1
|
Dobrinić P, Szczurek AT, Klose RJ. PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency. Nat Struct Mol Biol 2021; 28:811-824. [PMID: 34608337 PMCID: PMC7612713 DOI: 10.1038/s41594-021-00661-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 08/10/2021] [Indexed: 12/15/2022]
Abstract
The Polycomb repressive system plays a fundamental role in controlling gene expression during mammalian development. To achieve this, Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) bind target genes and use histone modification-dependent feedback mechanisms to form Polycomb chromatin domains and repress transcription. The inter-relatedness of PRC1 and PRC2 activity at these sites has made it difficult to discover the specific components of Polycomb chromatin domains that drive gene repression and to understand mechanistically how this is achieved. Here, by exploiting rapid degron-based approaches and time-resolved genomics, we kinetically dissect Polycomb-mediated repression and discover that PRC1 functions independently of PRC2 to counteract RNA polymerase II binding and transcription initiation. Using single-cell gene expression analysis, we reveal that PRC1 acts uniformly within the cell population and that repression is achieved by controlling transcriptional burst frequency. These important new discoveries provide a mechanistic and conceptual framework for Polycomb-dependent transcriptional control.
Collapse
Affiliation(s)
- Paula Dobrinić
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK.
| |
Collapse
|
2
|
Flora P, Dalal G, Cohen I, Ezhkova E. Polycomb Repressive Complex(es) and Their Role in Adult Stem Cells. Genes (Basel) 2021; 12:1485. [PMID: 34680880 PMCID: PMC8535826 DOI: 10.3390/genes12101485] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/13/2021] [Accepted: 09/22/2021] [Indexed: 12/31/2022] Open
Abstract
Populations of resident stem cells (SCs) are responsible for maintaining, repairing, and regenerating adult tissues. In addition to having the capacity to generate all the differentiated cell types of the tissue, adult SCs undergo long periods of quiescence within the niche to maintain themselves. The process of SC renewal and differentiation is tightly regulated for proper tissue regeneration throughout an organisms' lifetime. Epigenetic regulators, such as the polycomb group (PcG) of proteins have been implicated in modulating gene expression in adult SCs to maintain homeostatic and regenerative balances in adult tissues. In this review, we summarize the recent findings that elucidate the composition and function of the polycomb repressive complex machinery and highlight their role in diverse adult stem cell compartments.
Collapse
Affiliation(s)
- Pooja Flora
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA;
| | - Gil Dalal
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Idan Cohen
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Elena Ezhkova
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA;
| |
Collapse
|
3
|
Zhang YZ, Yuan J, Zhang L, Chen C, Wang Y, Zhang G, Peng L, Xie SS, Jiang J, Zhu JK, Du J, Duan CG. Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis. Nat Commun 2020; 11:6212. [PMID: 33277495 PMCID: PMC7718874 DOI: 10.1038/s41467-020-20089-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 11/12/2020] [Indexed: 01/07/2023] Open
Abstract
Histone 3 Lys 27 trimethylation (H3K27me3)-mediated epigenetic silencing plays a critical role in multiple biological processes. However, the H3K27me3 recognition and transcriptional repression mechanisms are only partially understood. Here, we report a mechanism for H3K27me3 recognition and transcriptional repression. Our structural and biochemical data showed that the BAH domain protein AIPP3 and the PHD proteins AIPP2 and PAIPP2 cooperate to read H3K27me3 and unmodified H3K4 histone marks, respectively, in Arabidopsis. The BAH-PHD bivalent histone reader complex silences a substantial subset of H3K27me3-enriched loci, including a number of development and stress response-related genes such as the RNA silencing effector gene ARGONAUTE 5 (AGO5). We found that the BAH-PHD module associates with CPL2, a plant-specific Pol II carboxyl terminal domain (CTD) phosphatase, to form the BAH-PHD-CPL2 complex (BPC) for transcriptional repression. The BPC complex represses transcription through CPL2-mediated CTD dephosphorylation, thereby causing inhibition of Pol II release from the transcriptional start site. Our work reveals a mechanism coupling H3K27me3 recognition with transcriptional repression through the alteration of Pol II phosphorylation states, thereby contributing to our understanding of the mechanism of H3K27me3-dependent silencing.
Collapse
Affiliation(s)
- Yi-Zhe Zhang
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Jianlong Yuan
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Lingrui Zhang
- grid.169077.e0000 0004 1937 2197Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907 USA
| | - Chunxiang Chen
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Yuhua Wang
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Guiping Zhang
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Li Peng
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Si-Si Xie
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Jing Jiang
- grid.256922.80000 0000 9139 560XState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
| | - Jian-Kang Zhu
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.169077.e0000 0004 1937 2197Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907 USA
| | - Jiamu Du
- grid.263817.9Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, 518055 Shenzhen, China
| | - Cheng-Guo Duan
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.256922.80000 0000 9139 560XState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
| |
Collapse
|
4
|
Gentile C, Kmita M. Polycomb Repressive Complexes in Hox Gene Regulation: Silencing and Beyond: The Functional Dynamics of Polycomb Repressive Complexes in Hox Gene Regulation. Bioessays 2020; 42:e1900249. [PMID: 32743818 DOI: 10.1002/bies.201900249] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 06/17/2020] [Indexed: 11/10/2022]
Abstract
The coordinated expression of the Hox gene family encoding transcription factors is critical for proper embryonic development and patterning. Major efforts have thus been dedicated to understanding mechanisms controlling Hox expression. In addition to the temporal and spatial sequential activation of Hox genes, proper embryonic development requires that Hox genes get differentially silenced in a cell-type specific manner as development proceeds. Factors contributing to Hox silencing include the polycomb repressive complexes (PRCs), which control gene expression through epigenetic modifications. This review focuses on PRC-dependent regulation of the Hox genes and is aimed at integrating the growing complexity of PRC functional properties in the context of Hox regulation. In particular, mechanisms underlying PRC binding dynamics as well as a series of studies that have revealed the impact of PRC on the 3D organization of the genome is discussed, which has a significant role on Hox regulation during development.
