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Mockenhaupt K, Tyc KM, McQuiston A, Gonsiewski AK, Zarei-Kheirabadi M, Hariprashad A, Biswas DD, Gupta AS, Olex AL, Singh SK, Waters MR, Dupree JL, Dozmorov MG, Kordula T. Yin Yang 1 controls cerebellar astrocyte maturation. Glia 2023; 71:2437-2455. [PMID: 37417428 PMCID: PMC10529878 DOI: 10.1002/glia.24434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 06/12/2023] [Accepted: 06/16/2023] [Indexed: 07/08/2023]
Abstract
Diverse subpopulations of astrocytes tile different brain regions to accommodate local requirements of neurons and associated neuronal circuits. Nevertheless, molecular mechanisms governing astrocyte diversity remain mostly unknown. We explored the role of a zinc finger transcription factor Yin Yang 1 (YY1) that is expressed in astrocytes. We found that specific deletion of YY1 from astrocytes causes severe motor deficits in mice, induces Bergmann gliosis, and results in simultaneous loss of GFAP expression in velate and fibrous cerebellar astrocytes. Single cell RNA-seq analysis showed that YY1 exerts specific effects on gene expression in subpopulations of cerebellar astrocytes. We found that although YY1 is dispensable for the initial stages of astrocyte development, it regulates subtype-specific gene expression during astrocyte maturation. Moreover, YY1 is continuously needed to maintain mature astrocytes in the adult cerebellum. Our findings suggest that YY1 plays critical roles regulating cerebellar astrocyte maturation during development and maintaining a mature phenotype of astrocytes in the adult cerebellum.
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Affiliation(s)
- Karli Mockenhaupt
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Katarzyna M. Tyc
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia
- Massey Cancer Center Bioinformatics Shared Resource Core, Virginia Commonwealth University, Richmond, Virginia
| | - Adam McQuiston
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, Virginia
| | - Alexandra K. Gonsiewski
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Masoumeh Zarei-Kheirabadi
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Avani Hariprashad
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Debolina D. Biswas
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Angela S. Gupta
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Amy L. Olex
- C. Kenneth and Dianne Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, Virginia
| | - Sandeep K. Singh
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Michael R. Waters
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Jeff L. Dupree
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, Virginia
- Research Service, Central Virginia VA Health Care System, Richmond, Virginia
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia
| | - Tomasz Kordula
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia
- The Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
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2
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Verma A, Arya R, Brahmachari V. Identification of a polycomb responsive region in human HoxA cluster and its long-range interaction with polycomb enriched genomic regions. Gene 2022; 845:146832. [PMID: 36007803 DOI: 10.1016/j.gene.2022.146832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 11/04/2022]
Abstract
Polycomb and Trithorax group proteins (PcG, TrxG) epigenetically regulate developmental genes. These proteins bind with specific DNA elements, the Polycomb Response Element (PRE). Apart from mutations in polycomb/ trithorax proteins, altered cis-elements like PRE underlie the modified function and thus disease etiology. PREs are well studied in Drosophila, while only a few human PREs have been reported. We have identified a polycomb responsive DNA element, hPRE-HoxA3, in the intron of the HoxA3 gene. The hPRE-HoxA3 represses luciferase reporter activity in a PcG-dependent manner. The endogenous hPRE-HoxA3 element recruits PcG proteins and is enriched with repressive H3K27me3 marks, demonstrating that hPRE-HoxA3 is a part of the PcG-dependent gene regulatory network. Furthermore, it interacts with D11-12, the well-known PRE in the human Hox cluster. hPRE-Hox3 is a part of the 3-dimensional chromosomal domain organization as it is involved in the long-range interaction with other PcG enriched regions of Hox A, B, C, and D clusters.
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Affiliation(s)
- Akanksha Verma
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007, India.
