51
|
Zoroddu S, Marchesi I, Bagella L. PRC2: an epigenetic multiprotein complex with a key role in the development of rhabdomyosarcoma carcinogenesis. Clin Epigenetics 2021; 13:156. [PMID: 34372908 PMCID: PMC8351429 DOI: 10.1186/s13148-021-01147-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/02/2021] [Indexed: 02/02/2023] Open
Abstract
Skeletal muscle formation represents a complex of highly organized and specialized systems that are still not fully understood. Epigenetic systems underline embryonic development, maintenance of stemness, and progression of differentiation. Polycomb group proteins play the role of gene silencing of stemness markers that regulate muscle differentiation. Enhancer of Zeste EZH2 is the catalytic subunit of the complex that is able to trimethylate lysine 27 of histone H3 and induce silencing of the involved genes. In embryonal Rhabdomyosarcoma and several other tumors, EZH2 is often deregulated and, in some cases, is associated with tumor malignancy. This review explores the molecular processes underlying the failure of muscle differentiation with a focus on the PRC2 complex. These considerations could open new studies aimed at the development of new cutting-edge therapeutic strategies in the onset of Rhabdomyosarcoma.
Collapse
Affiliation(s)
- Stefano Zoroddu
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100, Sassari, Italy
| | - Irene Marchesi
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100, Sassari, Italy
- Kitos Biotech Srls, Tramariglio, Alghero, SS, Italy
| | - Luigi Bagella
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/b, 07100, Sassari, Italy.
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA.
| |
Collapse
|
52
|
Freire-Benéitez V, Pomella N, Millner TO, Dumas AA, Niklison-Chirou MV, Maniati E, Wang J, Rajeeve V, Cutillas P, Marino S. Elucidation of the BMI1 interactome identifies novel regulatory roles in glioblastoma. NAR Cancer 2021; 3:zcab009. [PMID: 34316702 PMCID: PMC8210184 DOI: 10.1093/narcan/zcab009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/27/2021] [Accepted: 02/28/2021] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma (GBM) is the most common and aggressive intrinsic brain tumour in adults. Epigenetic mechanisms controlling normal brain development are often dysregulated in GBM. Among these, BMI1, a structural component of the Polycomb Repressive Complex 1 (PRC1), which promotes the H2AK119ub catalytic activity of Ring1B, is upregulated in GBM and its tumorigenic role has been shown in vitro and in vivo. Here, we have used protein and chromatin immunoprecipitation followed by mass spectrometry (MS) analysis to elucidate the protein composition of PRC1 in GBM and transcriptional silencing of defining interactors in primary patient-derived GIC lines to assess their functional impact on GBM biology. We identify novel regulatory functions in mRNA splicing and cholesterol transport which could represent novel targetable mechanisms in GBM.
Collapse
Affiliation(s)
- Verónica Freire-Benéitez
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, E1 2AT, London, UK
| | - Nicola Pomella
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, E1 2AT, London, UK
| | - Thomas O Millner
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, E1 2AT, London, UK
| | - Anaëlle A Dumas
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, E1 2AT, London, UK
| | - Maria Victoria Niklison-Chirou
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, E1 2AT, London, UK
| | - Eleni Maniati
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6AS UK
| | - Jun Wang
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6AS UK
| | - Vinothini Rajeeve
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6AS UK
| | - Pedro Cutillas
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6AS UK
| | - Silvia Marino
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, E1 2AT, London, UK
| |
Collapse
|
53
|
Brown K, Andrianakos H, Ingersoll S, Ren X. Single-molecule imaging of epigenetic complexes in living cells: insights from studies on Polycomb group proteins. Nucleic Acids Res 2021; 49:6621-6637. [PMID: 34009336 PMCID: PMC8266577 DOI: 10.1093/nar/gkab304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 12/30/2022] Open
Abstract
Chromatin-associated factors must locate, bind to, and assemble on specific chromatin regions to execute chromatin-templated functions. These dynamic processes are essential for understanding how chromatin achieves regulation, but direct quantification in living mammalian cells remains challenging. Over the last few years, live-cell single-molecule tracking (SMT) has emerged as a new way to observe trajectories of individual chromatin-associated factors in living mammalian cells, providing new perspectives on chromatin-templated activities. Here, we discuss the relative merits of live-cell SMT techniques currently in use. We provide new insights into how Polycomb group (PcG) proteins, master regulators of development and cell differentiation, decipher genetic and epigenetic information to achieve binding stability and highlight that Polycomb condensates facilitate target-search efficiency. We provide perspectives on liquid-liquid phase separation in organizing Polycomb targets. We suggest that epigenetic complexes integrate genetic and epigenetic information for target binding and localization and achieve target-search efficiency through nuclear organization.