Collapse
Affiliation(s)
- Claudia Gentile
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec, H2W 1R7, Canada.,Department of Experimental Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada.,Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215, USA
| | - Marie Kmita
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec, H2W 1R7, Canada.,Department of Experimental Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada.,Département de Médecine, Université de Montréal, Montréal, Quebec, H3C 3J7, Canada
| |
Collapse
|
5
|
Plasma cell differentiation is controlled by multiple cell division-coupled epigenetic programs. Nat Commun 2018; 9:1698. [PMID: 29703886 PMCID: PMC5923265 DOI: 10.1038/s41467-018-04125-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 04/05/2018] [Indexed: 12/13/2022] Open
Abstract
The genomic loci associated with B cell differentiation that are subject to transcriptional and epigenetic regulation in vivo are not well defined, leaving a gap in our understanding of the development of humoral immune responses. Here, using an in vivo T cell independent B cell differentiation model, we define a cellular division-dependent cis-regulatory element road map using ATAC-seq. Chromatin accessibility changes correlate with gene expression and reveal the reprogramming of transcriptional networks and the genes they regulate at specific cell divisions. A subset of genes in naive B cells display accessible promoters in the absence of transcription and are marked by H3K27me3, an EZH2 catalyzed repressive modification. Such genes encode regulators of cell division and metabolism and include the essential plasma cell transcription factor Blimp-1. Chemical inhibition of EZH2 results in enhanced plasma cell formation, increased expression of the above gene set, and premature expression of Blimp-1 ex vivo. These data provide insights into cell-division coupled epigenetic and transcriptional processes that program plasma cells. During B cell differentiation, the role of different genomic loci in transcriptional and epigenetic regulation in vivo is not well defined. Here the authors use an in vivo B cell differentiation model to map cellular division-dependent cis-regulatory element road map with ATAC-seq.
Collapse
|
6
|
|
7
|
Zouaz A, Auradkar A, Delfini MC, Macchi M, Barthez M, Ela Akoa S, Bastianelli L, Xie G, Deng WM, Levine SS, Graba Y, Saurin AJ. The Hox proteins Ubx and AbdA collaborate with the transcription pausing factor M1BP to regulate gene transcription. EMBO J 2017; 36:2887-2906. [PMID: 28871058 DOI: 10.15252/embj.201695751] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 08/02/2017] [Accepted: 08/07/2017] [Indexed: 11/09/2022] Open
Abstract
In metazoans, the pausing of RNA polymerase II at the promoter (paused Pol II) has emerged as a widespread and conserved mechanism in the regulation of gene transcription. While critical in recruiting Pol II to the promoter, the role transcription factors play in transitioning paused Pol II into productive Pol II is, however, little known. By studying how Drosophila Hox transcription factors control transcription, we uncovered a molecular mechanism that increases productive transcription. We found that the Hox proteins AbdA and Ubx target gene promoters previously bound by the transcription pausing factor M1BP, containing paused Pol II and enriched with promoter-proximal Polycomb Group (PcG) proteins, yet lacking the classical H3K27me3 PcG signature. We found that AbdA binding to M1BP-regulated genes results in reduction in PcG binding, the release of paused Pol II, increases in promoter H3K4me3 histone marks and increased gene transcription. Linking transcription factors, PcG proteins and paused Pol II states, these data identify a two-step mechanism of Hox-driven transcription, with M1BP binding leading to Pol II recruitment followed by AbdA targeting, which results in a change in the chromatin landscape and enhanced transcription.
Collapse
Affiliation(s)
- Amel Zouaz
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | - Ankush Auradkar
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | | | - Meiggie Macchi
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | - Marine Barthez
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | - Serge Ela Akoa
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | - Leila Bastianelli
- MGX-Montpellier GenomiX c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Gengqiang Xie
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Stuart S Levine
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yacine Graba
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| | - Andrew J Saurin
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Marseille, France
| |
Collapse
|
8
|
Du J, Zhang J, He T, Li Y, Su Y, Tie F, Liu M, Harte PJ, Zhu AJ. Stuxnet Facilitates the Degradation of Polycomb Protein during Development. Dev Cell 2017; 37:507-19. [PMID: 27326929 DOI: 10.1016/j.devcel.2016.05.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/29/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
Polycomb-group (PcG) proteins function to ensure correct deployment of developmental programs by epigenetically repressing target gene expression. Despite the importance, few studies have been focused on the regulation of PcG activity itself. Here, we report a Drosophila gene, stuxnet (stx), that controls Pc protein stability. We find that heightened stx activity leads to homeotic transformation, reduced Pc activity, and de-repression of PcG targets. Conversely, stx mutants, which can be rescued by decreased Pc expression, display developmental defects resembling hyperactivation of Pc. Our biochemical analyses provide a mechanistic basis for the interaction between stx and Pc; Stx facilitates Pc degradation in the proteasome, independent of ubiquitin modification. Furthermore, this mode of regulation is conserved in vertebrates. Mouse stx promotes degradation of Cbx4, an orthologous Pc protein, in vertebrate cells and induces homeotic transformation in Drosophila. Our results highlight an evolutionarily conserved mechanism of regulated protein degradation on PcG homeostasis and epigenetic activity.
Collapse
Affiliation(s)
- Juan Du
- State Key Laboratory of Membrane Biology, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Junzheng Zhang
- State Key Laboratory of Membrane Biology, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Tao He
- State Key Laboratory of Membrane Biology, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yajuan Li
- State Key Laboratory of Membrane Biology, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ying Su
- State Key Laboratory of Membrane Biology, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China
| | - Feng Tie
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Min Liu
- State Key Laboratory of Membrane Biology, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Peter J Harte
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Alan Jian Zhu
- State Key Laboratory of Membrane Biology, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
| |
Collapse
|
9
|
Wang X, Cao W, Zhang J, Yan M, Xu Q, Wu X, Wan L, Zhang Z, Zhang C, Qin X, Xiao M, Ye D, Liu Y, Han Z, Wang S, Mao L, Wei W, Chen W. A covalently bound inhibitor triggers EZH2 degradation through CHIP-mediated ubiquitination. EMBO J 2017; 36:1243-1260. [PMID: 28320739 PMCID: PMC5412902 DOI: 10.15252/embj.201694058] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 09/28/2016] [Accepted: 02/15/2017] [Indexed: 02/05/2023] Open
Abstract
Enhancer of zeste homolog 2 (EZH2) has been characterized as a critical oncogene and a promising drug target in human malignant tumors. The current EZH2 inhibitors strongly suppress the enhanced enzymatic function of mutant EZH2 in some lymphomas. However, the recent identification of a PRC2- and methyltransferase-independent role of EZH2 indicates that a complete suppression of all oncogenic functions of EZH2 is needed. Here, we report a unique EZH2-targeting strategy by identifying a gambogenic acid (GNA) derivative as a novel agent that specifically and covalently bound to Cys668 within the EZH2-SET domain, triggering EZH2 degradation through COOH terminus of Hsp70-interacting protein (CHIP)-mediated ubiquitination. This class of inhibitors significantly suppressed H3K27Me3 and effectively reactivated polycomb repressor complex 2 (PRC2)-silenced tumor suppressor genes. Moreover, the novel inhibitors significantly suppressed tumor growth in an EZH2-dependent manner, and tumors bearing a non-GNA-interacting C668S-EZH2 mutation exhibited resistance to the inhibitors. Together, our results identify the inhibition of the signaling pathway that governs GNA-mediated destruction of EZH2 as a promising anti-cancer strategy.
