1
|
Abstract
Epigenetic regulators are pivotal factors that influence and control T cell development. Recent findings continue to reveal additional elements of epigenetic modifications that play significant and crucial roles at different stages of T cell development. Through gaining a better understanding of the various epigenetic factors that influence the formation and survival of maturing T cells, new therapies can potentially be developed to combat diseases caused by dysregulated epigenetic chromatin modifications. In this review, we summarize the recent studies which shed light on the epigenetic regulation of T cell development especially at the critical stage of β-selection.
Collapse
Affiliation(s)
- Avik Dutta
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Harini Venkataganesh
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.,Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Paul E Love
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
2
|
Beurton F, Stempor P, Caron M, Appert A, Dong Y, Chen RAJ, Cluet D, Couté Y, Herbette M, Huang N, Polveche H, Spichty M, Bedet C, Ahringer J, Palladino F. Physical and functional interaction between SET1/COMPASS complex component CFP-1 and a Sin3S HDAC complex in C. elegans. Nucleic Acids Res 2019; 47:11164-11180. [PMID: 31602465 PMCID: PMC6868398 DOI: 10.1093/nar/gkz880] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 09/13/2019] [Accepted: 10/07/2019] [Indexed: 12/23/2022] Open
Abstract
The CFP1 CXXC zinc finger protein targets the SET1/COMPASS complex to non-methylated CpG rich promoters to implement tri-methylation of histone H3 Lys4 (H3K4me3). Although H3K4me3 is widely associated with gene expression, the effects of CFP1 loss vary, suggesting additional chromatin factors contribute to context dependent effects. Using a proteomics approach, we identified CFP1 associated proteins and an unexpected direct link between Caenorhabditis elegans CFP-1 and an Rpd3/Sin3 small (SIN3S) histone deacetylase complex. Supporting a functional connection, we find that mutants of COMPASS and SIN3 complex components genetically interact and have similar phenotypic defects including misregulation of common genes. CFP-1 directly binds SIN-3 through a region including the conserved PAH1 domain and recruits SIN-3 and the HDA-1/HDAC subunit to H3K4me3 enriched promoters. Our results reveal a novel role for CFP-1 in mediating interaction between SET1/COMPASS and a Sin3S HDAC complex at promoters.
Collapse
Affiliation(s)
- Flore Beurton
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Przemyslaw Stempor
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Matthieu Caron
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Alex Appert
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Yan Dong
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Ron A-j Chen
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - David Cluet
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Yohann Couté
- Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | - Marion Herbette
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Ni Huang
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Hélène Polveche
- INSERM UMR 861, I-STEM, 28, Rue Henri Desbruères, 91100 Corbeil-Essonnes, France
| | - Martin Spichty
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Cécile Bedet
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Julie Ahringer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Francesca Palladino
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| |
Collapse
|
3
|
Lin F, Meng X, Guo Y, Cao W, Liu W, Xia Q, Hui Z, Chen J, Hong S, Zhang X, Wu C, Wang D, Wang J, Lu L, Qian W, Wei L, Wang L. Epigenetic initiation of the T H17 differentiation program is promoted by Cxxc finger protein 1. SCIENCE ADVANCES 2019; 5:eaax1608. [PMID: 31633019 PMCID: PMC6785255 DOI: 10.1126/sciadv.aax1608] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/14/2019] [Indexed: 06/05/2023]
Abstract
IL-6/STAT3 signaling is known to initiate the TH17 differentiation program, but the upstream regulatory mechanisms remain minimally explored. Here, we show that Cxxc finger protein 1 (Cxxc1) promoted the generation of TH17 cells as an epigenetic regulator and prevented their differentiation into Treg cells. Mice with a T cell-specific deletion of Cxxc1 were protected from experimental autoimmune encephalomyelitis and were more susceptible to Citrobacter rodentium infection. Cxxc1 deficiency decreased IL-6Rα expression and impeded IL-6/STAT3 signaling, whereas the overexpression of IL-6Rα could partially reverse the defects in Cxxc1-deficient TH17 cells in vitro and in vivo. Genome-wide occupancy analysis revealed that Cxxc1 bound to Il6rα gene loci by maintaining the appropriate H3K4me3 modification of its promoter. Therefore, these data highlight that Cxxc1 as a key regulator governs the balance between TH17 and Treg cells by controlling the expression of IL-6Rα, which affects IL-6/STAT3 signaling and has an impact on TH17-related autoimmune diseases.
