transcriptomic and open chromatin data obtained from whole male and female individuals to evaluate the putative existence of a dosage compensation mechanism involving differential chromatin accessibility of the pea aphid’s X chromosome. Transcriptomic analyses first showed X/AA and XX/AA expression ratios for expressed genes close to 1 in males and females, respectively, suggesting dosage compensation in the pea aphid. Analyses of open chromatin data obtained by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE-seq) revealed a X chromosome chromatin accessibility globally and significantly higher in males than in females, while autosomes’ chromatin accessibility is similar between sexes. Moreover, chromatin environment of X-linked genes displaying similar expression levels in males and females—and thus likely to be compensated—is significantly more accessible in males. Conclusions Our results suggest the existence of an underlying epigenetic mechanism enhancing the X chromosome chromatin accessibility in males to allow X-linked gene dose correction between sexes in the pea aphid, similar to Drosophila. Our study gives new evidence into the comprehension of dosage compensation in link with chromatin biology in insects and newly in a major crop pest, taking benefits from both transcriptomic and open chromatin data. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0137-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gautier Richard
- EGI, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Domaine de la Motte, BP 35327, Le Rheu, France
| | - Fabrice Legeai
- BIPAA, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Campus Beaulieu, Rennes, France.,Genscale, INRIA, IRISA, Campus Beaulieu, Rennes, France
| | - Nathalie Prunier-Leterme
- EGI, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Domaine de la Motte, BP 35327, Le Rheu, France
| | - Anthony Bretaudeau
- BIPAA, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Campus Beaulieu, Rennes, France.,Genouest, INRIA, IRISA, Campus Beaulieu, Rennes, France
| | - Denis Tagu
- EGI, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Domaine de la Motte, BP 35327, Le Rheu, France
| | - Julie Jaquiéry
- CNRS, UMR 6553, EcoBio, University of Rennes 1, 35042 Rennes, France
| | - Gaël Le Trionnaire
- EGI, UMR 1349, INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Domaine de la Motte, BP 35327, Le Rheu, France
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56
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Liang Z, Brown KE, Carroll T, Taylor B, Vidal IF, Hendrich B, Rueda D, Fisher AG, Merkenschlager M. A high-resolution map of transcriptional repression. eLife 2017; 6. [PMID: 28318487 PMCID: PMC5373822 DOI: 10.7554/elife.22767] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/15/2017] [Indexed: 11/20/2022] Open
Abstract
Turning genes on and off is essential for development and homeostasis, yet little is known about the sequence and causal role of chromatin state changes during the repression of active genes. This is surprising, as defective gene silencing underlies developmental abnormalities and disease. Here we delineate the sequence and functional contribution of transcriptional repression mechanisms at high temporal resolution. Inducible entry of the NuRD-interacting transcriptional regulator Ikaros into mouse pre-B cell nuclei triggered immediate binding to target gene promoters. Rapid RNAP2 eviction, transcriptional shutdown, nucleosome invasion, and reduced transcriptional activator binding required chromatin remodeling by NuRD-associated Mi2beta/CHD4, but were independent of HDAC activity. Histone deacetylation occurred after transcriptional repression. Nevertheless, HDAC activity contributed to stable gene silencing. Hence, high resolution mapping of transcriptional repression reveals complex and interdependent mechanisms that underpin rapid transitions between transcriptional states, and elucidates the temporal order, functional role and mechanistic separation of NuRD-associated enzymatic activities. DOI:http://dx.doi.org/10.7554/eLife.22767.001
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Affiliation(s)
- Ziwei Liang
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom.,Epigenetics Section, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Karen E Brown
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom.,Epigenetics Section, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Thomas Carroll
- Epigenetics Section, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Benjamin Taylor
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom.,Epigenetics Section, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Isabel Ferreirós Vidal
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom.,Epigenetics Section, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Brian Hendrich
- Wellcome Trust - Medical Research Council Stem Cell Institute, Cambridge, United Kingdom.,Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - David Rueda
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom.,Integrative Biology Section, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Amanda G Fisher
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom.,Epigenetics Section, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom.,Epigenetics Section, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom.,Integrative Biology Section, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
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57
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Xist-dependent imprinted X inactivation and the early developmental consequences of its failure. Nat Struct Mol Biol 2017; 24:226-233. [PMID: 28134930 DOI: 10.1038/nsmb.3365] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 12/20/2016] [Indexed: 12/18/2022]
Abstract
The long noncoding RNA Xist is expressed from only the paternal X chromosome in mouse preimplantation female embryos and mediates transcriptional silencing of that chromosome. In females, absence of Xist leads to postimplantation lethality. Here, through single-cell RNA sequencing of early preimplantation mouse embryos, we found that the initiation of imprinted X-chromosome inactivation absolutely requires Xist. Lack of paternal Xist leads to genome-wide transcriptional misregulation in the early blastocyst and to failure to activate the extraembryonic pathway that is essential for postimplantation development. We also demonstrate that the expression dynamics of X-linked genes depends on the strain and parent of origin as well as on the location along the X chromosome, particularly at the first 'entry' sites of Xist. This study demonstrates that dosage-compensation failure has an effect as early as the blastocyst stage and reveals genetic and epigenetic contributions to orchestrating transcriptional silencing of the X chromosome during early embryogenesis.