Collapse
Affiliation(s)
- Xu Wang
- Faculty of Oral and Maxillofacial Surgery, Department of Oral and Maxillofacial Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Wei Cao
- Faculty of Oral and Maxillofacial Surgery, Department of Oral and Maxillofacial Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Jianjun Zhang
- Faculty of Oral and Maxillofacial Surgery, Department of Oral and Maxillofacial Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Ming Yan
- Faculty of Oral and Maxillofacial Surgery, Department of Oral and Maxillofacial Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Qin Xu
- Faculty of Oral and Maxillofacial Surgery, Department of Oral and Maxillofacial Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Xiangbing Wu
- Faculty of Oral and Maxillofacial Surgery, Department of Oral and Maxillofacial Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Lixin Wan
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Zhiyuan Zhang
- Faculty of Oral and Maxillofacial Surgery, Department of Oral and Maxillofacial Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Chenping Zhang
- Faculty of Oral and Maxillofacial Surgery, Department of Oral and Maxillofacial Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Xing Qin
- Faculty of Oral and Maxillofacial Surgery, Department of Oral and Maxillofacial Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Meng Xiao
- Faculty of Oral and Maxillofacial Surgery, Department of Oral and Maxillofacial Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Dongxia Ye
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Yuyang Liu
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Zeguang Han
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shaomeng Wang
- Comprehensive Cancer Center, Departments of Internal Medicine, Pharmacology and Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Li Mao
- Faculty of Oral and Maxillofacial Surgery, Department of Oral and Maxillofacial Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Oncology and Diagnostic Sciences, University of Maryland School of Dentistry, Baltimore, MD, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Wantao Chen
- Faculty of Oral and Maxillofacial Surgery, Department of Oral and Maxillofacial Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| |
Collapse
|
10
|
Abstract
In the past decade, deep-sequencing approaches have greatly improved our knowledge of the genome's potential and have become a crucial milestone for new discoveries in genomics. Transcription is the first step of gene expression; therefore, the detection and measurement of transcription rates is of great interest. Here, a detailed protocol for global run-on sequencing (GRO-seq) library preparation from Drosophila ovaries is described. The method relies on rapid isolation of nuclei with halted transcription, then restarting transcription in physiological conditions in the presence of a labeled nucleotide. The newly transcribed nascent RNA is then isolated and cloned using a small RNA cloning protocol. Although it is time-consuming, the global run-on method allows the user to profile the position, orientation and amount of transcriptionally engaged RNA polymerases across the genome, therefore providing a snapshot of genome-wide transcription.
Collapse
|
11
|
Entrevan M, Schuettengruber B, Cavalli G. Regulation of Genome Architecture and Function by Polycomb Proteins. Trends Cell Biol 2016; 26:511-525. [PMID: 27198635 DOI: 10.1016/j.tcb.2016.04.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 04/19/2016] [Accepted: 04/21/2016] [Indexed: 12/13/2022]
Abstract
Polycomb group (PcG) proteins dynamically define cellular identities through the epigenetic repression of key developmental regulatory genes. PcG proteins are recruited to specific regulatory elements to modify the chromatin surrounding them. In addition, they regulate the organization of their target genes in the 3D space of the nucleus, and this regulatory function of the 3D genome architecture is involved in cell differentiation and the maintenance of cellular memory. In this review we discuss recent advances in our understanding of how PcG proteins are recruited to chromatin to induce local and global changes in chromosome conformation and regulate their target genes.
Collapse
Affiliation(s)
- Marianne Entrevan
- Institute of Human Genetics, CNRS UPR1142 and University of Montpellier, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Bernd Schuettengruber
- Institute of Human Genetics, CNRS UPR1142 and University of Montpellier, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France.
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS UPR1142 and University of Montpellier, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France.
| |
Collapse
|
12
|
Sadasivam DA, Huang DH. Maintenance of Tissue Pluripotency by Epigenetic Factors Acting at Multiple Levels. PLoS Genet 2016; 12:e1005897. [PMID: 26926299 PMCID: PMC4771708 DOI: 10.1371/journal.pgen.1005897] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 02/04/2016] [Indexed: 01/24/2023] Open
Abstract
Pluripotent stem cells often adopt a unique developmental program while retaining certain flexibility. The molecular basis of such properties remains unclear. Using differentiation of pluripotent Drosophila imaginal tissues as assays, we examined the contribution of epigenetic factors in ectopic activation of Hox genes. We found that over-expression of Trithorax H3K4 methyltransferase can induce ectopic adult appendages by selectively activating the Hox genes Ultrabithorax and Sex comb reduced in wing and leg discs, respectively. This tissue-specific inducibility correlates with the presence of paused RNA polymerase II in the promoter-proximal region of these genes. Although the Antennapedia promoter is paused in eye-antenna discs, it cannot be induced by Trx without a reduction in histone variants or their chaperones, suggesting additional control by the nucleosomal architecture. Lineage tracing and pulse-chase experiments revealed that the active state of Hox genes is maintained substantially longer in mutants deficient for HIRA, a chaperone for the H3.3 variant. In addition, both HIRA and H3.3 appeared to act cooperatively with the Polycomb group of epigenetic repressors. These results support the involvement of H3.3-mediated nucleosome turnover in restoring the repressed state. We propose a regulatory framework integrating transcriptional pausing, histone modification, nucleosome architecture and turnover for cell lineage maintenance. During animal development, the primordia of different body parts undergo a series of transitions in which their developmental potency becomes more restricted. Hox genes encode a family of evolutionarily conserved transcriptional factors that are crucial for choosing different paths during transitions. Thus, the transcriptional status of Hox genes is directly linked to the maintenance and developmental direction of pluripotent tissues. As post-translational methylation of histone H3 is pivotal for transcriptional control, we could activate Hox genes and alter the subsequent development of some pluripotent Drosophila imaginal tissues by increasing the level of Trithorax that catalyzes activation-related methylation. However, other imaginal tissues remain refractory unless histone variants or their chaperones that directly affect nucleosome dynamics are simultaneously depleted. By monitoring the duration of Hox expression under these conditions, we found that the active state of Hox genes is substantially prolonged, resulting from effective conversion of promoter-associated paused RNA polymerase II into active transcription. Further analyses indicate that these factors are functionally linked to the Polycomb group of epigenetic factors that bestow long-term repression. Our studies demonstrate that developmental constraints are modulated by factors acting at multiple levels, offering a useful approach to tissue re-programming in regeneration medicine and stem cell research.
Collapse
Affiliation(s)
- Devendran A. Sadasivam
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Der-Hwa Huang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
| |
Collapse
|
13
|
Abstract
Epigenomics has grown exponentially, providing a better understanding of the mechanistic aspects of new and old phenomena originally described through genetics, as well as providing unexpected insights into the way chromatin modulates the genomic information. In this overview, some of the advances are selected for discussion and comment under six topics: (1) histone modifications, (2) weak interactions, (3) interplay with external inputs, (4) the role of RNA molecules, (5) chromatin folding and architecture, and, finally, (6) a view of the essential role of chromatin transactions in regulating the access to genomic DNA.