Collapse
MESH Headings
- Animals
- CD8-Positive T-Lymphocytes/cytology
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Cell Differentiation
- Citrobacter rodentium/physiology
- Encephalomyelitis, Autoimmune, Experimental/immunology
- Encephalomyelitis, Autoimmune, Experimental/metabolism
- Encephalomyelitis, Autoimmune, Experimental/pathology
- Enterobacteriaceae Infections/pathology
- Epigenesis, Genetic
- Female
- Histones/metabolism
- Interleukin-6/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Promoter Regions, Genetic
- Receptors, Interleukin-6/genetics
- Receptors, Interleukin-6/metabolism
- STAT3 Transcription Factor/metabolism
- Signal Transduction
- T-Lymphocytes, Regulatory/cytology
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- Th17 Cells/cytology
- Th17 Cells/immunology
- Th17 Cells/metabolism
- Trans-Activators/deficiency
- Trans-Activators/genetics
- Trans-Activators/metabolism
Collapse
Affiliation(s)
- Feng Lin
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University and Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Xiaoyu Meng
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University and Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Yixin Guo
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University and Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Wenqiang Cao
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University and Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Wanlu Liu
- Zhejiang University–University of Edinburgh Joint Institute, Zhejiang University, Haining, China
| | - Qiming Xia
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University and Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Zhaoyuan Hui
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University and Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Jian Chen
- Department of General Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shenghui Hong
- Laboratory Animal Center, Zhejiang University, Hangzhou, China
| | - Xuliang Zhang
- Laboratory Animal Center, Zhejiang University, Hangzhou, China
| | - Chuan Wu
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Di Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianli Wang
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University and Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Linrong Lu
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenbin Qian
- Institute of Hematology, Zhejiang University and Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Lie Wang
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University and Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, China
- Laboratory Animal Center, Zhejiang University, Hangzhou, China
| |
Collapse
|
4
|
Brown DA, Di Cerbo V, Feldmann A, Ahn J, Ito S, Blackledge NP, Nakayama M, McClellan M, Dimitrova E, Turberfield AH, Long HK, King HW, Kriaucionis S, Schermelleh L, Kutateladze TG, Koseki H, Klose RJ. The SET1 Complex Selects Actively Transcribed Target Genes via Multivalent Interaction with CpG Island Chromatin. Cell Rep 2018; 20:2313-2327. [PMID: 28877467 PMCID: PMC5603731 DOI: 10.1016/j.celrep.2017.08.030] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 07/19/2017] [Accepted: 08/06/2017] [Indexed: 12/24/2022] Open
Abstract
Chromatin modifications and the promoter-associated epigenome are important for the regulation of gene expression. However, the mechanisms by which chromatin-modifying complexes are targeted to the appropriate gene promoters in vertebrates and how they influence gene expression have remained poorly defined. Here, using a combination of live-cell imaging and functional genomics, we discover that the vertebrate SET1 complex is targeted to actively transcribed gene promoters through CFP1, which engages in a form of multivalent chromatin reading that involves recognition of non-methylated DNA and histone H3 lysine 4 trimethylation (H3K4me3). CFP1 defines SET1 complex occupancy on chromatin, and its multivalent interactions are required for the SET1 complex to place H3K4me3. In the absence of CFP1, gene expression is perturbed, suggesting that normal targeting and function of the SET1 complex are central to creating an appropriately functioning vertebrate promoter-associated epigenome. The CFP1/SET1 complex engages in dynamic and stable chromatin-binding events CFP1 uses multivalent chromatin interactions to select active CpG island promoters SET1A occupancy at CpG island promoters is predominately defined by CFP1 CFP1 targets SET1 to shape promoter-associated H3K4me3 and gene expression
Collapse
Affiliation(s)
- David A Brown
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Vincenzo Di Cerbo
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Angelika Feldmann
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Jaewoo Ahn
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-2 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Neil P Blackledge
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Manabu Nakayama
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-2 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Michael McClellan
- Ludwig Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Emilia Dimitrova
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | | | - Hannah K Long
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Hamish W King
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Skirmantas Kriaucionis
- Ludwig Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-2 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
| |
Collapse
|
5
|
Parvanov ED, Tian H, Billings T, Saxl RL, Spruce C, Aithal R, Krejci L, Paigen K, Petkov PM. PRDM9 interactions with other proteins provide a link between recombination hotspots and the chromosomal axis in meiosis. Mol Biol Cell 2016; 28:488-499. [PMID: 27932493 PMCID: PMC5341731 DOI: 10.1091/mbc.e16-09-0686] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/28/2016] [Accepted: 11/30/2016] [Indexed: 11/11/2022] Open
Abstract
In mammals, meiotic recombination occurs at 1- to 2-kb genomic regions termed hotspots, whose positions and activities are determined by PRDM9, a DNA-binding histone methyltransferase. We show that the KRAB domain of PRDM9 forms complexes with additional proteins to allow hotspots to proceed into the next phase of recombination. By a combination of yeast-two hybrid assay, in vitro binding, and coimmunoprecipitation from mouse spermatocytes, we identified four proteins that directly interact with PRDM9's KRAB domain, namely CXXC1, EWSR1, EHMT2, and CDYL. These proteins are coexpressed in spermatocytes at the early stages of meiotic prophase I, the limited period when PRDM9 is expressed. We also detected association of PRDM9-bound complexes with the meiotic cohesin REC8 and the synaptonemal complex proteins SYCP3 and SYCP1. Our results suggest a model in which PRDM9-bound hotspot DNA is brought to the chromosomal axis by the action of these proteins, ensuring the proper chromatin and spatial environment for subsequent recombination events.
Collapse
Affiliation(s)
- Emil D Parvanov
- Center for Genome Dynamics, Jackson Laboratory, Bar Harbor, ME 04609.,Department of Biology, Masaryk University, Brno, Czech Republic 625 00
| | - Hui Tian
- Center for Genome Dynamics, Jackson Laboratory, Bar Harbor, ME 04609
| | - Timothy Billings
- Center for Genome Dynamics, Jackson Laboratory, Bar Harbor, ME 04609
| | - Ruth L Saxl
- Center for Genome Dynamics, Jackson Laboratory, Bar Harbor, ME 04609
| | - Catrina Spruce
- Center for Genome Dynamics, Jackson Laboratory, Bar Harbor, ME 04609
| | - Rakesh Aithal
- Department of Biology, Masaryk University, Brno, Czech Republic 625 00
| | - Lumir Krejci
- Department of Biology, Masaryk University, Brno, Czech Republic 625 00 .,National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic 625 00
| | - Kenneth Paigen
- Center for Genome Dynamics, Jackson Laboratory, Bar Harbor, ME 04609
| | - Petko M Petkov
- Center for Genome Dynamics, Jackson Laboratory, Bar Harbor, ME 04609
| |
Collapse
|
6
|
Kurum E, Benayoun BA, Malhotra A, George J, Ucar D. Computational inference of a genomic pluripotency signature in human and mouse stem cells. Biol Direct 2016; 11:47. [PMID: 27639379 PMCID: PMC5027095 DOI: 10.1186/s13062-016-0148-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/03/2016] [Indexed: 12/18/2022] Open
Abstract
UNLABELLED Recent analyses of next-generation sequencing datasets have shown that cell-specific regulatory elements in stem cells are marked with distinguishable patterns of transcription factor (TF) binding and epigenetic marks. For example, we recently demonstrated that promoters of cell-specific genes are covered with expanded trimethylation of histone H3 at lysine 4 (H3K4me3) marks (i.e., broad H3K4me3 domains). Moreover, binding of specific TFs, such as OCT4, NANOG, and SOX2, have been shown to play a critical role in maintaining the pluripotency of stem cells. Despite these observations, a systematic exploration of genomic and epigenomic features of stem-cell-specific gene promoters has not been conducted. Advanced machine-learning models can capture distinguishable genomic and epigenomic characteristics of stem-cell-specific promoters by taking advantage of the wealth of publicly available datasets. Here, we propose a three-step framework to discover novel data characteristics of high-throughput next generation sequencing datasets that distinguish pluripotency genes in human and mouse embryonic stem cells (ESCs). Our framework involves: i) feature extraction to identify novel features of genomic datasets; ii) feature selection using a logistic regression model combined with the Least Absolute Shrinkage and Selection Operator (LASSO) method to find the most critical datasets and features; and iii) cross validation with features selected using LASSO method to assess the predictive power of selected data features in distinguishing pluripotency genes. We show that specific epigenetic marks, and specific features of these marks, are enriched at pluripotency gene promoters. Moreover, we also assess both the individual and combined effect of TF binding, epigenetic mark deposition, gene expression datasets for marking pluripotency genes. Our findings are consistent with the existence of a conserved, complex and integrative genomic signature in ESCs that can be exploited to flag important candidate pluripotency genes. They also validate our computational framework for fostering a deeper understanding of genomic datasets in stem cells, in the future, could be extended to study cell-type-specific genomic landscapes in other cell types. REVIEWERS This article was reviewed by Zoltan Gaspari and Piotr Zielenkiewicz.