Collapse
Affiliation(s)
- Kyle Brown
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | | | - Steven Ingersoll
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| |
Collapse
|
54
|
De Novo Polycomb Recruitment: Lessons from Latent Herpesviruses. Viruses 2021; 13:v13081470. [PMID: 34452335 PMCID: PMC8402699 DOI: 10.3390/v13081470] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/11/2022] Open
Abstract
The Human Herpesviruses persist in the form of a latent infection in specialized cell types. During latency, the herpesvirus genomes associate with cellular histone proteins and the viral lytic genes assemble into transcriptionally repressive heterochromatin. Although there is divergence in the nature of heterochromatin on latent herpesvirus genomes, in general, the genomes assemble into forms of heterochromatin that can convert to euchromatin to permit gene expression and therefore reactivation. This reversible form of heterochromatin is known as facultative heterochromatin and is most commonly characterized by polycomb silencing. Polycomb silencing is prevalent on the cellular genome and plays a role in developmentally regulated and imprinted genes, as well as X chromosome inactivation. As herpesviruses initially enter the cell in an un-chromatinized state, they provide an optimal system to study how de novo facultative heterochromatin is targeted to regions of DNA and how it contributes to silencing. Here, we describe how polycomb-mediated silencing potentially assembles onto herpesvirus genomes, synergizing what is known about herpesvirus latency with facultative heterochromatin targeting to the cellular genome. A greater understanding of polycomb silencing of herpesviruses will inform on the mechanism of persistence and reactivation of these pathogenic human viruses and provide clues regarding how de novo facultative heterochromatin forms on the cellular genome.
Collapse
|
55
|
Ghotbi E, Ye P, Ervin T, Kum A, Benes J, Jones RS. Polycomb-group recruitment to a Drosophila target gene is the default state that is inhibited by a transcriptional activator. SCIENCE ADVANCES 2021; 7:7/29/eabg1556. [PMID: 34272248 PMCID: PMC8284896 DOI: 10.1126/sciadv.abg1556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/25/2021] [Indexed: 06/13/2023]
Abstract
Polycomb-group (PcG) proteins are epigenetic regulators that maintain the transcriptional repression of target genes following their initial repression by transcription factors. PcG target genes are repressed in some cells, but active in others. Therefore, a mechanism must exist by which PcG proteins distinguish between the repressed and active states and only assemble repressive chromatin environments at target genes that are repressed. Here, we present experimental evidence that the repressed state of a Drosophila PcG target gene, giant (gt), is not identified by the presence of a repressor. Rather, de novo establishment of PcG-mediated silencing at gt is the default state that is prevented by the presence of an activator or coactivator, which may inhibit the catalytic activity of Polycomb-repressive complex 2 (PRC2).
Collapse
Affiliation(s)
- Elnaz Ghotbi
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Piao Ye
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Taylor Ervin
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Anni Kum
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Judith Benes
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Richard S Jones
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA.
| |
Collapse
|
56
|
Oss-Ronen L, Cohen I. Epigenetic regulation and signalling pathways in Merkel cell development. Exp Dermatol 2021; 30:1051-1064. [PMID: 34152646 DOI: 10.1111/exd.14415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 12/20/2022]
Abstract
Merkel cells are specialized epithelial cells connected to afferent nerve endings responsible for light-touch sensations, formed at specific locations in touch-sensitive regions of the mammalian skin. Although Merkel cells are descendants of the epidermal lineage, little is known about the mechanisms responsible for the development of these unique mechanosensory cells. Recent studies have highlighted that the Polycomb group (PcG) of proteins play a significant role in spatiotemporal regulation of Merkel cell formation. In addition, several of the major signalling pathways involved in skin development have been shown to regulate Merkel cell development as well. Here, we summarize the current understandings of the role of developmental regulators in Merkel cell formation, including the interplay between the epigenetic machinery and key signalling pathways, and the lineage-specific transcription factors involved in the regulation of Merkel cell development.
Collapse
Affiliation(s)
- Liat Oss-Ronen
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Idan Cohen
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Beer Sheva, Israel
| |
Collapse
|
57
|
Kitamura Y, Uranishi K, Hirasaki M, Nishimoto M, Suzuki A, Okuda A. Identification of germ cell-specific Mga variant mRNA that promotes meiosis via impediment of a non-canonical PRC1. Sci Rep 2021; 11:9737. [PMID: 33958653 PMCID: PMC8102552 DOI: 10.1038/s41598-021-89123-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/19/2021] [Indexed: 02/03/2023] Open
Abstract
A non-canonical PRC1 (PRC1.6) prevents precocious meiotic onset. Germ cells alleviate its negative effect by reducing their amount of MAX, a component of PRC1.6, as a prerequisite for their bona fide meiosis. Here, we found that germ cells produced Mga variant mRNA bearing a premature termination codon (PTC) during meiosis as an additional mechanism to impede the function of PRC1.6. The variant mRNA encodes an anomalous MGA protein that lacks the bHLHZ domain and thus functions as a dominant negative regulator of PRC1.6. Notwithstanding the presence of PTC, the Mga variant mRNA are rather stably present in spermatocytes and spermatids due to their intrinsic inefficient background of nonsense-mediated mRNA decay. Thus, our data indicate that meiosis is controlled in a multi-layered manner in which both MAX and MGA, which constitute the core of PRC1.6, are at least used as targets to deteriorate the integrity of the complex to ensure progression of meiosis.