Collapse
Affiliation(s)
- Vincenzo Pirrotta
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| |
Collapse
|
14
|
Aranda S, Mas G, Di Croce L. Regulation of gene transcription by Polycomb proteins. SCIENCE ADVANCES 2015; 1:e1500737. [PMID: 26665172 PMCID: PMC4672759 DOI: 10.1126/sciadv.1500737] [Citation(s) in RCA: 248] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 09/17/2015] [Indexed: 05/14/2023]
Abstract
The Polycomb group (PcG) of proteins defines a subset of factors that physically associate and function to maintain the positional identity of cells from the embryo to adult stages. PcG has long been considered a paradigmatic model for epigenetic maintenance of gene transcription programs. Despite intensive research efforts to unveil the molecular mechanisms of action of PcG proteins, several fundamental questions remain unresolved: How many different PcG complexes exist in mammalian cells? How are PcG complexes targeted to specific loci? How does PcG regulate transcription? In this review, we discuss the diversity of PcG complexes in mammalian cells, examine newly identified modes of recruitment to chromatin, and highlight the latest insights into the molecular mechanisms underlying the function of PcGs in transcription regulation and three-dimensional chromatin conformation.
Collapse
Affiliation(s)
- Sergi Aranda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Gloria Mas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
- Institucio Catalana de Recerca i Estudis Avançats, Pg Lluis Companys 23, Barcelona 08010, Spain
- Corresponding author. E-mail:
| |
Collapse
|
15
|
Lee JEA, Mitchell NC, Zaytseva O, Chahal A, Mendis P, Cartier-Michaud A, Parsons LM, Poortinga G, Levens DL, Hannan RD, Quinn LM. Defective Hfp-dependent transcriptional repression of dMYC is fundamental to tissue overgrowth in Drosophila XPB models. Nat Commun 2015; 6:7404. [PMID: 26074141 DOI: 10.1038/ncomms8404] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 05/06/2015] [Indexed: 02/06/2023] Open
Abstract
Nucleotide excision DNA repair (NER) pathway mutations cause neurodegenerative and progeroid disorders (xeroderma pigmentosum (XP), Cockayne syndrome (CS) and trichothiodystrophy (TTD)), which are inexplicably associated with (XP) or without (CS/TTD) cancer. Moreover, cancer progression occurs in certain patients, but not others, with similar C-terminal mutations in the XPB helicase subunit of transcription and NER factor TFIIH. Mechanisms driving overproliferation and, therefore, cancer associated with XPB mutations are currently unknown. Here using Drosophila models, we provide evidence that C-terminally truncated Hay/XPB alleles enhance overgrowth dependent on reduced abundance of RNA recognition motif protein Hfp/FIR, which transcriptionally represses the MYC oncogene homologue, dMYC. The data demonstrate that dMYC repression and dMYC-dependent overgrowth in the Hfp hypomorph is further impaired in the C-terminal Hay/XPB mutant background. Thus, we predict defective transcriptional repression of MYC by the Hfp orthologue, FIR, might provide one mechanism for cancer progression in XP/CS.
Collapse
Affiliation(s)
- Jue Er Amanda Lee
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Melbourne 3010, Australia
| | - Naomi C Mitchell
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Melbourne 3010, Australia
| | - Olga Zaytseva
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Melbourne 3010, Australia
| | - Arjun Chahal
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Melbourne 3010, Australia
| | - Peter Mendis
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Melbourne 3010, Australia
| | | | - Linda M Parsons
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Melbourne 3010, Australia
| | - Gretchen Poortinga
- Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne Victoria 3002, Australia
| | - David L Levens
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Ross D Hannan
- 1] Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne Victoria 3002, Australia [2] Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra Australian Capital Territory 2600, Australia
| | - Leonie M Quinn
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Melbourne 3010, Australia
| |
Collapse
|
16
|
Lee HG, Kahn TG, Simcox A, Schwartz YB, Pirrotta V. Genome-wide activities of Polycomb complexes control pervasive transcription. Genome Res 2015; 25:1170-81. [PMID: 25986499 PMCID: PMC4510001 DOI: 10.1101/gr.188920.114] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 05/15/2015] [Indexed: 11/24/2022]
Abstract
Polycomb group (PcG) complexes PRC1 and PRC2 are well known for silencing specific developmental genes. PRC2 is a methyltransferase targeting histone H3K27 and producing H3K27me3, essential for stable silencing. Less well known but quantitatively much more important is the genome-wide role of PRC2 that dimethylates ∼70% of total H3K27. We show that H3K27me2 occurs in inverse proportion to transcriptional activity in most non-PcG target genes and intergenic regions and is governed by opposing roaming activities of PRC2 and complexes containing the H3K27 demethylase UTX. Surprisingly, loss of H3K27me2 results in global transcriptional derepression proportionally greatest in silent or weakly transcribed intergenic and genic regions and accompanied by an increase of H3K27ac and H3K4me1. H3K27me2 therefore sets a threshold that prevents random, unscheduled transcription all over the genome and even limits the activity of highly transcribed genes. PRC1-type complexes also have global roles. Unexpectedly, we find a pervasive distribution of histone H2A ubiquitylated at lysine 118 (H2AK118ub) outside of canonical PcG target regions, dependent on the RING/Sce subunit of PRC1-type complexes. We show, however, that H2AK118ub does not mediate the global PRC2 activity or the global repression and is predominantly produced by a new complex involving L(3)73Ah, a homolog of mammalian PCGF3.
Collapse
Affiliation(s)
- Hun-Goo Lee
- Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Tatyana G Kahn
- Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA; Molecular Biology, Umeå University, NUS, 901 87 Umeå, Sweden
| | - Amanda Simcox
- Molecular Genetics, Ohio State University, Columbus, Ohio, USA
| | - Yuri B Schwartz
- Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA; Molecular Biology, Umeå University, NUS, 901 87 Umeå, Sweden
| | - Vincenzo Pirrotta
- Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
| |
Collapse
|
17
|
Miller MS, Rialdi A, Ho JSY, Tilove M, Martinez-Gil L, Moshkina NP, Peralta Z, Noel J, Melegari C, Maestre AM, Mitsopoulos P, Madrenas J, Heinz S, Benner C, Young JAT, Feagins AR, Basler CF, Fernandez-Sesma A, Becherel OJ, Lavin MF, van Bakel H, Marazzi I. Senataxin suppresses the antiviral transcriptional response and controls viral biogenesis. Nat Immunol 2015; 16:485-94. [PMID: 25822250 PMCID: PMC4406851 DOI: 10.1038/ni.3132] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 02/27/2015] [Indexed: 12/14/2022]
Abstract
The human helicase senataxin (SETX) has been linked to the neurodegenerative diseases amyotrophic lateral sclerosis (ALS4) and ataxia with oculomotor apraxia (AOA2). Here we identified a role for SETX in controlling the antiviral response. Cells that had undergone depletion of SETX and SETX-deficient cells derived from patients with AOA2 had higher expression of antiviral mediators in response to infection than did wild-type cells. Mechanistically, we propose a model whereby SETX attenuates the activity of RNA polymerase II (RNAPII) at genes stimulated after a virus is sensed and thus controls the magnitude of the host response to pathogens and the biogenesis of various RNA viruses (e.g., influenza A virus and West Nile virus). Our data indicate a potentially causal link among inborn errors in SETX, susceptibility to infection and the development of neurologic disorders.