Collapse
Affiliation(s)
- Esra Kurum
- Department of Statistics, University of California, Riverside, Riverside, CA, USA
| | | | - Ankit Malhotra
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Joshy George
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA.
| |
Collapse
|
7
|
Mahadevan J, Skalnik DG. Efficient differentiation of murine embryonic stem cells requires the binding of CXXC finger protein 1 to DNA or methylated histone H3-Lys4. Gene 2016; 594:1-9. [PMID: 27590438 DOI: 10.1016/j.gene.2016.08.048] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 08/04/2016] [Accepted: 08/29/2016] [Indexed: 01/03/2023]
Abstract
Mammalian CXXC finger protein 1 (Cfp1) is a DNA-binding protein that is a component of the Setd1 histone methyltransferase complexes and is a critical epigenetic regulator of both histone and cytosine methylation. Murine embryonic stem (ES) cells lacking Cfp1 exhibit a loss of histone H3-Lys4 tri-methylation (H3K4me3) at many CpG islands, and a mis-localization of this epigenetic mark to heterochromatic sub-nuclear domains. Furthermore, these cells fail to undergo cellular differentiation in vitro. These defects are rescued upon introduction of a Cfp1-expression vector. Cfp1 contains an N-terminal plant homeodomain (PHD), a motif frequently observed in chromatin associated proteins that functions as a reader module of histone marks. Here, we report that the Cfp1 PHD domain directly and specifically binds to histone H3K4me1/me2/me3 marks. Introduction of individual mutations at key Cfp1 PHD residues (Y28, D44, or W49) ablates this histone interaction both in vitro and in vivo. The W49A point mutation does not affect the ability of Cfp1 to rescue appropriate restriction of histone H3K4me3 to euchromatic sub-nuclear domains or in vitro cellular differentiation in Cfp1-null ES cells. Similarly, a mutated form of Cfp1 that lacks DNA-binding activity (C169A) rescues in vitro cellular differentiation. However, rescue of Cfp1-null ES cells with a double mutant form of Cfp1 (W49A, C169A) results in partially defective in vitro differentiation. These data define the Cfp1 PHD domain as a reader of histone H3K4me marks and provide evidence that this activity is involved in the regulation of lineage commitment in ES cells.
Collapse
Affiliation(s)
- Jyothi Mahadevan
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - David G Skalnik
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Biology Department, School of Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, United States.
| |
Collapse
|
8
|
Cao W, Guo J, Wen X, Miao L, Lin F, Xu G, Ma R, Yin S, Hui Z, Chen T, Guo S, Chen W, Huang Y, Liu Y, Wang J, Wei L, Wang L. CXXC finger protein 1 is critical for T-cell intrathymic development through regulating H3K4 trimethylation. Nat Commun 2016; 7:11687. [PMID: 27210293 PMCID: PMC4879243 DOI: 10.1038/ncomms11687] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 04/19/2016] [Indexed: 02/07/2023] Open
Abstract
T-cell development in the thymus is largely controlled by an epigenetic program, involving in both DNA methylation and histone modifications. Previous studies have identified Cxxc1 as a regulator of both cytosine methylation and histone 3 lysine 4 trimethylation (H3K4me3). However, it is unknown whether Cxxc1 plays a role in thymocyte development. Here we show that T-cell development in the thymus is severely impaired in Cxxc1-deficient mice. Furthermore, we identify genome-wide Cxxc1-binding sites and H3K4me3 modification sites in wild-type and Cxxc1-deficient thymocytes. Our results demonstrate that Cxxc1 directly controls the expression of key genes important for thymocyte survival such as RORγt and for T-cell receptor signalling including Zap70 and CD8, through maintaining the appropriate H3K4me3 on their promoters. Importantly, we show that RORγt, a direct target of Cxxc1, can rescue the survival defects in Cxxc1-deficient thymocytes. Our data strongly support a critical role of Cxxc1 in thymocyte development.