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58
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Mulugeta E, Wassenaar E, Sleddens-Linkels E, van IJcken WFJ, Heard E, Grootegoed JA, Just W, Gribnau J, Baarends WM. Genomes of Ellobius species provide insight into the evolutionary dynamics of mammalian sex chromosomes. Genome Res 2016; 26:1202-10. [PMID: 27510564 PMCID: PMC5052041 DOI: 10.1101/gr.201665.115] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 07/11/2016] [Indexed: 11/24/2022]
Abstract
The X and Y sex chromosomes of placental mammals show hallmarks of a tumultuous evolutionary past. The X Chromosome has a rich and conserved gene content, while the Y Chromosome has lost most of its genes. In the Transcaucasian mole vole Ellobius lutescens, the Y Chromosome including Sry has been lost, and both females and males have a 17,X diploid karyotype. Similarly, the closely related Ellobius talpinus, has a 54,XX karyotype in both females and males. Here, we report the sequencing and assembly of the E. lutescens and E. talpinus genomes. The results indicate that the loss of the Y Chromosome in E. lutescens and E. talpinus occurred in two independent events. Four functional homologs of mouse Y-Chromosomal genes were detected in both female and male E. lutescens, of which three were also detected in the E. talpinus genome. One of these is Eif2s3y, known as the only Y-derived gene that is crucial for successful male meiosis. Female and male E. lutescens can carry one and the same X Chromosome with a largely conserved gene content, including all genes known to function in X Chromosome inactivation. The availability of the genomes of these mole vole species provides unique models to study the dynamics of sex chromosome evolution.
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Affiliation(s)
- Eskeatnaf Mulugeta
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands; Institut Curie, Genetics and Developmental Biology Unit, 75248, Paris, France
| | - Evelyne Wassenaar
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
| | | | | | - Edith Heard
- Institut Curie, Genetics and Developmental Biology Unit, 75248, Paris, France
| | - J Anton Grootegoed
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
| | - Walter Just
- Institute of Human Genetics, University of Ulm, 89081, Ulm, Germany
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, 3015CN, Rotterdam, The Netherlands
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59
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Lomvardas S, Maniatis T. Histone and DNA Modifications as Regulators of Neuronal Development and Function. Cold Spring Harb Perspect Biol 2016; 8:8/7/a024208. [PMID: 27371659 DOI: 10.1101/cshperspect.a024208] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DNA and histone modifications, together with constraints imposed by nuclear architecture, contribute to the transcriptional regulatory landscape of the nervous system. Here, we provide select examples showing how these regulatory layers, often referred to as epigenetic, contribute to neuronal differentiation and function. We describe the interplay between DNA methylation and Polycomb-mediated repression during neuronal differentiation, the role of DNA methylation and long-range enhancer-promoter interactions in Protocadherin promoter choice, and the contribution of heterochromatic silencing and nuclear organization in singular olfactory receptor expression. Finally, we explain how the activity-dependent expression of a histone variant determines the longevity of olfactory sensory neurons.