Collapse
Affiliation(s)
- Matthew S Miller
- 1] Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [2] Department of Biochemistry and Biomedical Sciences, Institute for Infectious Diseases Research, McMaster Immunology Research Centre, McMaster University, Hamilton, Canada
| | - Alexander Rialdi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jessica Sook Yuin Ho
- Laboratory of Methyltransferases in Development and Disease, Institute of Molecular and Cell Biology, Singapore
| | - Micah Tilove
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Luis Martinez-Gil
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Natasha P Moshkina
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Zuleyma Peralta
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Justine Noel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Camilla Melegari
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ana M Maestre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Panagiotis Mitsopoulos
- Microbiome and Disease Tolerance Centre, Department of Microbiology and Immunology, McGill University, Montreal, Canada
| | - Joaquín Madrenas
- Microbiome and Disease Tolerance Centre, Department of Microbiology and Immunology, McGill University, Montreal, Canada
| | - Sven Heinz
- The Salk Institute for Biological Studies, La Jolla, California, USA
| | - Chris Benner
- The Salk Institute for Biological Studies, La Jolla, California, USA
| | | | - Alicia R Feagins
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ana Fernandez-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Olivier J Becherel
- The University of Queensland, UQ Centre for Clinical Research, Herston, Australia
| | - Martin F Lavin
- The University of Queensland, UQ Centre for Clinical Research, Herston, Australia
| | - Harm van Bakel
- 1] Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [2] Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ivan Marazzi
- 1] Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [2] Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| |
Collapse
|
18
|
Fuda NJ, Guertin MJ, Sharma S, Danko CG, Martins AL, Siepel A, Lis JT. GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters. PLoS Genet 2015; 11:e1005108. [PMID: 25815464 PMCID: PMC4376892 DOI: 10.1371/journal.pgen.1005108] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 02/26/2015] [Indexed: 11/28/2022] Open
Abstract
Previous studies have shown that GAGA Factor (GAF) is enriched on promoters with paused RNA Polymerase II (Pol II), but its genome-wide function and mechanism of action remain largely uncharacterized. We assayed the levels of transcriptionally-engaged polymerase using global run-on sequencing (GRO-seq) in control and GAF-RNAi Drosophila S2 cells and found promoter-proximal polymerase was significantly reduced on a large subset of paused promoters where GAF occupancy was reduced by knock down. These promoters show a dramatic increase in nucleosome occupancy upon GAF depletion. These results, in conjunction with previous studies showing that GAF directly interacts with nucleosome remodelers, strongly support a model where GAF directs nucleosome displacement at the promoter and thereby allows the entry Pol II to the promoter and pause sites. This action of GAF on nucleosomes is at least partially independent of paused Pol II because intergenic GAF binding sites with little or no Pol II also show GAF-dependent nucleosome displacement. In addition, the insulator factor BEAF, the BEAF-interacting protein Chriz, and the transcription factor M1BP are strikingly enriched on those GAF-associated genes where pausing is unaffected by knock down, suggesting insulators or the alternative promoter-associated factor M1BP protect a subset of GAF-bound paused genes from GAF knock-down effects. Thus, GAF binding at promoters can lead to the local displacement of nucleosomes, but this activity can be restricted or compensated for when insulator protein or M1BP complexes also reside at GAF bound promoters. Transcriptional regulation is critical for proper gene expression in response to environmental changes and developmental programs. Eukaryotes have evolved multiple mechanisms by which transcription factors regulate transcription. One mechanism is the reorganization of chromatin to allow Pol II recruitment. Another is the release of promoter-proximal paused Pol II, where Pol II transcription that is halted 20–60 bases downstream of the transcription start site (TSS) is allowed to enter into productive elongation through the gene body. The Drosophila transcription factor GAF binds to genes that undergo pausing and interacts with nucleosome remodelers and the pausing factor NELF. Thus, GAF can regulate multiple points necessary for transcription, but its mechanistic role is not fully understood genome-wide. We depleted GAF from cells and examined the genome-wide changes in Pol II and nucleosome distributions across genes. We found that GAF depletion reduces polymerase density at genes where GAF binds just upstream of the TSS, and results in nucleosomes moving into the promoter region. Our results show that GAF is important for maintaining the promoter accessibility, allowing Pol II to be recruited to promoters and enter the pause sites downstream of the TSS. Thus, GAF is critical for providing the chromatin environment necessary for the proper control of gene expression.
Collapse
Affiliation(s)
- Nicholas J. Fuda
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Michael J. Guertin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Sumeet Sharma
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Charles G. Danko
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - André L. Martins
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - John T. Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| |
Collapse
|
19
|
Dorsett D, Kassis JA. Checks and balances between cohesin and polycomb in gene silencing and transcription. Curr Biol 2014; 24:R535-9. [PMID: 24892918 PMCID: PMC4104651 DOI: 10.1016/j.cub.2014.04.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The cohesin protein complex was discovered for its roles in sister chromatid cohesion and segregation, and the Polycomb group (PcG) proteins for their roles in epigenetic gene silencing during development. Cohesin also controls gene transcription via multiple mechanisms. Genetic and molecular evidence from Drosophila argue that cohesin and the PRC1 PcG complex interact to control transcription of many active genes that are critical for development, and that via these interactions cohesin also controls the availability of PRC1 for gene silencing.
Collapse
Affiliation(s)
- Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA.
| | - Judith A Kassis
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
20
|
Derkacheva M, Hennig L. Variations on a theme: Polycomb group proteins in plants. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2769-84. [PMID: 24336446 DOI: 10.1093/jxb/ert410] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Polycomb group (PcG) proteins evolved early in evolution, probably in the common ancestor of animals and plants. In some unicellular organisms, such as Chlamydomonas and Tetrahymena, PcG proteins silence genes in heterochromatin, suggesting an ancestral function in genome defence. In angiosperms, the PcG system controls many developmental transitions. A PcG function in the vernalization response evolved especially in Brassicaceaea. Thus, the role of PcG proteins has changed during evolution to match novel needs. Recent studies identified many proteins associated with plant PcG protein complexes. Possible functions of these interactions are discussed here. We highlight recent findings about recruitment of PcG proteins in plants in comparison with animal system. Through the new data, a picture emerges in which PcG protein complexes do not function in sequential linear pathways but as dynamically interacting networks allowing stabilizing feedback loops. We discuss how the interplay between different PcG protein complexes can enable establishment, maintenance, and epigenetic inheritance of H3K27me3.