Collapse
Affiliation(s)
- Wenqiang Cao
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jing Guo
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiaofeng Wen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Li Miao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Feng Lin
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Guanxin Xu
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ruoyu Ma
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Shengxia Yin
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhaoyuan Hui
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Tingting Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Shixin Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Wei Chen
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA.,Division of Pulmonary Medicine, Allergy and Immunology, Department of Pediatrics, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania 15224, USA
| | - Yingying Huang
- Core Facilities, College of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Jianli Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Lie Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| |
Collapse
|
9
|
Bledau AS, Schmidt K, Neumann K, Hill U, Ciotta G, Gupta A, Torres DC, Fu J, Kranz A, Stewart AF, Anastassiadis K. The H3K4 methyltransferase Setd1a is first required at the epiblast stage, whereas Setd1b becomes essential after gastrulation. Development 2014; 141:1022-35. [PMID: 24550110 DOI: 10.1242/dev.098152] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Histone 3 lysine 4 (H3K4) methylation is a universal epigenetic mark. In mammals, there are six H3K4 methyltransferases related to yeast Set1 and fly Trithorax, including two orthologs of Set1: Setd1a and Setd1b. Here we show that mouse Setd1a is required for gastrulation, whereas Setd1b-deficient embryos survive to E11.5 but are grossly retarded. Setd1a knockout embryos implant but do not proceed past the epiblast. Furthermore, Setd1a is not required until the inner cell mass has formed, at which stage it has replaced Mll2 as the major H3K4 methyltransferase. Setd1a is required for embryonic, epiblast and neural stem cell survival and neural stem cell reprogramming, whereas Setd1b is dispensable. Deletion of Setd1a in embryonic stem cells resulted in rapid losses of bulk H3K4 methylation, pluripotency gene expression and proliferation, with G1 pileup. Setd1b overexpression could not rescue the proliferation defects caused by loss of Setd1a in embryonic stem cells. The precise developmental requirement for Setd1a suggests that gastrulation is regulated by a switch between the major H3K4 methyltransferases.
Collapse
Affiliation(s)
- Anita S Bledau
- Stem Cell Engineering, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Baubec T, Schübeler D. Genomic patterns and context specific interpretation of DNA methylation. Curr Opin Genet Dev 2014; 25:85-92. [PMID: 24614011 DOI: 10.1016/j.gde.2013.11.015] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 11/29/2013] [Indexed: 12/21/2022]
Abstract
Methylation of CpG dinucleotides is a reversible modification of DNA that is highly prevalent throughout mammalian genomes. Recent advances generated genomic DNA methylation maps during cellular differentiation at unprecedented resolution. Combined with functional assays this revealed that dynamics in DNA methylation coincide with changes in regulatory activity and that transcription factors play an important role in shaping methylation patterns. This tightly links DNA methylation with underlying DNA sequence features and suggests that a substantial fraction of methylation changes occur downstream of gene regulation. Here we discuss our current understanding of the context-dependent readout of DNA methylation and criteria that need to be fulfilled for this modification to be instructive for gene regulation.
Collapse
Affiliation(s)
- Tuncay Baubec
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland.
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, Basel 4058, Switzerland; University of Basel, Faculty of Science, Petersplatz 1, Basel 4003, Switzerland.
| |
Collapse
|
11
|
Woo S, Lee A, Denis V, Chen CA, Yum S. Transcript response of soft coral (Scleronephthya gracillimum) on exposure to polycyclic aromatic hydrocarbons. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:901-910. [PMID: 23832774 DOI: 10.1007/s11356-013-1958-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 06/24/2013] [Indexed: 06/02/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are the most persistent organic pollutants in worldwide aquatic environments. The extensive isolation of genes responsive to PAH pollution in soft coral (Scleronephthya gracillimum) is described herein. Soft coral colonies were exposed to 100 μg/L of a standard mixture of PAHs. Gene candidates with transcript levels that changed in response to PAH exposure were identified by differential display polymerase chain reaction (DD-PCR). There were 37 types of candidate genes identified, of which 20 were upregulated in expression and 17 were downregulated. The functions of the genes identified included oxidative stress response, ribosomal structure maintenance, molecular chaperone activity, protein kinase activation and tumorigenesis, defense mechanisms, transcription, and other biological responses. mRNA quantification was carried out using real-time quantitative PCR in eight selected genes: cytosolic malate dehydrogenase, protein disulfide isomerase, ribosomal protein L6, ral guanine nucleotide dissociation stimulator-like 1, poly(ADP-ribose) polymerase 4, peptidylglycine α-hydroxylating monooxygenase, a disintegrin and metalloproteinase (ADAM) metallopeptidase protein, and eukaryotic initiation factor 4 gamma 3. Changes in transcript levels were consistent with DD-PCR results. The gene candidates isolated in this study were differentially expressed and therefore have potential as molecular biomarkers for understanding coral responses to environmental stressors.
Collapse
Affiliation(s)
- Seonock Woo
- South Sea Environment Research Division, Korea Institute of Ocean Science and Technology, Geoje, 656-830, Republic of Korea
| | | | | | | | | |
Collapse
|
12
|
Schweikert G, Cseke B, Clouaire T, Bird A, Sanguinetti G. MMDiff: quantitative testing for shape changes in ChIP-Seq data sets. BMC Genomics 2013; 14:826. [PMID: 24267901 PMCID: PMC4008153 DOI: 10.1186/1471-2164-14-826] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 11/15/2013] [Indexed: 12/21/2022] Open
Abstract
Background Cell-specific gene expression is controlled by epigenetic modifications and transcription factor binding. While genome-wide maps for these protein-DNA interactions have become widely available, quantitative comparison of the resulting ChIP-Seq data sets remains challenging. Current approaches to detect differentially bound or modified regions are mainly borrowed from RNA-Seq data analysis, thus focusing on total counts of fragments mapped to a region, ignoring any information encoded in the shape of the peaks. Results Here, we present MMDiff, a robust, broadly applicable method for detecting differences between sequence count data sets. Based on quantifying shape changes in signal profiles, it overcomes challenges imposed by the highly structured nature of the data and the paucity of replicates. We first use a simulated data set to compare the performance of MMDiff with results obtained by four alternative methods. We demonstrate that MMDiff excels when peak profiles change between samples. We next use MMDiff to re-analyse a recent data set of the histone modification H3K4me3 elucidating the establishment of this prominent epigenomic marker. Our empirical analysis shows that the method yields reproducible results across experiments, and is able to detect functional important changes in histone modifications. To further explore the broader applicability of MMDiff, we apply it to two ENCODE data sets: one investigating the histone modification H3K27ac and one measuring the genome-wide binding of the transcription factor CTCF. In both cases, MMDiff proves to be complementary to count-based methods. In addition, we can show that MMDiff is capable of directly detecting changes of homotypic binding events at neighbouring binding sites. MMDiff is readily available as a Bioconductor package. Conclusions Our results demonstrate that higher order features of ChIP-Seq peaks carry relevant and often complementary information to total counts, and hence are important in assessing differential histone modifications and transcription factor binding. We have developed a new computational method, MMDiff, that is capable of exploring these features and therefore closes an existing gap in the analysis of ChIP-Seq data sets.