Collapse
Affiliation(s)
- Yuka Kitamura
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1, Yamane Hidaka, Saitama, 350-1241, Japan
| | - Kousuke Uranishi
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1, Yamane Hidaka, Saitama, 350-1241, Japan
| | - Masataka Hirasaki
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1, Yamane Hidaka, Saitama, 350-1241, Japan
- Department of Clinical Cancer Genomics, International Medical Center, Saitama Medical University, 1397-1, Yamane Hidaka, Saitama, 350-1241, Japan
| | - Masazumi Nishimoto
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1, Yamane Hidaka, Saitama, 350-1241, Japan
- Biomedical Research Center, Saitama Medical University, 1397-1, Yamane Hidaka, Saitama, 350-1241, Japan
| | - Ayumu Suzuki
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1, Yamane Hidaka, Saitama, 350-1241, Japan.
| | - Akihiko Okuda
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1, Yamane Hidaka, Saitama, 350-1241, Japan.
| |
Collapse
|
58
|
Assumpção ALFV, Fu G, Singh DK, Lu Z, Kuehnl AM, Welch R, Ong IM, Wen R, Pan X. A lineage-specific requirement for YY1 Polycomb Group protein function in early T cell development. Development 2021; 148:dev.197319. [PMID: 33766932 DOI: 10.1242/dev.197319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 03/12/2021] [Indexed: 01/22/2023]
Abstract
Yin Yang 1 (YY1) is a ubiquitous transcription factor and mammalian Polycomb Group protein (PcG) with important functions for regulating lymphocyte development and stem cell self-renewal. YY1 mediates stable PcG-dependent transcriptional repression via recruitment of PcG proteins that result in histone modifications. Many questions remain unanswered regarding how cell- and tissue-specificity is achieved by PcG proteins. Here, we demonstrate that a conditional knockout of Yy1 in the hematopoietic system results in an early T cell developmental blockage at the double negative (DN) 1 stage with reduced Notch1 signaling. There is a lineage-specific requirement for YY1 PcG function. YY1 PcG domain is required for T and B cell development but not necessary for myeloid cells. YY1 functions in early T cell development are multicomponent and involve both PcG-dependent and -independent regulations. Although YY1 promotes early T cell survival through its PcG function, its function to promote the DN1-to-DN2 transition and Notch1 expression and signaling is independent of its PcG function. Our results reveal how a ubiquitously expressed PcG protein mediates lineage-specific and context-specific functions to control early T cell development.
Collapse
Affiliation(s)
- Anna L F V Assumpção
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA.,Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA
| | - Guoping Fu
- Versiti, Blood Research Institute, 8701 Watertown Plank Road, Milwaukee, WI 53223, USA
| | - Deependra K Singh
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA.,Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA
| | - Zhanping Lu
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA.,Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA
| | - Ashley M Kuehnl
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA.,Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA
| | - Rene Welch
- Department of Obstetrics and Gynecology, University of Wisconsin School of Medicine and Public Health, 750 Highland Ave, Madison, WI 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, 610 Walnut St, Madison, WI 53726, USA
| | - Irene M Ong
- Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA.,Department of Obstetrics and Gynecology, University of Wisconsin School of Medicine and Public Health, 750 Highland Ave, Madison, WI 53705, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, 610 Walnut St, Madison, WI 53726, USA
| | - Renren Wen
- Versiti, Blood Research Institute, 8701 Watertown Plank Road, Milwaukee, WI 53223, USA
| | - Xuan Pan
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, 2015 Linden Dr., Madison, WI 57306, USA.,Carbone Cancer Center, UW-Madison Blood Research Program, Madison, WI 53705, USA
| |
Collapse
|
59
|
Chen Z, Djekidel MN, Zhang Y. Distinct dynamics and functions of H2AK119ub1 and H3K27me3 in mouse preimplantation embryos. Nat Genet 2021; 53:551-563. [PMID: 33821005 PMCID: PMC8092361 DOI: 10.1038/s41588-021-00821-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 02/17/2021] [Indexed: 11/09/2022]
Abstract
Polycomb repressive complexes 1 and 2 (PRC1/2) maintain transcriptional silencing of developmental genes largely by catalyzing the formation of mono-ubiquitinated histone H2A at lysine 119 (H2AK119ub1) and trimethylated histone H3 at lysine 27 (H3K27me3), respectively. How Polycomb domains are reprogrammed during mammalian preimplantation development remains largely unclear. Here we show that, although H2AK119ub1 and H3K27me3 are highly colocalized in gametes, they undergo differential reprogramming dynamics following fertilization. H3K27me3 maintains thousands of maternally biased domains until the blastocyst stage, whereas maternally biased H2AK119ub1 distribution in zygotes is largely equalized at the two-cell stage. Notably, while maternal PRC2 depletion has a limited effect on global H2AK119ub1 in early embryos, it disrupts allelic H2AK119ub1 at H3K27me3 imprinting loci including Xist. By contrast, acute H2AK119ub1 depletion in zygotes does not affect H3K27me3 imprinting maintenance, at least by the four-cell stage. Importantly, loss of H2AK119ub1, but not H3K27me3, causes premature activation of developmental genes during zygotic genome activation (ZGA) and subsequent embryonic arrest. Thus, our study reveals distinct dynamics and functions of H3K27me3 and H2AK119ub1 in mouse preimplantation embryos.