Collapse
Affiliation(s)
- Maria Derkacheva
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden Department of Biology and Zurich-Basel Plant Science Center, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Lars Hennig
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden Department of Biology and Zurich-Basel Plant Science Center, ETH Zurich, CH-8092, Zurich, Switzerland Science for Life Laboratory, SE-75007 Uppsala, Sweden
| |
Collapse
|
21
|
Stapel LC, Vastenhouw NL. Message control in developmental transitions; deciphering chromatin's role using zebrafish genomics. Brief Funct Genomics 2013; 13:106-20. [PMID: 24170706 DOI: 10.1093/bfgp/elt045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Now that the sequencing of genomes has become routine, understanding how a given genome is used in different ways to obtain cell type diversity in an organism is the next frontier. How specific transcription programs are established during vertebrate embryogenesis, however, remains poorly understood. Transcription is influenced by chromatin structure, which determines the accessibility of DNA-binding proteins to the genome. Although large-scale genomics approaches have uncovered specific features of chromatin structure that are diagnostic for different cell types and developmental stages, our functional understanding of chromatin in transcriptional regulation during development is very limited. In recent years, zebrafish embryogenesis has emerged as an excellent vertebrate model system to investigate the functional relationship between chromatin organization, gene regulation and development in a dynamic environment. Here, we review how studies in zebrafish have started to improve our understanding of the role of chromatin structure in genome activation and pluripotency and in the potential inheritance of transcriptional states from parent to progeny.
Collapse
Affiliation(s)
- L Carine Stapel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany.
| | | |
Collapse
|
22
|
Herz HM, Garruss A, Shilatifard A. SET for life: biochemical activities and biological functions of SET domain-containing proteins. Trends Biochem Sci 2013; 38:621-39. [PMID: 24148750 DOI: 10.1016/j.tibs.2013.09.004] [Citation(s) in RCA: 225] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 09/06/2013] [Accepted: 09/12/2013] [Indexed: 01/23/2023]
Affiliation(s)
- Hans-Martin Herz
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | | | | |
Collapse
|
23
|
Spicuglia S, Maqbool MA, Puthier D, Andrau JC. An update on recent methods applied for deciphering the diversity of the noncoding RNA genome structure and function. Methods 2013; 63:3-17. [DOI: 10.1016/j.ymeth.2013.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/02/2013] [Accepted: 04/04/2013] [Indexed: 12/17/2022] Open
|
24
|
Abstract
Histone modifications and chromatin-associated protein complexes are crucially involved in the control of gene expression, supervising cell fate decisions and differentiation. Many promoters in embryonic stem (ES) cells harbor a distinctive histone modification signature that combines the activating histone H3 Lys 4 trimethylation (H3K4me3) mark and the repressive H3K27me3 mark. These bivalent domains are considered to poise expression of developmental genes, allowing timely activation while maintaining repression in the absence of differentiation signals. Recent advances shed light on the establishment and function of bivalent domains; however, their role in development remains controversial, not least because suitable genetic models to probe their function in developing organisms are missing. Here, we explore avenues to and from bivalency and propose that bivalent domains and associated chromatin-modifying complexes safeguard proper and robust differentiation.
Collapse
Affiliation(s)
- Philipp Voigt
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | | | | |
Collapse
|
25
|
Saunders A, Core LJ, Sutcliffe C, Lis JT, Ashe HL. Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription. Genes Dev 2013; 27:1146-58. [PMID: 23699410 DOI: 10.1101/gad.215459.113] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Cascades of zygotic gene expression pattern the anterior-posterior (AP) and dorsal-ventral (DV) axes of the early Drosophila embryo. Here, we used the global run-on sequencing assay (GRO-seq) to map the genome-wide RNA polymerase distribution during early Drosophila embryogenesis, thus providing insights into how genes are regulated. We identify widespread promoter-proximal pausing yet show that the presence of paused polymerase does not necessarily equate to direct regulation through pause release to productive elongation. Our data reveal that a subset of early Zelda-activated genes is regulated at the level of polymerase recruitment, whereas other Zelda target and axis patterning genes are predominantly regulated through pause release. In contrast to other signaling pathways, we found that bone morphogenetic protein (BMP) target genes are collectively more highly paused than BMP pathway components and show that BMP target gene expression requires the pause-inducing negative elongation factor (NELF) complex. Our data also suggest that polymerase pausing allows plasticity in gene activation throughout embryogenesis, as transiently repressed and transcriptionally silenced genes maintain and lose promoter polymerases, respectively. Finally, we provide evidence that the major effect of pausing is on the levels, rather than timing, of transcription. These data are discussed in terms of the efficiency of transcriptional activation required across cell populations during developmental time constraints.
Collapse
Affiliation(s)
- Abbie Saunders
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | | | | | | | | |
Collapse
|
26
|
Role of polycomb proteins in regulating HSV-1 latency. Viruses 2013; 5:1740-57. [PMID: 23860385 PMCID: PMC3738959 DOI: 10.3390/v5071740] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 07/04/2013] [Accepted: 07/04/2013] [Indexed: 12/26/2022] Open
Abstract
Herpes simplex virus (HSV) establishes a latent infection within sensory neurons of humans. Latency is characterized by the transcriptional repression of lytic genes by the condensation of lytic gene regions into heterochromatin. Recent data suggest that facultative heterochromatin predominates, and that cellular Polycomb proteins are involved in the establishment and maintenance of transcriptional repression during latency. This review summarizes these data and discusses the implication of viral and cellular factors in regulating heterochromatin composition.
Collapse
|
27
|
Lindner M, Simonini S, Kooiker M, Gagliardini V, Somssich M, Hohenstatt M, Simon R, Grossniklaus U, Kater MM. TAF13 interacts with PRC2 members and is essential for Arabidopsis seed development. Dev Biol 2013; 379:28-37. [PMID: 23506837 DOI: 10.1016/j.ydbio.2013.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Revised: 02/28/2013] [Accepted: 03/01/2013] [Indexed: 11/24/2022]
Abstract
TBP-Associated Factors (TAFs) are components of complexes like TFIID, TFTC, SAGA/STAGA and SMAT that are important for the activation of transcription, either by establishing the basic transcription machinery or by facilitating histone acetylation. However, in Drosophila embryos several TAFs were shown to be associated with the Polycomb Repressive Complex 1 (PRC1), even though the role of this interaction remains unclear. Here we show that in Arabidopsis TAF13 interacts with MEDEA and SWINGER, both members of a plant variant of Polycomb Repressive Complex 2 (PRC2). PRC2 variants play important roles during the plant life cycle, including seed development. The taf13 mutation causes seed defects, showing embryo arrest at the 8-16 cell stage and over-proliferation of the endosperm in the chalazal region, which is typical for Arabidopsis PRC2 mutants. Our data suggest that TAF13 functions together with PRC2 in transcriptional regulation during seed development.