Collapse
Affiliation(s)
- Gabriele Schweikert
- School of Informatics, University of Edinburgh, 10 Crichton Street, Edinburgh EH89AB, UK.
| | | | | | | | | |
Collapse
|
13
|
Glant TT, Besenyei T, Kádár A, Kurkó J, Tryniszewska B, Gál J, Soós G, Szekanecz Z, Hoffmann G, Block JA, Katz RS, Mikecz K, Rauch TA. Differentially expressed epigenome modifiers, including aurora kinases A and B, in immune cells in rheumatoid arthritis in humans and mouse models. ACTA ACUST UNITED AC 2013; 65:1725-35. [PMID: 23653330 DOI: 10.1002/art.37986] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 04/16/2013] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To identify epigenetic factors that are implicated in the pathogenesis of rheumatoid arthritis (RA), and to explore the therapeutic potential of the targeted inhibition of these factors. METHODS Polymerase chain reaction (PCR) arrays were used to investigate the expression profile of genes that encode key epigenetic regulator enzymes. Mononuclear cells from RA patients and mice were monitored for gene expression changes, in association with arthritis development in murine models of RA. Selected genes were further characterized by quantitative reverse transcription-PCR, Western blot, and flow cytometry methods. The targeted inhibition of the up-regulated enzymes was studied in arthritic mice. RESULTS A set of genes with arthritis-specific expression was identified by the PCR arrays. Aurora kinases A and B, both of which were highly expressed in arthritic mice and treatment-naive RA patients, were selected for detailed analysis. Elevated aurora kinase expression was accompanied by increased phosphorylation of histone H3, which promotes proliferation of T lymphocytes. Treatment with VX-680, a pan-aurora kinase inhibitor, promoted B cell apoptosis, provided significant protection against disease onset, and attenuated inflammatory reactions in arthritic mice. CONCLUSION Arthritis development is accompanied by changes in expression of a number of epigenome-modifying enzymes. Drug-induced down-regulation of the aurora kinases, among other targets, seems to be sufficient to treat experimental arthritis. Development of new therapeutics that target aurora kinases can potentially improve RA management.
Collapse
|
14
|
Cfp1 integrates both CpG content and gene activity for accurate H3K4me3 deposition in embryonic stem cells. Genes Dev 2012; 26:1714-28. [PMID: 22855832 DOI: 10.1101/gad.194209.112] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Trimethylation of histone H3 Lys 4 (H3K4me3) is a mark of active and poised promoters. The Set1 complex is responsible for most somatic H3K4me3 and contains the conserved subunit CxxC finger protein 1 (Cfp1), which binds to unmethylated CpGs and links H3K4me3 with CpG islands (CGIs). Here we report that Cfp1 plays unanticipated roles in organizing genome-wide H3K4me3 in embryonic stem cells. Cfp1 deficiency caused two contrasting phenotypes: drastic loss of H3K4me3 at expressed CGI-associated genes, with minimal consequences for transcription, and creation of "ectopic" H3K4me3 peaks at numerous regulatory regions. DNA binding by Cfp1 was dispensable for targeting H3K4me3 to active genes but was required to prevent ectopic H3K4me3 peaks. The presence of ectopic peaks at enhancers often coincided with increased expression of nearby genes. This suggests that CpG targeting prevents "leakage" of H3K4me3 to inappropriate chromatin compartments. Our results demonstrate that Cfp1 is a specificity factor that integrates multiple signals, including promoter CpG content and gene activity, to regulate genome-wide patterns of H3K4me3.
Collapse
|
15
|
Orkin SH, Hochedlinger K. Chromatin connections to pluripotency and cellular reprogramming. Cell 2011; 145:835-50. [PMID: 21663790 DOI: 10.1016/j.cell.2011.05.019] [Citation(s) in RCA: 303] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Indexed: 12/15/2022]
Abstract
The pluripotent state of embryonic stem cells (ESCs) provides a unique perspective on regulatory programs that govern self-renewal and differentiation and somatic cell reprogramming. Here, we review the highly connected protein and transcriptional networks that maintain pluripotency and how they are intertwined with factors that affect chromatin structure and function. The complex interrelationships between pluripotency and chromatin factors are illustrated by X chromosome inactivation, regulatory control by noncoding RNAs, and environmental influences on cell states. Manipulation of cell state through the process of transdifferentiation suggests that environmental cues may direct transcriptional programs as cells enter a transiently "plastic" state during reprogramming.
Collapse
Affiliation(s)
- Stuart H Orkin
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
| | | |
Collapse
|
16
|
The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain. Nat Commun 2011; 2:227. [PMID: 21407193 PMCID: PMC3072069 DOI: 10.1038/ncomms1237] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 02/09/2011] [Indexed: 12/18/2022] Open
Abstract
CFP1 is a CXXC domain-containing protein and an essential component of the SETD1 histone H3K4 methyltransferase complex. CXXC domain proteins direct different chromatin-modifying activities to various chromatin regions. Here, we report crystal structures of the CFP1 CXXC domain in complex with six different CpG DNA sequences. The crescent-shaped CFP1 CXXC domain is wedged into the major groove of the CpG DNA, distorting the B-form DNA, and interacts extensively with the major groove of the DNA. The structures elucidate the molecular mechanism of the non-methylated CpG-binding specificity of the CFP1 CXXC domain. The CpG motif is confined by a tripeptide located in a rigid loop, which only allows the accommodation of the non-methylated CpG dinucleotide. Furthermore, we demonstrate that CFP1 has a preference for a guanosine nucleotide following the CpG motif.