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Affiliation(s)
- Stavros Lomvardas
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032
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60
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Gall Trošelj K, Novak Kujundzic R, Ugarkovic D. Polycomb repressive complex's evolutionary conserved function: the role of EZH2 status and cellular background. Clin Epigenetics 2016; 8:55. [PMID: 27239242 PMCID: PMC4882774 DOI: 10.1186/s13148-016-0226-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 05/04/2016] [Indexed: 02/07/2023] Open
Abstract
When assembled in multiprotein polycomb repressive complexes (PRCs), highly evolutionary conserved polycomb group (PcG) proteins epigenetically control gene activity. Although the composition of PRCs may vary considerably, it is well established that the embryonic ectoderm development (EED) 1, suppressor of zeste (SUZ) 12, and methyltransferase enhancer of zeste (EZH2)-containing complex, PRC2, which is abundant in highly proliferative cells (including cancer cells), establishes a repressive methylation mark on histone 3 (H3K27me3). From the perspective of molecular cancer pathogenesis, this effect, when directed towards a promoter of tumor suppressor genes, represents pro-tumorigenic effect. This mode of action was shown in several cancer models. However, EZH2 function extends beyond this scenario. The highly specific cellular background, related to the origin of cell and numerous external stimuli during a given time-window, may be the trigger for EZH2 interaction with other proteins, not necessarily histones. This is particularly relevant for cancer. This review provides a critical overview of the evolutional importance of PRC and discusses several important aspects of EZH2 functioning within PRC. The review also deals with mutational studies on EZH2. Due to the existence of several protein (and messenger RNA (mRNA)) isoforms, these mutations were stratified, using the protein sequence which is considered canonical. This approach showed that there is an urgent need for the uniformed positioning of currently known EZH2 mutations (somatic-in tumors, as well as germline mutations in the Weaver's syndrome). Finally, we discuss EZH2 function with respect to amount of trimethylated H3K27, in a specific cellular milieu, through presenting the most recent data related to EZH2-H3K27m3 relationship in cancer. All these points are significant in considering EZH2 as a therapeutic target.
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Affiliation(s)
- Koraljka Gall Trošelj
- />Division of Molecular Medicine, Laboratory for Epigenomics, Rudjer Boskovic Institute, Bijenicka cesta 54, 10 000 Zagreb, Croatia
| | - Renata Novak Kujundzic
- />Division of Molecular Medicine, Laboratory for Epigenomics, Rudjer Boskovic Institute, Bijenicka cesta 54, 10 000 Zagreb, Croatia
| | - Djurdjica Ugarkovic
- />Division of Molecular Biology, Laboratory for Evolutionary Genetics, Rudjer Boskovic Institute, Bijenicka cesta 54, 10 000 Zagreb, Croatia
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61
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Almouzni G, Cedar H. Maintenance of Epigenetic Information. Cold Spring Harb Perspect Biol 2016; 8:8/5/a019372. [PMID: 27141050 DOI: 10.1101/cshperspect.a019372] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The genome is subject to a diverse array of epigenetic modifications from DNA methylation to histone posttranslational changes. Many of these marks are somatically stable through cell division. This article focuses on our knowledge of the mechanisms governing the inheritance of epigenetic marks, particularly, repressive ones, when the DNA and chromatin template are duplicated in S phase. This involves the action of histone chaperones, nucleosome-remodeling enzymes, histone and DNA methylation binding proteins, and chromatin-modifying enzymes. Last, the timing of DNA replication is discussed, including the question of whether this constitutes an epigenetic mark that facilitates the propagation of epigenetic marks.