Collapse
Affiliation(s)
- Zhiyuan Chen
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Mohamed Nadhir Djekidel
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, WAB-149G, Boston, MA, USA.
| |
Collapse
|
60
|
Giaimo BD, Robert-Finestra T, Oswald F, Gribnau J, Borggrefe T. Chromatin Regulator SPEN/SHARP in X Inactivation and Disease. Cancers (Basel) 2021; 13:cancers13071665. [PMID: 33916248 PMCID: PMC8036811 DOI: 10.3390/cancers13071665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Carcinogenesis is a multistep process involving not only the activation of oncogenes and disabling tumor suppressor genes, but also epigenetic modulation of gene expression. X chromosome inactivation (XCI) is a paradigm to study heterochromatin formation and maintenance. The double dosage of X chromosomal genes in female mammals is incompatible with early development. XCI is an excellent model system for understanding the establishment of facultative heterochromatin initiated by the expression of a 17,000 nt long non-coding RNA, known as Xinactivespecifictranscript (Xist), on the X chromosome. This review focuses on the molecular mechanisms of how epigenetic modulators act in a step-wise manner to establish facultative heterochromatin, and we put these in the context of cancer biology and disease. An in depth understanding of XCI will allow a better characterization of particular types of cancer and hopefully facilitate the development of novel epigenetic therapies. Abstract Enzymes, such as histone methyltransferases and demethylases, histone acetyltransferases and deacetylases, and DNA methyltransferases are known as epigenetic modifiers that are often implicated in tumorigenesis and disease. One of the best-studied chromatin-based mechanism is X chromosome inactivation (XCI), a process that establishes facultative heterochromatin on only one X chromosome in females and establishes the right dosage of gene expression. The specificity factor for this process is the long non-coding RNA Xinactivespecifictranscript (Xist), which is upregulated from one X chromosome in female cells. Subsequently, Xist is bound by the corepressor SHARP/SPEN, recruiting and/or activating histone deacetylases (HDACs), leading to the loss of active chromatin marks such as H3K27ac. In addition, polycomb complexes PRC1 and PRC2 establish wide-spread accumulation of H3K27me3 and H2AK119ub1 chromatin marks. The lack of active marks and establishment of repressive marks set the stage for DNA methyltransferases (DNMTs) to stably silence the X chromosome. Here, we will review the recent advances in understanding the molecular mechanisms of how heterochromatin formation is established and put this into the context of carcinogenesis and disease.
Collapse
Affiliation(s)
- Benedetto Daniele Giaimo
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
- Correspondence: (B.D.G.); (T.B.); Tel.: +49-641-9947-400 (T.B.)
| | - Teresa Robert-Finestra
- Department of Developmental Biology, Erasmus MC, Oncode Institute, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (T.R.-F.); (J.G.)
| | - Franz Oswald
- Center for Internal Medicine, Department of Internal Medicine I, University Medical Center Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany;
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, Oncode Institute, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands; (T.R.-F.); (J.G.)
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
- Correspondence: (B.D.G.); (T.B.); Tel.: +49-641-9947-400 (T.B.)
| |
Collapse
|
61
|
Avni D, Avni O. Extracellular Vesicles: Schistosomal Long-Range Precise Weapon to Manipulate the Immune Response. Front Cell Infect Microbiol 2021; 11:649480. [PMID: 33869080 PMCID: PMC8044974 DOI: 10.3389/fcimb.2021.649480] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
Schistosomiasis (Bilharziasis), a neglected tropical disease that affects more than 240 million people around the world, is caused by infection with the helminth parasite Schistosoma. As part of their secretome, schistosomes release extracellular vesicles (EVs) that modulate the host immune response. The EV-harbored miRNAs upregulate the innate immune response of the M1 pathway and downregulate the differentiation toward the adaptive Th2 immunity. A schistosomal egg-derived miRNA increases the percentage of regulatory T cells. This schistosomal-inducible immunoediting process generates ultimately a parasitic friendly environment that is applied carefully as restrained Th2 response is crucial for the host survival and successful excretion of the eggs. Evidence indicates a selective targeting of schistosomal EVs, however, the underlying mechanisms are unclear yet. The effects of the schistosomes on the host immune system is in accordance with the hygiene hypothesis, attributing the dramatic increase in recent decades in allergy and other diseases associated with imbalanced immune response, to the reduced exposure to infectious agents that co-evolved with humans during evolution. Deciphering the bioactive cargo, function, and selective targeting of the parasite-secreted EVs may facilitate the development of novel tools for diagnostics and delivered therapy to schistosomiasis, as well as to immune-associated disorders.
Collapse
Affiliation(s)
- Dror Avni
- Laboratory of Molecular Cell Biology, Sheba Medical Center, Tel Hashomer, Israel.,Laboratory for the Study of Tropical Diseases, Sheba Medical Center, Tel Hashomer, Israel.,Department of Medicine C, Sheba Medical Center, Tel Hashomer, Israel
| | - Orly Avni
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| |
Collapse
|
62
|
Cohen I, Bar C, Liu H, Valdes VJ, Zhao D, Galbo PM, Silva JM, Koseki H, Zheng D, Ezhkova E. Polycomb complexes redundantly maintain epidermal stem cell identity during development. Genes Dev 2021; 35:354-366. [PMID: 33602871 PMCID: PMC7919412 DOI: 10.1101/gad.345363.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022]
Abstract
In this study, Cohen et al. sought to understand the functional contribution of PRC1 and PRC2, which largely overlap in their genomic binding and cooperate to establish repressive chromatin domains demarcated by H2AK119ub and H3K27me3, to gene repression. By using the developing murine epidermis as a paradigm, they uncovered a previously unappreciated functional redundancy between Polycomb complexes, and their findings show how PRC1 and PRC2 function as two independent counterparts, providing a repressive safety net that protects and preserves lineage identity. Polycomb repressive complex 1 (PRC1) and PRC2 are critical epigenetic developmental regulators. PRC1 and PRC2 largely overlap in their genomic binding and cooperate to establish repressive chromatin domains demarcated by H2AK119ub and H3K27me3. However, the functional contribution of each complex to gene repression has been a subject of debate, and understanding of its physiological significance requires further studies. Here, using the developing murine epidermis as a paradigm, we uncovered a previously unappreciated functional redundancy between Polycomb complexes. Coablation of PRC1 and PRC2 in embryonic epidermal progenitors resulted in severe defects in epidermal stratification, a phenotype not observed in the single PRC1-null or PRC2-null epidermis. Molecular dissection indicated a loss of epidermal identity that was coupled to a strong derepression of nonlineage transcription factors, otherwise repressed by either PRC1 or PRC2 in the absence of its counterpart. Ectopic expression of subsets of PRC1/2-repressed nonepidermal transcription factors in wild-type epidermal stem cells was sufficient to suppress epidermal identity genes, highlighting the importance of functional redundancy between PRC1 and PRC2. Altogether, our studies show how PRC1 and PRC2 function as two independent counterparts, thereby providing a repressive safety net that protects and preserves lineage identity.