| | - Richa Arya
- Current address- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
| | - Vani Brahmachari
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007, India
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Du J, Kirk B, Zeng J, Ma J, Wang Q. Three classes of response elements for human PRC2 and MLL1/2-Trithorax complexes. Nucleic Acids Res 2018; 46:8848-8864. [PMID: 29992232 PMCID: PMC6158500 DOI: 10.1093/nar/gky595] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 12/15/2022] Open
Abstract
Polycomb group (PcG) and Trithorax group (TrxG) proteins are essential for maintaining epigenetic memory in both embryonic stem cells and differentiated cells. To date, how they are localized to hundreds of specific target genes within a vertebrate genome had remained elusive. Here, by focusing on short cis-acting DNA elements of single functions, we discovered three classes of response elements in human genome: Polycomb response elements (PREs), Trithorax response elements (TREs) and Polycomb/Trithorax response elements (P/TREs). In particular, the four PREs (PRE14, 29, 39 and 48) are the first set of, to our knowledge, bona fide vertebrate PREs ever discovered, while many previously reported Drosophila or vertebrate PREs are likely P/TREs. We further demonstrated that YY1 and CpG islands are specifically enriched in the four TREs (PRE30, 41, 44 and 55), but not in the PREs. The three classes of response elements as unraveled in this study should guide further global investigation and open new doors for a deeper understanding of PcG and TrxG mechanisms in vertebrates.
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Affiliation(s)
- Junqing Du
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Brian Kirk
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jia Zeng
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jianpeng Ma
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, TX 77030, USA
| | - Qinghua Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Maini J, Ghasemi M, Yandhuri D, Thakur SS, Brahmachari V. Human PRE-PIK3C2B, an intronic cis-element with dual function of activation and repression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:196-204. [PMID: 27932267 DOI: 10.1016/j.bbagrm.2016.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 10/28/2016] [Accepted: 12/02/2016] [Indexed: 02/01/2023]
Abstract
The Polycomb/Trithorax Responsive Elements (PRE/TREs) are the cis-regulatory sequences that interact with both repressive (PcG) as well as activating (TrxG) complexes. However, most of the mammalian PREs are demonstrated to interact with the repressive polycomb (PcG) complexes only. We have carried out an unbiased search for proteins interacting with human PRE-PIK3C2B (hPRE-PIK3C2B) based on DNA affinity purification followed by mass spectrometry and identified MLL, MLL4 and WDR87 among other proteins in three biological replicates in HEK, U87 and HeLa cell lines. The hPRE-PIK3C2B interacts with the members of multiple activating complexes (COMPASS-like). The increase in the interaction of MLL and MLL4 on depletion of YY1 and the increase in the enrichment of YY1 and EZH2 upon MLL knockdown at the hPRE-PIK3C2B indicate the dual occupancy and suggest a concentration dependent enrichment of the activator or the repressor complex at hPRE-PIK3C2B. Further, we show that the hPRE-PIK3C2B interacts with the Drosophila homologues of PcG and TrxG proteins in transgenic flies. Here, we found that there is an increased enrichment of Pc (Polycomb) in comparison to Trx (TrxG protein) at hPRE-PIK3C2B in the Drosophila transgenic flies and this seems to be the default state while the balance is tipped towards the trithorax complex in PcG mutants. To the best of our knowledge, this is one of the early demonstrations of human PRE acting as a TRE without any sequence alteration.
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Affiliation(s)
- Jayant Maini
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India
| | - Mohsen Ghasemi
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India
| | - Deepti Yandhuri
- CSIR-Centre for Cellular & Molecular Biology, Uppal Road, Habsiguda, Hyderabad 500007, India
| | - Suman S Thakur
- CSIR-Centre for Cellular & Molecular Biology, Uppal Road, Habsiguda, Hyderabad 500007, India
| | - Vani Brahmachari
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India.
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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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Svoboda LK, Harris A, Bailey NJ, Schwentner R, Tomazou E, von Levetzow C, Magnuson B, Ljungman M, Kovar H, Lawlor ER. Overexpression of HOX genes is prevalent in Ewing sarcoma and is associated with altered epigenetic regulation of developmental transcription programs. Epigenetics 2015; 9:1613-25. [PMID: 25625846 DOI: 10.4161/15592294.2014.988048] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The polycomb proteins BMI-1 and EZH2 are highly overexpressed by Ewing sarcoma (ES), a tumor of stem cell origin that is driven by EWS-ETS fusion oncogenes, most commonly EWS-FLI1. In the current study we analyzed expression of transcription programs that are controlled by polycomb proteins during embryonic development to determine if they are abnormal in ES. Our results show that polycomb target gene expression in ES deviates from normal tissues and stem cells and that, as expected, most targets are relatively repressed. However, we also discovered a paradoxical up regulation of numerous polycomb targets and these were highly enriched for homeobox (HOX) genes. Comparison of HOX profiles between malignant and non-malignant tissues revealed a distinctive HOX profile in ES, which was characterized by overexpression of posterior HOXD genes. In addition, ectopic expression of EWS-FLI1 during stem cell differentiation led to aberrant up regulation of posterior HOXD genes. Mechanistically, this up regulation was associated with altered epigenetic regulation. Specifically, ES and EWS-FLI1+ stem cells displayed a relative loss of polycomb-dependent H3K27me3 and gain of trithorax-dependent H3K4me3 at the promoters of posterior HOXD genes and also at the HOXD11.12 polycomb response element. In addition, a striking correlation was evident between HOXD13 and other genes whose regulation is coordinately regulated during embryonic development by distal enhancer elements. Together, these studies demonstrate that epigenetic regulation of polycomb target genes, in particular HOXD genes, is altered in ES and that these changes are mediated downstream of EWS-FLI1.