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Affiliation(s)
- Geneviève Almouzni
- Department of Nuclear Dynamics and Genome Plasticity, Institut Curie, Section de recherche, 75231 Paris Cedex 05, France
| | - Howard Cedar
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Ein Kerem, Jerusalem, Israel 91120
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62
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Payer B. Developmental regulation of X-chromosome inactivation. Semin Cell Dev Biol 2016; 56:88-99. [PMID: 27112543 DOI: 10.1016/j.semcdb.2016.04.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/13/2016] [Accepted: 04/21/2016] [Indexed: 12/01/2022]
Abstract
With the emergence of sex-determination by sex chromosomes, which differ in composition and number between males and females, appeared the need to equalize X-chromosomal gene dosage between the sexes. Mammals have devised the strategy of X-chromosome inactivation (XCI), in which one of the two X-chromosomes is rendered transcriptionally silent in females. In the mouse, the best-studied model organism with respect to XCI, this inactivation process occurs in different forms, imprinted and random, interspersed by periods of X-chromosome reactivation (XCR), which is needed to switch between the different modes of XCI. In this review, I describe the recent advances with respect to the developmental control of XCI and XCR and in particular their link to differentiation and pluripotency. Furthermore, I review the mechanisms, which influence the timing and choice, with which one of the two X-chromosomes is chosen for inactivation during random XCI. This has an impact on how females are mosaics with regard to which X-chromosome is active in different cells, which has implications on the severity of diseases caused by X-linked mutations.
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Affiliation(s)
- Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra (UPF), Dr. Aiguader, 88, Barcelona 08003, Spain.
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63
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Torday JS, Miller WB. Biologic relativity: Who is the observer and what is observed? PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 121:29-34. [PMID: 26980522 DOI: 10.1016/j.pbiomolbio.2016.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/01/2016] [Accepted: 03/10/2016] [Indexed: 02/06/2023]
Abstract
When quantum physics and biological phenomena are analogously explored, it emerges that biologic causation must also be understood independently of its overt appearance. This is similar to the manner in which Bohm characterized the explicate versus the implicate order as overlapping frames of ambiguity. Placed in this context, the variables affecting epigenetic inheritance can be properly assessed as a key mechanistic principle of evolution that significantly alters our understanding of homeostasis, pleiotropy, and heterochrony, and the purposes of sexual reproduction. Each of these become differing manifestations of a new biological relativity in which biologic space-time becomes its own frame. In such relativistic cellular contexts, it is proper to question exactly who has observer status, and who and what are being observed. Consideration within this frame reduces biology to cellular information sharing through cell-cell communication to resolve ambiguities at every scope and scale. In consequence, it becomes implicit that eukaryotic evolution derives from the unicellular state, remaining consistently adherent to it in a continuous evolutionary arc based upon elemental, non-stochastic physiologic first principles. Furthermore, the entire cell including its cytoskeletal apparatus and membranes that participate in the resolution of biological uncertainties must be considered as having equivalent primacy with genomes in evolutionary terms.
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Affiliation(s)
- John S Torday
- Evolutionary Medicine, UCLA, 1124 West Carson Street, Torrance, CA 90502-2006, USA.
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64
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Patel DJ. A Structural Perspective on Readout of Epigenetic Histone and DNA Methylation Marks. Cold Spring Harb Perspect Biol 2016; 8:a018754. [PMID: 26931326 DOI: 10.1101/cshperspect.a018754] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This article outlines the protein modules that target methylated lysine histone marks and 5mC DNA marks, and the molecular principles underlying recognition. The article focuses on the structural basis underlying readout of isolated marks by single reader molecules, as well as multivalent readout of multiple marks by linked reader cassettes at the histone tail and nucleosome level. Additional topics addressed include the role of histone mimics, cross talk between histone marks, technological developments at the genome-wide level, advances using chemical biology approaches, the linkage between histone and DNA methylation, the role for regulatory lncRNAs, and the promise of chromatin-based therapeutic modalities.
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Affiliation(s)
- Dinshaw J Patel
- Structural Biology Department, Memorial Sloan-Kettering Cancer Center, New York, New York 10065
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65
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Abstract
Genetic causes for human disorders are being discovered at an unprecedented pace. A growing subclass of disease-causing mutations involves changes in the epigenome or in the abundance and activity of proteins that regulate chromatin structure. This article focuses on research that has uncovered human diseases that stem from such epigenetic deregulation. Disease may be caused by direct changes in epigenetic marks, such as DNA methylation, commonly found to affect imprinted gene regulation. Also described are disease-causing genetic mutations in epigenetic modifiers that either affect chromatin in trans or have a cis effect in altering chromatin configuration.