Collapse
Affiliation(s)
- Matias Lindner
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. Mol Cell 2013; 49:808-24. [PMID: 23473600 DOI: 10.1016/j.molcel.2013.02.013] [Citation(s) in RCA: 552] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chromatin modification by Polycomb proteins provides an essential strategy for gene silencing in higher eukaryotes. Polycomb repressive complexes (PRCs) silence key developmental regulators and are centrally integrated in the transcriptional circuitry of stem cells. PRC2 trimethylates histone H3 on lysine 27 (H3K27me3), and PRC1-type complexes ubiquitylate histone H2A and compact polynucleosomes. How PRCs are deployed to select and silence genomic targets is the subject of intense investigation. We review advances on targeting, modulation, and functions of PRC1 and PRC2 and progress on defining the transcriptional steps they impact. Recent findings emphasize PRC1 targeting independent of H3K27me3, nonenzymatic PRC1-mediated compaction, and connections between PRCs and noncoding RNAs. Systematic analyses of Polycomb complexes and associated histone modifications during DNA replication and mitosis have also emerged. The stage is now set to reveal fundamental epigenetic mechanisms that determine how Polycomb target genes are silenced and how Polycomb silence is preserved through cell-cycle progression.
Collapse
|
29
|
Gaertner B, Johnston J, Chen K, Wallaschek N, Paulson A, Garruss AS, Gaudenz K, De Kumar B, Krumlauf R, Zeitlinger J. Poised RNA polymerase II changes over developmental time and prepares genes for future expression. Cell Rep 2012; 2:1670-83. [PMID: 23260668 DOI: 10.1016/j.celrep.2012.11.024] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 09/29/2012] [Accepted: 11/27/2012] [Indexed: 01/20/2023] Open
Abstract
Poised RNA polymerase II (Pol II) is predominantly found at developmental control genes and is thought to allow their rapid and synchronous induction in response to extracellular signals. How the recruitment of poised RNA Pol II is regulated during development is not known. By isolating muscle tissue from Drosophila embryos at five stages of differentiation, we show that the recruitment of poised Pol II occurs at many genes de novo and this makes them permissive for future gene expression. A comparison with other tissues shows that these changes are stage specific and not tissue specific. In contrast, Polycomb group repression is tissue specific, and in combination with Pol II (the balanced state) marks genes with highly dynamic expression. This suggests that poised Pol II is temporally regulated and is held in check in a tissue-specific fashion. We compare our data with findings in mammalian embryonic stem cells and discuss a framework for predicting developmental programs on the basis of the chromatin state.
Collapse
Affiliation(s)
- Bjoern Gaertner
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat Rev Genet 2012; 13:720-31. [PMID: 22986266 DOI: 10.1038/nrg3293] [Citation(s) in RCA: 906] [Impact Index Per Article: 69.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent years have witnessed a sea change in our understanding of transcription regulation: whereas traditional models focused solely on the events that brought RNA polymerase II (Pol II) to a gene promoter to initiate RNA synthesis, emerging evidence points to the pausing of Pol II during early elongation as a widespread regulatory mechanism in higher eukaryotes. Current data indicate that pausing is particularly enriched at genes in signal-responsive pathways. Here the evidence for pausing of Pol II from recent high-throughput studies will be discussed, as well as the potential interconnected functions of promoter-proximally paused Pol II.
Collapse
|
31
|
Lagha M, Bothma JP, Levine M. Mechanisms of transcriptional precision in animal development. Trends Genet 2012; 28:409-16. [PMID: 22513408 PMCID: PMC4257495 DOI: 10.1016/j.tig.2012.03.006] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 03/08/2012] [Accepted: 03/09/2012] [Indexed: 10/28/2022]
Abstract
We review recently identified mechanisms of transcriptional control that ensure reliable and reproducible patterns of gene expression in natural populations of developing embryos, despite inherent fluctuations in gene regulatory processes, variations in genetic backgrounds and exposure to diverse environmental conditions. These mechanisms are not responsible for switching genes on and off. Instead, they control the fine-tuning of gene expression and ensure regulatory precision. Several such mechanisms are discussed, including redundant binding sites within transcriptional enhancers, shadow enhancers, and 'poised' enhancers and promoters, as well as the role of 'redundant' gene interactions within regulatory networks. We propose that such regulatory mechanisms provide population fitness and 'fine-tune' the spatial and temporal control of gene expression.
Collapse
Affiliation(s)
- Mounia Lagha
- Center for Integrative Genomics, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | | | | |
Collapse
|
32
|
Transcriptional repression via antilooping in the Drosophila embryo. Proc Natl Acad Sci U S A 2012; 109:9460-4. [PMID: 22645339 DOI: 10.1073/pnas.1102625108] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcriptional repressors are thought to inhibit gene expression by interfering with the binding or function of RNA Polymerase II, perhaps by promoting local chromatin condensation. Here, we present evidence for a distinctive mechanism of repression, whereby sequence-specific repressors prevent the looping of distal enhancers to the promoter. Particular efforts focus on the Snail repressor, which plays a conserved role in promoting epithelial-mesenchyme transitions in both invertebrates and vertebrates, including mesoderm invagination in Drosophila, neural crest migration in vertebrates, and tumorigenesis in mammals. Chromosome conformation capture experiments were used to examine enhancer looping at Snail target genes in wild-type and mutant embryos. These studies suggest that the Snail repressor blocks the formation of fruitful enhancer-promoter interactions when bound to a distal enhancer. This higher-order mechanism of transcriptional repression has broad implications for the control of gene activity in metazoan development.