Collapse
Affiliation(s)
- Idan Cohen
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Carmit Bar
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Hequn Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Victor J Valdes
- Department of Cell Biology and Development, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Dejian Zhao
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Yale Center for Genome Analysis, Yale University, New Haven, Connecticut 06510, USA.,Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Phillip M Galbo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Jose M Silva
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), Tsurumi-ku, Yokohama 230-0045, Japan.,AMED-CREST, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Neurology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Elena Ezhkova
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| |
Collapse
|
63
|
Huseyin MK, Klose RJ. Live-cell single particle tracking of PRC1 reveals a highly dynamic system with low target site occupancy. Nat Commun 2021; 12:887. [PMID: 33563969 PMCID: PMC7873255 DOI: 10.1038/s41467-021-21130-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 01/13/2021] [Indexed: 01/04/2023] Open
Abstract
Polycomb repressive complex 1 (PRC1) is an essential chromatin-based repressor of gene transcription. How PRC1 engages with chromatin to identify its target genes and achieve gene repression remains poorly defined, representing a major hurdle to our understanding of Polycomb system function. Here, we use genome engineering and single particle tracking to dissect how PRC1 binds to chromatin in live mouse embryonic stem cells. We observe that PRC1 is highly dynamic, with only a small fraction stably interacting with chromatin. By integrating subunit-specific dynamics, chromatin binding, and abundance measurements, we discover that PRC1 exhibits low occupancy at target sites. Furthermore, we employ perturbation approaches to uncover how specific components of PRC1 define its kinetics and chromatin binding. Together, these discoveries provide a quantitative understanding of chromatin binding by PRC1 in live cells, suggesting that chromatin modification, as opposed to PRC1 complex occupancy, is central to gene repression.
Collapse
Affiliation(s)
- Miles K Huseyin
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
| |
Collapse
|
64
|
Li X, Ji G, Zhou J, Du J, Li X, Shi W, Hu Y, Zhou W, Hao A. Pcgf1 Regulates Early Neural Tube Development Through Histone Methylation in Zebrafish. Front Cell Dev Biol 2021; 8:581636. [PMID: 33575252 PMCID: PMC7870693 DOI: 10.3389/fcell.2020.581636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/15/2020] [Indexed: 11/13/2022] Open
Abstract
The neural induction constitutes the initial step in the generation of the neural tube. Pcgf1, as one of six Pcgf paralogs, is a maternally expressed gene, but its role and mechanism in early neural induction during neural tube development have not yet been explored. In this study, we found that zebrafish embryos exhibited a small head and reduced or even absence of telencephalon after inhibiting the expression of Pcgf1. Moreover, the neural induction process of zebrafish embryos was abnormally activated, and the subsequent NSC self-renewal was inhibited after injecting the Pcgf1 MO. The results of in vitro also showed that knockdown of Pcgf1 increased the expression levels of the neural markers Pax6, Pou3f1, and Zfp521, but decreased the expression levels of the pluripotent markers Oct4, Hes1, and Nanog, which further confirmed that Pcgf1 was indispensable for maintaining the pluripotency of P19 cells. To gain a better understanding of the role of Pcgf1 in early development, we analyzed mRNA profiles from Pcgf1-deficient P19 cells using RNA-seq. We found that the differentially expressed genes were enriched in many functional categories, which related to the development phenotype, and knockdown of Pcgf1 increased the expression of histone demethylases. Finally, our results showed that Pcgf1 loss-of-function decreased the levels of transcriptional repression mark H3K27me3 at the promoters of Ngn1 and Otx2, and the levels of transcriptional activation mark H3K4me3 at the promoters of Pou5f3 and Nanog. Together, our findings reveal that Pcgf1 might function as both a facilitator for pluripotent maintenance and a repressor for neural induction.