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Affiliation(s)
- Huda Y Zoghbi
- Howard Hughes Medical Institute, Baylor College of Medicine, and Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
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66
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Ramírez F, Lingg T, Toscano S, Lam KC, Georgiev P, Chung HR, Lajoie BR, de Wit E, Zhan Y, de Laat W, Dekker J, Manke T, Akhtar A. High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila. Mol Cell 2016; 60:146-62. [PMID: 26431028 DOI: 10.1016/j.molcel.2015.08.024] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 07/20/2015] [Accepted: 08/25/2015] [Indexed: 01/08/2023]
Abstract
Dosage compensation mechanisms provide a paradigm to study the contribution of chromosomal conformation toward targeting and spreading of epigenetic regulators over a specific chromosome. By using Hi-C and 4C analyses, we show that high-affinity sites (HAS), landing platforms of the male-specific lethal (MSL) complex, are enriched around topologically associating domain (TAD) boundaries on the X chromosome and harbor more long-range contacts in a sex-independent manner. Ectopically expressed roX1 and roX2 RNAs target HAS on the X chromosome in trans and, via spatial proximity, induce spreading of the MSL complex in cis, leading to increased expression of neighboring autosomal genes. We show that the MSL complex regulates nucleosome positioning at HAS, therefore acting locally rather than influencing the overall chromosomal architecture. We propose that the sex-independent, three-dimensional conformation of the X chromosome poises it for exploitation by the MSL complex, thereby facilitating spreading in males.
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Affiliation(s)
- Fidel Ramírez
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Lingg
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Sarah Toscano
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Kin Chung Lam
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Plamen Georgiev
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Ho-Ryun Chung
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Bryan R Lajoie
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Elzo de Wit
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Ye Zhan
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | - Wouter de Laat
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA; Howard Hughes Medical Institute
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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67
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Abstract
Induced pluripotency defines the process by which somatic cells are converted into induced pluripotent stem cells (iPSCs) upon overexpression of a small set of transcription factors. In this article, we put transcription factor-induced pluripotency into a historical context, review current methods to generate iPSCs, and discuss mechanistic insights that have been gained into the process of reprogramming. In addition, we focus on potential therapeutic applications of induced pluripotency and emerging technologies to efficiently engineer the genomes of human pluripotent cells for scientific and therapeutic purposes.
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Affiliation(s)
- Konrad Hochedlinger
- Howard Hughes Medical Institute at Massachusetts General Hospital, Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Medical School, Boston, Massachusetts 02114
| | - Rudolf Jaenisch
- Whitehead Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
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68
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Abstract
Epigenetic mechanisms play an essential role in the germline and imprinting cycle. Germ cells show extensive epigenetic programming in preparation for the generation of the totipotent state, which in turn leads to the establishment of pluripotent cells in blastocysts. The latter are the cells from which pluripotent embryonic stem cells are derived and maintained in culture. Following blastocyst implantation, postimplantation epiblast cells develop, which give rise to all somatic cells as well as primordial germ cells, the precursors of sperm and eggs. Pluripotent stem cells in culture can be induced to undergo differentiation into somatic cells and germ cells in culture. Understanding the natural cycles of epigenetic reprogramming that occur in the germline will allow the generation of better and more versatile stem cells for both therapeutic and research purposes.
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Affiliation(s)
- Wolf Reik
- The Babraham Institute, Babraham Research Campus, Cambridge CB2 3EG, United Kingdom Wellcome Trust Cancer Research UK Gurdon Institute & Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - M Azim Surani
- Wellcome Trust Cancer Research UK Gurdon Institute & Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
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69
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Abstract
MOF was first identified in Drosophila melanogaster as an important component of the dosage compensation complex. As a member of MYST family of histone acetyltransferase, MOF specifically deposits the acetyl groups to histone H4 lysine 16. Throughout evolution, MOF and its mammalian ortholog have retained highly conserved substrate specificity and similar enzymatic activities. MOF plays important roles in dosage compensation, ESC self-renewal, DNA damage and repair, cell survival, and gene expression regulation. Dysregulation of MOF has been implicated in tumor formation and progression of many types of human cancers. This review will discuss the structure and activity of mammalian hMOF as well as its function in H4K16 acetylation, DNA damage response, stem cell pluripotency, and carcinogenesis.