Collapse
|
33
|
Vastenhouw NL, Schier AF. Bivalent histone modifications in early embryogenesis. Curr Opin Cell Biol 2012; 24:374-86. [PMID: 22513113 DOI: 10.1016/j.ceb.2012.03.009] [Citation(s) in RCA: 211] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 02/08/2023]
Abstract
Histone modifications influence the interactions of transcriptional regulators with chromatin. Studies in embryos and embryonic stem (ES) cells have uncovered histone modification patterns that are diagnostic for different cell types and developmental stages. For example, bivalent domains consisting of regions of H3 lysine 27 trimethylation (H3K27me3) and H3 lysine 4 trimethylation (H3K4me3) mark lineage control genes in ES cells and zebrafish blastomeres. Such bivalent domains have garnered attention because the H3K27me3 mark might help repress lineage-regulatory genes during pluripotency while the H3K4me3 mark could poise genes for activation upon differentiation. Despite the prominence of the bivalent domain concept, studies in other model organisms have questioned its universal nature, and the function of bivalent domains has remained unclear. Histone marks are also associated with developmental regulatory genes in sperm. These observations have raised the possibility that specific histone modification patterns might persist from parent to offspring, but it is unclear whether histone marks are inherited or formed de novo. Here, we review the potential roles of H3K4me3 and H3K27me3 marks in embryos and ES cells and discuss how histone marks might be established, maintained and resolved during embryonic development.
Collapse
Affiliation(s)
- Nadine L Vastenhouw
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.
| | | |
Collapse
|
34
|
Nahkuri S, Paro R. The role of noncoding RNAs in chromatin regulation during differentiation. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 1:743-52. [PMID: 23799570 DOI: 10.1002/wdev.41] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A myriad of nuclear noncoding RNAs (ncRNAs) have been discovered since the paradigm of RNAs as plain conveyors of protein translation was discarded. There is increasing evidence that at vital intersections of developmental pathways, ncRNAs target the chromatin modulating machinery to its site of action. However, the mechanistic details of processes involved are still largely unclear, and well-characterized metazoan ncRNA species implicated in chromatin regulation during differentiation remain few. Nevertheless, four major categories are slowly emerging: cis-acting antisense ncRNAs that flag the neighboring genes for the propagation of chromatin marks; allele-specific ncRNAs that perform similar tasks, but target larger loci that typically vary in size from hundreds of thousands of base pairs to a whole chromosome; structural ncRNAs proposed to act as scaffolds that couple chromatin shaping complexes of distinct functionalities; and cofactor ncRNAs with a capacity to inhibit or activate essential components of the intertwined chromatin and transcription apparatuses.
Collapse
Affiliation(s)
- Satu Nahkuri
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | | |
Collapse
|
35
|
Inner workings and regulatory inputs that control Polycomb repressive complex 2. Chromosoma 2012; 121:221-34. [PMID: 22349693 DOI: 10.1007/s00412-012-0361-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 01/09/2012] [Accepted: 01/10/2012] [Indexed: 01/27/2023]
Abstract
Polycomb repressive complex 2 (PRC2) is a conserved multisubunit enzyme that methylates histone H3 on lysine-27. This chromatin modification is a hallmark of target genes transcriptionally silenced by the Polycomb system. At its core, PRC2 activity depends upon the SET domain active site of its catalytic subunit, EZH2, as well as critical stimulatory inputs from noncatalytic subunits, especially EED and SU(Z)12. We review recent progress on this core PRC2 machinery, including key features of the active site, control mechanisms that operate via EZH2 phosphorylation, and subunit elements and architectures that influence PRC2 function. Among these, we highlight work identifying an EED regulatory site that enables PRC2 to bind pre-existing methylated H3-K27 and stimulate enzyme output. These advances illuminate basic inner workings of PRC2 and also provide insights that could aid design of PRC2 inhibitors. The chromatin landscape that PRC2 encounters in vivo is decorated with many histone modifications that accompany active transcription, such as H3-K4 methylation. It has long been assumed that these "active" modifications oppose PRC2 at some level but, until recently, mechanisms of this antagonistic cross-talk have been elusive. We discuss new findings that illuminate how H3-K4 and H3-K36 methylation, H3-K27 acetylation, and H3-S28 phosphorylation each exert a negative impact on PRC2 function. The emerging picture presents PRC2 as a cooperative multipart machine, intricately outfitted to sense and respond to the local chromatin environment and other cues. This PRC2 design ensures flexibility and fine tuning of its fundamental gene silencing roles in diverse biological contexts.
Collapse
|
36
|
Transcriptional activators and activation mechanisms. Protein Cell 2011; 2:879-88. [PMID: 22180087 DOI: 10.1007/s13238-011-1101-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 08/22/2011] [Indexed: 10/14/2022] Open
Abstract
Transcriptional activators are required to turn on the expression of genes in a eukaryotic cell. Activators bound to the enhancer can facilitate either the recruitment of RNA polymerase II to the promoter or its elongation. This article examines a few selected issues in understanding activator functions and activation mechanisms.
Collapse
|
37
|
Stepanik VA, Harte PJ. A mutation in the E(Z) methyltransferase that increases trimethylation of histone H3 lysine 27 and causes inappropriate silencing of active Polycomb target genes. Dev Biol 2011; 364:249-58. [PMID: 22182520 DOI: 10.1016/j.ydbio.2011.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Revised: 11/12/2011] [Accepted: 12/01/2011] [Indexed: 01/08/2023]
Abstract
Drosophila Polycomb Repressive Complex 2 (PRC2) is a lysine methyltransferase that trimethylates histone H3 lysine 27 (H3K27me3), a modification essential for Polycomb silencing. Mutations in its catalytic subunit, E(Z), that abolish its methyltransferase activity disrupt Polycomb silencing, causing derepression of Polycomb target genes in cells where they are normally silenced. In contrast, the unusual E(z) mutant allele Trithorax mimic (E(z)(Trm)) causes dominant homeotic phenotypes similar to those caused by mutations in trithorax (trx), an antagonist of Polycomb silencing. This suggests that E(z)(Trm) causes inappropriate silencing of Polycomb target genes in cells where they are normally active. Here we show that E(z)(Trm) mutants have an elevated level of H3K27me3 and reduced levels of H3K27me1 and H3K27me2, modifications also carried out by E(Z). This suggests that the E(z)(Trm) mutation increases the H3K27 trimethylation efficiency of E(Z). Acetylated H3K27 (H3K27ac), a mark of transcriptionally active genes that directly antagonizes H3K27 methylation by E(Z), is also reduced in E(z)(Trm) mutants, consistent with their elevated H3K27me3 level causing inappropriate silencing. In 0-4h E(z)(Trm) embryos, H3K27me3 accumulates prematurely and to high levels and does so at the expense of H3K27ac, which is normally present at high levels in early embryos. Despite their high level of H3K27me3, expression of Abd-B initiates normally in homozygous E(z)(Trm) embryos, but is substantially lower than in wild type embryos by completion of germ band retraction. These results suggest that increased H3K27 trimethylation activity of E(Z)(Trm) causes the premature accumulation of H3K27me3 in early embryogenesis, "predestining" initially active Polycomb target genes to silencing once Polycomb silencing is initiated.
Collapse
Affiliation(s)
- Vincent A Stepanik
- Department of Genetics, Case Western Reserve University, Cleveland, OH, USA.
| | | |
Collapse
|