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Key Words
- ARMS, alveolar rhabdomyosarcoma
- BM-MSC, adult bone marrow-derived mesenchymal stem cells
- ChIP, chromatin immunoprecipitation
- ChIP-seq, chromatin immunoprecipitation/high throughput sequencing
- ERMS, embryonal rhabdomyosarcoma
- ES, Ewing sarcoma
- Ewing sarcoma
- GCR, global control region
- HOX
- HOX, homeobox
- MSC, mesenchymal stem cells
- NC-MSC, neural crest stem cell-derived mesenchymal stem cells
- NCSC, neural crest stem cells
- OS, osteosarcoma
- PCA, principal components analysis
- PRE, polycomb response element
- RT-PCR, reverse transcriptase polymerase chain reaction
- epigenetic
- hESC, human embryonic stem cells
- polycomb
- qPCR, quantitative polymerase chain reaction
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Affiliation(s)
- Laurie K Svoboda
- a Translational Oncology Program and the Departments of Pediatric and Communicable Diseases; University of Michigan ; Ann Arbor , MI USA
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Context-dependent actions of Polycomb repressors in cancer. Oncogene 2015; 35:1341-52. [DOI: 10.1038/onc.2015.195] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/15/2015] [Accepted: 05/05/2015] [Indexed: 12/21/2022]
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Kallappagoudar S, Yadav RK, Lowe BR, Partridge JF. Histone H3 mutations--a special role for H3.3 in tumorigenesis? Chromosoma 2015; 124:177-89. [PMID: 25773741 PMCID: PMC4446520 DOI: 10.1007/s00412-015-0510-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 02/19/2015] [Accepted: 02/26/2015] [Indexed: 12/31/2022]
Abstract
Brain tumors are the most common solid tumors in children. Pediatric high-grade glioma (HGG) accounts for ∼8–12 % of these brain tumors and is a devastating disease as 70–90 % of patients die within 2 years of diagnosis. The failure to advance therapy for these children over the last 30 years is largely due to limited knowledge of the molecular basis for these tumors and a lack of disease models. Recently, sequencing of tumor cells revealed that histone H3 is frequently mutated in pediatric HGG, with up to 78 % of diffuse intrinsic pontine gliomas (DIPGs) carrying K27M and 36 % of non-brainstem gliomas carrying either K27M or G34R/V mutations. Although mutations in many chromatin modifiers have been identified in cancer, this was the first demonstration that histone mutations may be drivers of disease. Subsequent studies have identified high-frequency mutation of histone H3 to K36M in chondroblastomas and to G34W/L in giant cell tumors of bone, which are diseases of adolescents and young adults. Interestingly, the G34 mutations, the K36M mutations, and the majority of K27M mutations occur in genes encoding the replacement histone H3.3. Here, we review the peculiar characteristics of histone H3.3 and use this information as a backdrop to highlight current thinking about how the identified mutations may contribute to disease development.
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Affiliation(s)
- Satish Kallappagoudar
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
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Ma RG, Zhang Y, Sun TT, Cheng B. Epigenetic regulation by polycomb group complexes: focus on roles of CBX proteins. J Zhejiang Univ Sci B 2015; 15:412-28. [PMID: 24793759 DOI: 10.1631/jzus.b1400077] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Polycomb group (PcG) complexes are epigenetic regulatory complexes that conduct transcriptional repression of target genes via modifying the chromatin. The two best characterized forms of PcG complexes, polycomb repressive complexes 1 and 2 (PRC1 and PRC2), are required for maintaining the stemness of embryonic stem cells and many types of adult stem cells. The spectra of target genes for PRCs are dynamically changing with cell differentiation, which is essential for proper decisions on cell fate during developmental processes. Chromobox (CBX) family proteins are canonical components in PRC1, responsible for targeting PRC1 to the chromatin. Recent studies highlight the function specifications among CBX family members in undifferentiated and differentiated stem cells, which reveal the interplay between compositional diversity and functional specificity of PRC1. In this review, we summarize the current knowledge about targeting and functional mechanisms of PRCs, emphasizing the recent breakthroughs related to CBX proteins under a number of physiological and pathological conditions.