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Affiliation(s)
- Qiao Yi Chen
- Department of Environmental Medicine, NYU School of Medicine, Tuxedo, NY, USA
| | - Max Costa
- Department of Environmental Medicine, NYU School of Medicine, Tuxedo, NY, USA
| | - Hong Sun
- Department of Environmental Medicine, NYU School of Medicine, Tuxedo, NY, USA
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70
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Abstract
To accommodate genomes in the limited space of the cell nucleus and ensure the correct execution of gene expression programs, genomes are packaged in complex fashion in the three-dimensional cell nucleus. As a consequence of the extensive higher-order organization of chromosomes, distantly located genomic regions on the same or distinct chromosomes undergo long-range interactions. This article discusses the nature of long interactions, mechanisms of their formation, and their emerging functional roles in gene regulation and genome maintenance.
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Affiliation(s)
- Job Dekker
- University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
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71
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Abstract
SUMMARY The involvement of RNA interference (RNAi) in heterochromatin formation has become clear largely through studies in the fission yeast Schizosaccharomyces pombe and plants like Arabidopsis thaliana. This article discusses how heterochromatic small interfering RNAs are produced and how the RNAi machinery participates in the formation and function of heterochromatin.
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Affiliation(s)
| | - Danesh Moazed
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115-5730
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72
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Abstract
Dosage compensation in Drosophila increases the transcription of genes on the single X chromosome in males to equal that of both X chromosomes in females. Site-specific histone acetylation by the male-specific lethal (MSL) complex is thought to play a fundamental role in the increased transcriptional output of the male X. Nucleation and sequence-independent spreading of the complex to active genes serves as a model for understanding the targeting and function of epigenetic chromatin-modifying complexes. Interestingly, two noncoding RNAs are key for MSL assembly and spreading to active genes along the length of the X chromosome.
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Affiliation(s)
- John C Lucchesi
- Department of Biology, O. W. Rollins Research Center, Emory University, Atlanta, Georgia 30322
| | - Mitzi I Kuroda
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
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73
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Abstract
Histones package and compact DNA by assembling into nucleosome core particles. Most histones are synthesized at S phase for rapid deposition behind replication forks. In addition, the replacement of histones deposited during S phase by variants that can be deposited independently of replication provide the most fundamental level of chromatin differentiation. Alternative mechanisms for depositing different variants can potentially establish and maintain epigenetic states. Variants have also evolved crucial roles in chromosome segregation, transcriptional regulation, DNA repair, and other processes. Investigations into the evolution, structure, and metabolism of histone variants provide a foundation for understanding the participation of chromatin in important cellular processes and in epigenetic memory.
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Affiliation(s)
- Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024
| | - M Mitchell Smith
- Department of Microbiology, University of Virginia, Charlottesville, Virginia 22908
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74
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Grossniklaus U, Paro R. Transcriptional silencing by polycomb-group proteins. Cold Spring Harb Perspect Biol 2014; 6:a019331. [PMID: 25367972 DOI: 10.1101/cshperspect.a019331] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Polycomb-group (PcG) genes encode chromatin proteins involved in stable and heritable transcriptional silencing. PcG proteins participate in distinct multimeric complexes that deposit, or bind to, specific histone modifications (e.g., H3K27me3 and H2AK119ub1) to prevent gene activation and maintain repressed chromatin domains. PcG proteins are evolutionary conserved and play a role in processes ranging from vernalization and seed development in plants, over X-chromosome inactivation in mammals, to the maintenance of stem cell identity. PcG silencing is medically relevant as it is often observed in human disorders, including cancer, and tissue regeneration, which involve the reprogramming of PcG-controlled target genes.
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Affiliation(s)
- Ueli Grossniklaus
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, CH-8008 Zürich, Switzerland
| | - Renato Paro
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
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75
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Abstract
Numerous studies over the past decade have identified increasing numbers of long noncoding RNAs (lncRNAs) across many organisms. Research since has shown that lncRNAs constitute an important layer of genome regulation in diverse biological processes and disease. Here, we discuss the common emerging theme of lncRNAs interfacing with epigenetic machinery. This, in turn, modulates the activity and localization of the epigenetic machinery during cell fate specification.