Collapse
Affiliation(s)
- Xinyue Li
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Mental Disorders, Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Guangyu Ji
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Mental Disorders, Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Juan Zhou
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Mental Disorders, Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jingyi Du
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Mental Disorders, Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xian Li
- Department of Foot and Ankle Surgery, Cheeloo College of Medicine, The Second Hospital, Shandong University, Jinan, China
| | - Wei Shi
- Department of Blood Transfusion, Qilu Hospital of Shandong University, Jinan, China
| | - Yong Hu
- Department of Foot and Ankle Surgery, Cheeloo College of Medicine, The Second Hospital, Shandong University, Jinan, China
| | - Wenjuan Zhou
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Mental Disorders, Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Aijun Hao
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Mental Disorders, Department of Anatomy and Histoembryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| |
Collapse
|
65
|
Chaouch A, Lasko P. Drosophila melanogaster: a fruitful model for oncohistones. Fly (Austin) 2021; 15:28-37. [PMID: 33423597 DOI: 10.1080/19336934.2020.1863124] [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: 10/22/2022] Open
Abstract
Drosophila melanogaster has proven to be a powerful genetic model to study human disease. Approximately 75% of human disease-associated genes have homologs in the fruit fly and regulatory pathways are highly conserved in Drosophila compared to humans. Drosophila is an established model organism for the study of genetics and developmental biology related to human disease and has also made a great contribution to epigenetic research. Many key factors that regulate chromatin condensation through effects on histone post-translational modifications were first discovered in genetic screens in Drosophila. Recently, the importance of chromatin regulators in cancer progression has been uncovered, leading to a rapid expansion in the knowledge on how perturbations of chromatin can result in the pathogenesis of human cancer. In this review, we provide examples of how Drosophila melanogaster has contributed to better understanding the detrimental effects of mutant forms of histones, called 'oncohistones', that are found in different human tumours.
Collapse
Affiliation(s)
- Amel Chaouch
- Department of Biology, McGill University , Montréal, Québec, Canada
| | - Paul Lasko
- Department of Biology, McGill University , Montréal, Québec, Canada.,Department of Human Genetics, Radboudumc , Nijmegen, Netherlands
| |
Collapse
|
66
|
Boeren J, Gribnau J. Xist-mediated chromatin changes that establish silencing of an entire X chromosome in mammals. Curr Opin Cell Biol 2020; 70:44-50. [PMID: 33360102 DOI: 10.1016/j.ceb.2020.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/17/2020] [Accepted: 11/22/2020] [Indexed: 12/19/2022]
Abstract
X chromosome inactivation (XCI) ensures an equal gene dosage between the sexes in placental mammals. Xist, a modular multi-domain X-encoded long non-coding RNA coats the X chromosome in cis during XCI. Xist recruits chromatin remodelers and repressor complexes ensuring silencing of the inactive X (Xi). Here, we review the recent work focused on the role of Xist functional repeats and interacting RNA-binding factors in the establishment of the silent state. Xist orchestrates recruitment of remodelers and repressors that first facilitate removal of the active chromatin landscape and subsequently direct the transition into a repressive heterochromatic environment. Some of these factors affect silencing on a chromosome-wide scale, while others display gene-specific silencing defects. The temporal order of recruitment shows each silencing step is party dependent on one another. After the Xi is established, many of the factors are dispensable, and a different repertoire of proteins ensure the silenced Xi is maintained and propagated.
Collapse
Affiliation(s)
- Jeffrey Boeren
- Department of Developmental Biology, Erasmus University Medical Center, the Netherlands; Oncode Institute, Erasmus University Medical Center, the Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus University Medical Center, the Netherlands; Oncode Institute, Erasmus University Medical Center, the Netherlands.
| |
Collapse
|
67
|
Liu X. A Structural Perspective on Gene Repression by Polycomb Repressive Complex 2. Subcell Biochem 2020; 96:519-562. [PMID: 33252743 DOI: 10.1007/978-3-030-58971-4_17] [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: 03/30/2023]
Abstract
Polycomb Repressive Complex 2 (PRC2) is a major repressive chromatin complex formed by the Polycomb Group (PcG) proteins. PRC2 mediates trimethylation of histone H3 lysine 27 (H3K27me3), a hallmark of gene silencing. PRC2 is a key regulator of development, impacting many fundamental biological processes, like stem cell differentiation in mammals and vernalization in plants. Misregulation of PRC2 function is linked to a variety of human cancers and developmental disorders. In correlation with its diverse roles in development, PRC2 displays a high degree of compositional complexity and plasticity. Structural biology research over the past decade has shed light on the molecular mechanisms of the assembly, catalysis, allosteric activation, autoinhibition, chemical inhibition, dimerization and chromatin targeting of various developmentally regulated PRC2 complexes. In addition to these aspects, structure-function analysis is also discussed in connection with disease data in this chapter.
Collapse
Affiliation(s)
- Xin Liu
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
| |
Collapse
|
68
|
Polycomb group-mediated histone H2A monoubiquitination in epigenome regulation and nuclear processes. Nat Commun 2020; 11:5947. [PMID: 33230107 PMCID: PMC7683540 DOI: 10.1038/s41467-020-19722-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 10/12/2020] [Indexed: 12/19/2022] Open
Abstract
Histone posttranslational modifications are key regulators of chromatin-associated processes including gene expression, DNA replication and DNA repair. Monoubiquitinated histone H2A, H2Aub (K118 in Drosophila or K119 in vertebrates) is catalyzed by the Polycomb group (PcG) repressive complex 1 (PRC1) and reversed by the PcG-repressive deubiquitinase (PR-DUB)/BAP1 complex. Here we critically assess the current knowledge regarding H2Aub deposition and removal, its crosstalk with PcG repressive complex 2 (PRC2)-mediated histone H3K27 methylation, and the recent attempts toward discovering its readers and solving its enigmatic functions. We also discuss mounting evidence of the involvement of H2A ubiquitination in human pathologies including cancer, while highlighting some knowledge gaps that remain to be addressed. Histone H2A monoubiquitination on lysine 119 in vertebrate and lysine 118 in Drosophila (H2Aub) is an epigenomic mark usually associated with gene repression by Polycomb group factors. Here the authors review the current knowledge on the deposition and removal of H2Aub, its function in transcription and other DNA-associated processes as well as its relevance to human disease.