Collapse
|
17
|
Islam ABMMK, Richter WF, Lopez-Bigas N, Benevolenskaya EV. Selective targeting of histone methylation. Cell Cycle 2011; 10:413-24. [PMID: 21270517 DOI: 10.4161/cc.10.3.14705] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Histones are post-translationally modified by multiple histone-modifying enzymes, which in turn influences gene expression. Much of the work in the field to date has focused on genetic, biochemical and structural characterization of these enzymes. The most recent genome-wide methods provide insights into specific recruitment of histone-modifying enzymes in vivo and, therefore, onto mechanisms of establishing a differential expression pattern. Here we focus on the recruitment mechanisms of the enzymes involved in the placement of two contrasting histone marks, histone H3 lysine 4 (H3K4) methylation and histone H3 lysine 27 (H3K27) methylation. We describe distribution of their binding sites and show that recruitment of different histone-modifying proteins can be coordinated, opposed, or alternating. Specifically, genomic sites of the H3K4 histone demethylase KDM5A become accessible to its homolog KDM5B in cells with a lowered KDM5A level. The currently available data on recruitment of H3K4/H3K27 modifying enzymes suggests that the formed protein complexes are targeted in a sequential and temporal manner, but that additional, still unknown, interactions contribute to targeting specificity.
Collapse
Affiliation(s)
- Abul B M M K Islam
- Research Unit on Biomedical Informatics, Department of Experimental Health and Sciences, PRBB, Universitat Pompeu Fabra, Barcelona, Spain
| | | | | | | |
Collapse
|
18
|
Smith E, Shilatifard A. The chromatin signaling pathway: diverse mechanisms of recruitment of histone-modifying enzymes and varied biological outcomes. Mol Cell 2011; 40:689-701. [PMID: 21145479 DOI: 10.1016/j.molcel.2010.11.031] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 09/10/2010] [Accepted: 10/07/2010] [Indexed: 12/14/2022]
Abstract
Posttranslational modifications of histones are coupled in the regulation of the cellular processes involving chromatin, such as transcription, replication, repair, and genome stability. Recent biochemical and genetic studies have clearly demonstrated that many aspects of chromatin, in addition to posttranslational modifications of histones, provide surfaces that can interact with effectors and the modifying machineries in a context-dependent manner, all as a part of the "chromatin signaling pathway." Here, we have reviewed recent findings on the molecular basis for the recruitment of the chromatin-modifying machineries and their diverse and varied biological outcomes.
Collapse
Affiliation(s)
- Edwin Smith
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | | |
Collapse
|
19
|
Natural history of eukaryotic DNA methylation systems. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 101:25-104. [PMID: 21507349 DOI: 10.1016/b978-0-12-387685-0.00002-0] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Methylation of cytosines and adenines in DNA is a widespread epigenetic mark in both prokaryotes and eukaryotes. In eukaryotes, it has a profound influence on chromatin structure and dynamics. Recent advances in genomics and biochemistry have considerably elucidated the functions and provenance of these DNA modifications. DNA methylases appear to have emerged first in bacterial restriction-modification (R-M) systems from ancient RNA-modifying enzymes, in transitions that involved acquisition of novel catalytic residues and DNA-recognition features. DNA adenine methylases appear to have been acquired by ciliates, heterolobosean amoeboflagellates, and certain chlorophyte algae. Six distinct clades of cytosine methylases, including the DNMT1, DNMT2, and DNMT3 clades, were acquired by eukaryotes through independent lateral transfer of their precursors from bacteria or bacteriophages. In addition to these, multiple adenine and cytosine methylases were acquired by several families of eukaryotic transposons. In eukaryotes, the DNA-methylase module was often combined with distinct modified and unmodified peptide recognition domains and other modules mediating specialized interactions, for example, the RFD module of DNMT1 which contains a permuted Sm domain linked to a helix-turn-helix domain. In eukaryotes, the evolution of DNA methylases appears to have proceeded in parallel to the elaboration of histone-modifying enzymes and the RNAi system, with functions related to counter-viral and counter-transposon defense, and regulation of DNA repair and differential gene expression being their primary ancestral functions. Diverse DNA demethylation systems that utilize base-excision repair via DNA glycosylases and cytosine deaminases appear to have emerged in multiple eukaryotic lineages. Comparative genomics suggests that the link between cytosine methylation and DNA glycosylases probably emerged first in a novel R-M system in bacteria. Recent studies suggest that the 5mC is not a terminal DNA modification, with enzymes of the Tet/JBP family of 2-oxoglutarate- and iron-dependent dioxygenases further hydroxylating it to form 5-hydroxymethylcytosine (5hmC). These enzymes emerged first in bacteriophages and appear to have been transferred to eukaryotes on one or more occasions. Eukaryotes appear to have recruited three major types of DNA-binding domains (SRA/SAD, TAM/MBD, and CXXC) in discriminating DNA with methylated or unmethylated cytosines. Analysis of the domain architectures of these domains and the DNA methylases suggests that early in eukaryotic evolution they developed a close functional link with SET-domain methylases and Jumonji-related demethylases that operate on peptides in chromatin proteins. In several eukaryotes, other functional connections were elaborated in the form of various combinations between domains related to DNA methylation and those involved in ATP-dependent chromatin remodeling and RNAi. In certain eukaryotes, such as mammals and angiosperms, novel dependencies on the DNA methylation system emerged, which resulted in it affecting unexpected aspects of the biology of these organisms such as parent-offspring interactions. In genomic terms, this was reflected in the emergence of new proteins related to methylation, such as Stella. The well-developed methylation systems of certain heteroloboseans, stramenopiles, chlorophytes, and haptophyte indicate that these might be new model systems to explore the relevance of DNA modifications in eukaryotes.