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Affiliation(s)
- Rong-gang Ma
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
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Bonasio R, Lecona E, Narendra V, Voigt P, Parisi F, Kluger Y, Reinberg D. Interactions with RNA direct the Polycomb group protein SCML2 to chromatin where it represses target genes. eLife 2014; 3:e02637. [PMID: 24986859 PMCID: PMC4074974 DOI: 10.7554/elife.02637] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Polycomb repressive complex-1 (PRC1) is essential for the epigenetic regulation of gene expression. SCML2 is a mammalian homolog of Drosophila SCM, a Polycomb-group protein that associates with PRC1. In this study, we show that SCML2A, an SCML2 isoform tightly associated to chromatin, contributes to PRC1 localization and also directly enforces repression of certain Polycomb target genes. SCML2A binds to PRC1 via its SPM domain and interacts with ncRNAs through a novel RNA-binding region (RBR). Targeting of SCML2A to chromatin involves the coordinated action of the MBT domains, RNA binding, and interaction with PRC1 through the SPM domain. Deletion of the RBR reduces the occupancy of SCML2A at target genes and overexpression of a mutant SCML2A lacking the RBR causes defects in PRC1 recruitment. These observations point to a role for ncRNAs in regulating SCML2 function and suggest that SCML2 participates in the epigenetic control of transcription directly and in cooperation with PRC1.DOI: http://dx.doi.org/10.7554/eLife.02637.001.
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Affiliation(s)
- Roberto Bonasio
- Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, New York University School of Medicine, New York, United States
| | - Emilio Lecona
- Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, New York University School of Medicine, New York, United States
| | - Varun Narendra
- Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, New York University School of Medicine, New York, United States
| | - Philipp Voigt
- Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, New York University School of Medicine, New York, United States
| | - Fabio Parisi
- Department of Pathology, Yale University School of Medicine, New Haven, United States Yale Cancer Center, Yale University School of Medicine, New Haven, United States
| | - Yuval Kluger
- Department of Pathology, Yale University School of Medicine, New Haven, United States Yale Cancer Center, Yale University School of Medicine, New Haven, United States
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, Howard Hughes Medical Institute, New York University School of Medicine, New York, United States
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Cheedipudi S, Genolet O, Dobreva G. Epigenetic inheritance of cell fates during embryonic development. Front Genet 2014; 5:19. [PMID: 24550937 PMCID: PMC3912789 DOI: 10.3389/fgene.2014.00019] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 01/21/2014] [Indexed: 01/25/2023] Open
Abstract
During embryonic development a large number of widely differing and specialized cell types with identical genomes are generated from a single totipotent zygote. Tissue specific transcription factors cooperate with epigenetic modifiers to establish cellular identity in differentiated cells and epigenetic regulatory mechanisms contribute to the maintenance of distinct chromatin states and cell-type specific gene expression patterns, a phenomenon referred to as epigenetic memory. This is accomplished via the stable maintenance of various epigenetic marks through successive rounds of cell division. Preservation of DNA methylation patterns is a well-established mechanism of epigenetic memory, but more recently it has become clear that many other epigenetic modifications can also be maintained following DNA replication and cell division. In this review, we present an overview of the current knowledge regarding the role of histone lysine methylation in the establishment and maintenance of stable epigenetic states.
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Affiliation(s)
- Sirisha Cheedipudi
- Origin of Cardiac Cell Lineages Group, Max Planck Institute for Heart and Lung Research Bad Nauheim, Germany ; Medical Faculty, J. W. Goethe University Frankfurt Frankfurt, Germany
| | - Oriana Genolet
- Origin of Cardiac Cell Lineages Group, Max Planck Institute for Heart and Lung Research Bad Nauheim, Germany ; Medical Faculty, J. W. Goethe University Frankfurt Frankfurt, Germany
| | - Gergana Dobreva
- Origin of Cardiac Cell Lineages Group, Max Planck Institute for Heart and Lung Research Bad Nauheim, Germany ; Medical Faculty, J. W. Goethe University Frankfurt Frankfurt, Germany
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