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Affiliation(s)
- John L Rinn
- Harvard University, Department of Stem Cell and Regenerative Biology, Cambridge, Massachusetts 02138
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76
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Abstract
DNA methylation is one of the best characterized epigenetic modifications. In mammals it is involved in various biological processes including the silencing of transposable elements, regulation of gene expression, genomic imprinting, and X-chromosome inactivation. This article describes how DNA methylation serves as a cellular memory system and how it is dynamically regulated through the action of the DNA methyltransferase (DNMT) and ten eleven translocation (TET) enzymes. Its role in the regulation of gene expression, through its interplay with histone modifications, is also described, and its implication in human diseases discussed. The exciting areas of investigation that will likely become the focus of research in the coming years are outlined in the summary.
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Affiliation(s)
- En Li
- China Novartis Institutes for BioMedical Research, Pudong New Area, Shanghai 201203, China
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77
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Strome S, Kelly WG, Ercan S, Lieb JD. Regulation of the X chromosomes in Caenorhabditis elegans. Cold Spring Harb Perspect Biol 2014; 6:6/3/a018366. [PMID: 24591522 DOI: 10.1101/cshperspect.a018366] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Dosage compensation, which regulates the expression of genes residing on the sex chromosomes, has provided valuable insights into chromatin-based mechanisms of gene regulation. The nematode Caenorhabditis elegans has adopted various strategies to down-regulate and even nearly silence the X chromosomes. This article discusses the different chromatin-based strategies used in somatic tissues and in the germline to modulate gene expression from the C. elegans X chromosomes and compares these strategies to those used by other organisms to cope with similar X-chromosome dosage differences.
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Affiliation(s)
- Susan Strome
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California 95064
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78
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Abstract
Genomic imprinting affects a subset of genes in mammals and results in a monoallelic, parental-specific expression pattern. Most of these genes are located in clusters that are regulated through the use of insulators or long noncoding RNAs (lncRNAs). To distinguish the parental alleles, imprinted genes are epigenetically marked in gametes at imprinting control elements through the use of DNA methylation at the very least. Imprinted gene expression is subsequently conferred through lncRNAs, histone modifications, insulators, and higher-order chromatin structure. Such imprints are maintained after fertilization through these mechanisms despite extensive reprogramming of the mammalian genome. Genomic imprinting is an excellent model for understanding mammalian epigenetic regulation.
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Affiliation(s)
- Denise P Barlow
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, CeMM, 1090 Vienna, Austria
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79
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Abstract
Much of what we know about the role of epigenetics in the determination of phenotype has come from studies of inbred mice. Some unusual expression patterns arising from endogenous and transgenic murine alleles, such as the Agouti coat color alleles, have allowed the study of variegation, variable expressivity, transgenerational epigenetic inheritance, parent-of-origin effects, and position effects. These phenomena have taught us much about gene silencing and the probabilistic nature of epigenetic processes. Based on some of these alleles, large-scale mutagenesis screens have broadened our knowledge of epigenetic control by identifying and characterizing novel genes involved in these processes.
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Affiliation(s)
- Marnie Blewitt
- Walter and Eliza Hall Institute, Melbourne, 3052 Victoria, Australia
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80
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Elgin SCR, Reuter G. Position-effect variegation, heterochromatin formation, and gene silencing in Drosophila. Cold Spring Harb Perspect Biol 2013; 5:a017780. [PMID: 23906716 DOI: 10.1101/cshperspect.a017780] [Citation(s) in RCA: 309] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Position-effect variegation (PEV) results when a gene normally in euchromatin is juxtaposed with heterochromatin by rearrangement or transposition. When heterochromatin packaging spreads across the heterochromatin/euchromatin border, it causes transcriptional silencing in a stochastic pattern. PEV is intensely studied in Drosophila using the white gene. Screens for dominant mutations that suppress or enhance white variegation have identified many conserved epigenetic factors, including the histone H3 lysine 9 methyltransferase SU(VAR)3-9. Heterochromatin protein HP1a binds H3K9me2/3 and interacts with SU(VAR)3-9, creating a core memory system. Genetic, molecular, and biochemical analysis of PEV in Drosophila has contributed many key findings concerning establishment and maintenance of heterochromatin with concomitant gene silencing.
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Affiliation(s)
- Sarah C R Elgin
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
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