Collapse
|
20
|
Mendenhall EM, Koche RP, Truong T, Zhou VW, Issac B, Chi AS, Ku M, Bernstein BE. GC-rich sequence elements recruit PRC2 in mammalian ES cells. PLoS Genet 2010; 6:e1001244. [PMID: 21170310 PMCID: PMC3000368 DOI: 10.1371/journal.pgen.1001244] [Citation(s) in RCA: 326] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 11/09/2010] [Indexed: 11/22/2022] Open
Abstract
Polycomb proteins are epigenetic regulators that localize to developmental loci in the early embryo where they mediate lineage-specific gene repression. In Drosophila, these repressors are recruited to sequence elements by DNA binding proteins associated with Polycomb repressive complex 2 (PRC2). However, the sequences that recruit PRC2 in mammalian cells have remained obscure. To address this, we integrated a series of engineered bacterial artificial chromosomes into embryonic stem (ES) cells and examined their chromatin. We found that a 44 kb region corresponding to the Zfpm2 locus initiates de novo recruitment of PRC2. We then pinpointed a CpG island within this locus as both necessary and sufficient for PRC2 recruitment. Based on this causal demonstration and prior genomic analyses, we hypothesized that large GC-rich elements depleted of activating transcription factor motifs mediate PRC2 recruitment in mammals. We validated this model in two ways. First, we showed that a constitutively active CpG island is able to recruit PRC2 after excision of a cluster of activating motifs. Second, we showed that two 1 kb sequence intervals from the Escherichia coli genome with GC-contents comparable to a mammalian CpG island are both capable of recruiting PRC2 when integrated into the ES cell genome. Our findings demonstrate a causal role for GC-rich sequences in PRC2 recruitment and implicate a specific subset of CpG islands depleted of activating motifs as instrumental for the initial localization of this key regulator in mammalian genomes. Key developmental genes are precisely turned on or off during development, thus creating a complex, multi-tissue embryo. The mechanism that keeps genes off, or repressed, is crucial to proper development. In embryonic stem cells, Polycomb repressive complex 2 (PRC2) is recruited to the promoters of these developmental genes and helps to maintain repression in the appropriate tissues through development. How PRC2 is initially recruited to these genes in the early embryo remains elusive. Here we experimentally demonstrate that stretches of GC-rich DNA, termed CpG islands, can initiate recruitment of PRC2 in embryonic stem cells when they are transcriptionally-inactive. Surprisingly, we find that GC-rich DNA from bacterial genomes can also initiate recruitment of PRC2 in embryonic stem cells. This supports a model where inactive GC-rich DNA can itself suffice to recruit PRC2 even in the absence of more complex DNA sequence motifs.
Collapse
Affiliation(s)
- Eric M. Mendenhall
- Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Richard P. Koche
- Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Thanh Truong
- Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Vicky W. Zhou
- Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Biju Issac
- Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Andrew S. Chi
- Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Neuro-Oncology Division, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Manching Ku
- Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Bradley E. Bernstein
- Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
21
|
Abstract
AbstractNumerous epigenetic modifications have been identified and correlated with transcriptionally active euchromatin or repressed heterochromatin and many enzymes responsible for the addition and removal of these marks have been characterized. However, less is known regarding how these enzymes are regulated and targeted to appropriate genomic locations. Mammalian CXXC finger protein 1 is an epigenetic regulator that was originally identified as a protein that binds specifically to any DNA sequence containing an unmethylated CpG dinucleotide. Mouse embryos lacking CXXC finger protein 1 die prior to gastrulation, and embryonic stem cells lacking CXXC finger protein 1 are viable but are unable to achieve cellular differentiation and lineage commitment. CXXC finger protein 1 is a regulator of both cytosine and histone methylation. It physically interacts with DNA methyltransferase 1 and facilitates maintenance cytosine methylation. Rescue studies reveal that CXXC finger protein 1 contains redundant functional domains that are sufficient to support cellular differentiation and proper levels of cytosine methylation. CXXC finger protein 1 is also a component of the Setd1 histone H3-Lys4 methyltransferase complexes and functions to target these enzymes to unmethylated CpG islands. Depletion of CXXC finger protein 1 leads to loss of histone H3-Lys4 tri-methylation at CpG islands and inappropriate drifting of this euchromatin mark into areas of hetero-chromatin. Thus, one function of CXXC finger protein 1 is to serve as an effector protein that interprets cytosine methylation patterns and facilitates crosstalk with histone-modifying enzymes.
Collapse
Affiliation(s)
- David G. Skalnik
- 1Wells Center for Pediatric Research, Section of Pediatric Hematology/Oncology, Departments of Pediatrics and Biochemistry and Molecular Biology, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN 46202, USA
| |
Collapse
|
22
|
Cheng X, Blumenthal RM. Coordinated chromatin control: structural and functional linkage of DNA and histone methylation. Biochemistry 2010; 49:2999-3008. [PMID: 20210320 DOI: 10.1021/bi100213t] [Citation(s) in RCA: 157] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
One of the most fundamental questions in the control of gene expression in mammals is how epigenetic methylation patterns of DNA and histones are established, erased, and recognized. This central process in controlling metazoan gene expression includes coordinated covalent modifications of DNA and its associated histones. This review focuses on recent developments in characterizing the functional links between the methylation status of the DNA and of two particularly important histone marks. Mammalian DNA methylation is intricately connected to the presence of unmodified lysine 4 and methylated lysine 9 residues in histone H3. An interconnected network of methyltransferases, demethylases, and accessory proteins is responsible for changing or maintaining the modification status of specific regions of chromatin. The structural and functional interactions among members of this network are critical to processes that include imprinting and differentiation, dysregulation of which is associated with disorders ranging from inflammation to cancer.
Collapse
Affiliation(s)
- Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA.
| | | |
Collapse
|
23
|
Thompson RF, Fazzari MJ, Greally JM. Experimental approaches to the study of epigenomic dysregulation in ageing. Exp Gerontol 2010; 45:255-68. [PMID: 20060885 DOI: 10.1016/j.exger.2009.12.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2009] [Revised: 12/19/2009] [Accepted: 12/28/2009] [Indexed: 12/25/2022]
Abstract
In this review, we describe how normal ageing may involve the acquisition of epigenetic errors over time, akin to the accumulation of genetic mutations with ageing. We describe how such experiments are currently performed, their limitations technically and analytically and their application to ageing research.