Collapse
|
69
|
Geng Z, Gao Z. Mammalian PRC1 Complexes: Compositional Complexity and Diverse Molecular Mechanisms. Int J Mol Sci 2020; 21:E8594. [PMID: 33202645 PMCID: PMC7697839 DOI: 10.3390/ijms21228594] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022] Open
Abstract
Polycomb group (PcG) proteins function as vital epigenetic regulators in various biological processes, including pluripotency, development, and carcinogenesis. PcG proteins form multicomponent complexes, and two major types of protein complexes have been identified in mammals to date, Polycomb Repressive Complexes 1 and 2 (PRC1 and PRC2). The PRC1 complexes are composed in a hierarchical manner in which the catalytic core, RING1A/B, exclusively interacts with one of six Polycomb group RING finger (PCGF) proteins. This association with specific PCGF proteins allows for PRC1 to be subdivided into six distinct groups, each with their own unique modes of action arising from the distinct set of associated proteins. Historically, PRC1 was considered to be a transcription repressor that deposited monoubiquitylation of histone H2A at lysine 119 (H2AK119ub1) and compacted local chromatin. More recently, there is increasing evidence that demonstrates the transcription activation role of PRC1. Moreover, studies on the higher-order chromatin structure have revealed a new function for PRC1 in mediating long-range interactions. This provides a different perspective regarding both the transcription activation and repression characteristics of PRC1. This review summarizes new advancements regarding the composition of mammalian PRC1 and accompanying explanations of how diverse PRC1-associated proteins participate in distinct transcription regulation mechanisms.
Collapse
Affiliation(s)
- Zhuangzhuang Geng
- Departments of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA;
| | - Zhonghua Gao
- Departments of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA;
- Penn State Hershey Cancer Institute, Hershey, PA 17033, USA
- The Stem Cell and Regenerative Biology Program, Penn State College of Medicine, Hershey, PA 17033, USA
| |
Collapse
|
70
|
Yang Y, Li G. Post-translational modifications of PRC2: signals directing its activity. Epigenetics Chromatin 2020; 13:47. [PMID: 33129354 PMCID: PMC7603765 DOI: 10.1186/s13072-020-00369-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 10/23/2020] [Indexed: 12/23/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) is a chromatin-modifying enzyme that catalyses the methylation of histone H3 at lysine 27 (H3K27me1/2/3). This complex maintains gene transcriptional repression and plays an essential role in the maintenance of cellular identity as well as normal organismal development. The activity of PRC2, including its genomic targeting and catalytic activity, is controlled by various signals. Recent studies have revealed that these signals involve cis chromatin features, PRC2 facultative subunits and post-translational modifications (PTMs) of PRC2 subunits. Overall, these findings have provided insight into the biochemical signals directing PRC2 function, although many mysteries remain.
Collapse
Affiliation(s)
- Yiqi Yang
- Faculty of Health Sciences, University of Macau, Macau, China.,Cancer Centre, Faculty of Health Sciences, University of Macau, Macau, China.,Centre of Reproduction, Development and Aging, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Gang Li
- Faculty of Health Sciences, University of Macau, Macau, China. .,Cancer Centre, Faculty of Health Sciences, University of Macau, Macau, China. .,Centre of Reproduction, Development and Aging, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China.
| |
Collapse
|
71
|
Strejčková B, Čegan R, Pecinka A, Milec Z, Šafář J. Identification of polycomb repressive complex 1 and 2 core components in hexaploid bread wheat. BMC PLANT BIOLOGY 2020; 20:175. [PMID: 33050875 PMCID: PMC7557041 DOI: 10.1186/s12870-020-02384-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Polycomb repressive complexes 1 and 2 play important roles in epigenetic gene regulation by posttranslationally modifying specific histone residues. Polycomb repressive complex 2 is responsible for the trimethylation of lysine 27 on histone H3; Polycomb repressive complex 1 catalyzes the monoubiquitination of histone H2A at lysine 119. Both complexes have been thoroughly studied in Arabidopsis, but the evolution of polycomb group gene families in monocots, particularly those with complex allopolyploid origins, is unknown. RESULTS Here, we present the in silico identification of the Polycomb repressive complex 1 and 2 (PRC2, PRC1) subunits in allohexaploid bread wheat, the reconstruction of their evolutionary history and a transcriptional analysis over a series of 33 developmental stages. We identified four main subunits of PRC2 [E(z), Su(z), FIE and MSI] and three main subunits of PRC1 (Pc, Psc and Sce) and determined their chromosomal locations. We found that most of the genes coding for subunit proteins are present as paralogs in bread wheat. Using bread wheat RNA-seq data from different tissues and developmental stages throughout plant ontogenesis revealed variable transcriptional activity for individual paralogs. Phylogenetic analysis showed a high level of protein conservation among temperate cereals. CONCLUSIONS The identification and chromosomal location of the Polycomb repressive complex 1 and 2 core components in bread wheat may enable a deeper understanding of developmental processes, including vernalization, in commonly grown winter wheat.