Collapse
Affiliation(s)
- Reid F Thompson
- Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | | |
Collapse
|
24
|
Tate CM, Lee JH, Skalnik DG. CXXC finger protein 1 restricts the Setd1A histone H3K4 methyltransferase complex to euchromatin. FEBS J 2009; 277:210-23. [PMID: 19951360 DOI: 10.1111/j.1742-4658.2009.07475.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CXXC finger protein 1 (Cfp1), encoded by the CXXC1 gene, is a component of the euchromatic Setd1A histone H3K4 methyltransferase complex, and is a critical regulator of histone methylation, cytosine methylation, cellular differentiation, and vertebrate development. Murine embryonic stem (ES) cells lacking Cfp1 (CXXC1(-/-)) are viable but show increased levels of global histone H3K4 methylation, suggesting that Cfp1 functions to inhibit or restrict the activity of the Setd1A histone H3K4 methyltransferase complex. The studies reported here reveal that ES cells lacking Cfp1 contain decreased levels of Setd1A and show subnuclear mislocalization of both Setd1A and trimethylation of histone H3K4 with regions of heterochromatin. Remarkably, structure-function studies reveal that expression of either the N-terminal fragment of Cfp1 (amino acids 1-367) or the C-terminal fragment of Cfp1 (amino acids 361-656) is sufficient to restore appropriate levels of Setd1A in CXXC1(-/-) ES cells. Furthermore, functional analysis of various Cfp1 point mutations reveals that retention of either Cfp1 DNA-binding activity or association with the Setd1 histone H3K4 methyltransferase complex is required to restore normal Setd1A levels. In contrast, expression of full-length Cfp1 in CXXC1(-/-) ES cells is required to restrict Setd1A and histone H3K4 trimethylation to euchromatin, indicating that both Cfp1 DNA-binding activity and interaction with the Setd1A complex are required for appropriate genomic targeting of the Setd1A complex. These studies illustrate the complexity of Cfp1 function, and identify Cfp1 as a regulator of Setd1A genomic targeting.
Collapse
Affiliation(s)
- Courtney M Tate
- Herman B. Wells Center for Pediatric Research, Section of Pediatric Hematology/Oncology, Departments of Pediatrics and Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | | |
Collapse
|
25
|
South PF, Fingerman IM, Mersman DP, Du HN, Briggs SD. A conserved interaction between the SDI domain of Bre2 and the Dpy-30 domain of Sdc1 is required for histone methylation and gene expression. J Biol Chem 2009; 285:595-607. [PMID: 19897479 DOI: 10.1074/jbc.m109.042697] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In Saccharomyces cerevisiae, lysine 4 on histone H3 (H3K4) is methylated by the Set1 complex (Set1C or COMPASS). Besides the catalytic Set1 subunit, several proteins that form the Set1C (Swd1, Swd2, Swd3, Spp1, Bre2, and Sdc1) are also needed to mediate proper H3K4 methylation. Until this study, it has been unclear how individual Set1C members interact and how this interaction may impact histone methylation and gene expression. In this study, Bre2 and Sdc1 are shown to directly interact, and it is shown that the association of this heteromeric complex is needed for proper H3K4 methylation and gene expression to occur. Interestingly, mutational and biochemical analysis identified the C terminus of Bre2 as a critical protein-protein interaction domain that binds to the Dpy-30 domain of Sdc1. Using the human homologs of Bre2 and Sdc1, ASH2L and DPY-30, respectively, we demonstrate that the C terminus of ASH2L also interacts with the Dpy-30 domain of DPY-30, suggesting that this protein-protein interaction is maintained from yeast to humans. Because of the functionally conserved nature of the C terminus of Bre2 and ASH2L, this region was named the SDI (Sdc1 Dpy-30 interaction) domain. Finally, we show that the SDI-Dpy-30 domain interaction is physiologically important for the function of Set1 in vivo, because specific disruption of this interaction prevents Bre2 and Sdc1 association with Set1, resulting in H3K4 methylation defects and decreases in gene expression. Overall, these and other mechanistic studies on how H3K4 methyltransferase complexes function will likely provide insights into how human MLL and SET1-like complexes or overexpression of ASH2L leads to oncogenesis.
Collapse
Affiliation(s)
- Paul F South
- Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, USA
| | | | | | | | | |
Collapse
|
26
|
Tate CM, Fishel ML, Holleran JL, Egorin MJ, Skalnik DG. Embryonic stem cells lacking the epigenetic regulator Cfp1 are hypersensitive to DNA-damaging agents and exhibit decreased Ape1/Ref-1 protein expression and endonuclease activity. DNA Repair (Amst) 2009; 8:1411-23. [PMID: 19836314 DOI: 10.1016/j.dnarep.2009.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 09/17/2009] [Accepted: 09/23/2009] [Indexed: 02/08/2023]
Abstract
Modulation of chromatin structure plays an important role in the recruitment and function of DNA repair proteins. CXXC finger protein 1 (Cfp1), encoded by the CXXC1 gene, is essential for mammalian development and is an important regulator of chromatin structure. Murine embryonic stem (ES) cells lacking Cfp1 (CXXC1(-/-)) are viable but demonstrate a dramatic decrease in cytosine methylation, altered histone methylation, and an inability to differentiate. We find that ES cells lacking Cfp1 are hypersensitive to a variety of DNA-damaging agents. In addition, CXXC1(-/-) ES cells accumulate more DNA damage and exhibit decreased protein expression and endonuclease activity of AP endonuclease (Ape1/Ref-1), an enzyme involved in DNA base excision repair. Expression in CXXC1(-/-) ES cells of either the amino half of Cfp1 (amino acids 1-367) or the carboxyl half of Cfp1 (amino acids 361-656) restores normal Ape1/Ref-1 protein expression and rescues the hypersensitivity to DNA-damaging agents, demonstrating that Cfp1 contains redundant functional domains. Furthermore, retention of either the DNA-binding activity of Cfp1 or interaction with the Setd1A and Setd1B histone H3-Lys4 methyltransferase complexes is required to restore normal sensitivity of CXXC1(-/-) ES cells to DNA-damaging agents. These results implicate Cfp1 as a regulator of DNA repair processes.
Collapse
Affiliation(s)
- Courtney M Tate
- Herman B Wells Center for Pediatric Research, Section of Pediatric Hematology/Oncology, Department of Pediatrics, Indiana University School of Medicine, 1044W. Walnut St. R4-W312, Indianapolis, IN 46202, USA
| | | | | | | | | |
Collapse
|