Collapse
Affiliation(s)
- Beáta Strejčková
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Radim Čegan
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900, Olomouc, Czech Republic
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, 61200, Brno, Czech Republic
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Zbyněk Milec
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 77900, Olomouc, Czech Republic.
| |
Collapse
|
72
|
Chetverina DA, Lomaev DV, Erokhin MM. Polycomb and Trithorax Group Proteins: The Long Road from Mutations in Drosophila to Use in Medicine. Acta Naturae 2020; 12:66-85. [PMID: 33456979 PMCID: PMC7800605 DOI: 10.32607/actanaturae.11090] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Polycomb group (PcG) and Trithorax group (TrxG) proteins are evolutionarily conserved factors responsible for the repression and activation of the transcription of multiple genes in Drosophila and mammals. Disruption of the PcG/TrxG expression is associated with many pathological conditions, including cancer, which makes them suitable targets for diagnosis and therapy in medicine. In this review, we focus on the major PcG and TrxG complexes, the mechanisms of PcG/TrxG action, and their recruitment to chromatin. We discuss the alterations associated with the dysfunction of a number of factors of these groups in oncology and the current strategies used to develop drugs based on small-molecule inhibitors.
Collapse
Affiliation(s)
- D. A. Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - D. V. Lomaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - M. M. Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| |
Collapse
|
73
|
Menon MP, Hua KF. The Long Non-coding RNAs: Paramount Regulators of the NLRP3 Inflammasome. Front Immunol 2020; 11:569524. [PMID: 33101288 PMCID: PMC7546312 DOI: 10.3389/fimmu.2020.569524] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/24/2020] [Indexed: 12/17/2022] Open
Abstract
The NOD LRR pyrin domain containing protein 3 (NLRP3) inflammasome is a cytosolic multi-proteins conglomerate with intrinsic ATPase activity. Their predominant presence in the immune cells emphasizes its significant role in immune response. The downstream effector proteins IL-1β and IL-18 are responsible for the biological functions of the NLRP3 inflammasome upon encountering the alarmins and microbial ligands. Although the NLRP3 inflammasome is essential for host defense during infections, uncontrolled activation and overproduction of IL-1β and IL-18 increase the risk of developing autoimmune and metabolic disorders. Emerging evidences suggest the action of lncRNAs in regulating the activity of NLRP3 inflammasome in various disease conditions. The long non-coding RNA (lncRNA) is an emerging field of study and evidence on their regulatory role in various diseases is grabbing attention. Recent studies emphasize the functions of lncRNAs in the fine control of the NLRP3 inflammasome at nuclear and cytoplasmic levels by interfering in chromatin architecture, gene transcription and translation. Recently, lncRNAs are also found to control the activity of various regulators of NLRP3 inflammasome. Understanding the precise role of lncRNA in controlling the activity of NLRP3 inflammasome helps us to design targeted therapies for multiple inflammatory diseases. The present review is a novel attempt to consolidate the substantial role of lncRNAs in the regulation of the NLRP3 inflammasome. A deeper insight on the NLRP3 inflammasome regulation by lncRNAs will help in developing targeted and beneficial therapeutics in the future.
Collapse
Affiliation(s)
- Mridula P Menon
- Department of Biotechnology and Animal Science, National Ilan University, Yilan, Taiwan
| | - Kuo-Feng Hua
- Department of Biotechnology and Animal Science, National Ilan University, Yilan, Taiwan.,Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan.,Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| |
Collapse
|
74
|
Courtney AJ, Kamei M, Ferraro AR, Gai K, He Q, Honda S, Lewis ZA. Normal Patterns of Histone H3K27 Methylation Require the Histone Variant H2A.Z in Neurospora crassa. Genetics 2020; 216:51-66. [PMID: 32651262 PMCID: PMC7463285 DOI: 10.1534/genetics.120.303442] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/05/2020] [Indexed: 12/14/2022] Open
Abstract
Neurospora crassa contains a minimal Polycomb repression system, which provides rich opportunities to explore Polycomb-mediated repression across eukaryotes and enables genetic studies that can be difficult in plant and animal systems. Polycomb Repressive Complex 2 is a multi-subunit complex that deposits mono-, di-, and trimethyl groups on lysine 27 of histone H3, and trimethyl H3K27 is a molecular marker of transcriptionally repressed facultative heterochromatin. In mouse embryonic stem cells and multiple plant species, H2A.Z has been found to be colocalized with H3K27 methylation. H2A.Z is required for normal H3K27 methylation in these experimental systems, though the regulatory mechanisms are not well understood. We report here that Neurospora crassa mutants lacking H2A.Z or SWR-1, the ATP-dependent histone variant exchanger, exhibit a striking reduction in levels of H3K27 methylation. RNA-sequencing revealed downregulation of eed, encoding a subunit of PRC2, in an hH2Az mutant compared to wild type, and overexpression of EED in a ΔhH2Az;Δeed background restored most H3K27 methylation. Reduced eed expression leads to region-specific losses of H3K27 methylation, suggesting that differential dependence on EED concentration is critical for normal H3K27 methylation at certain regions in the genome.
Collapse
Affiliation(s)
- Abigail J Courtney
- Department of Microbiology, University of Georgia, Athens, Georgia 30602
| | - Masayuki Kamei
- Department of Microbiology, University of Georgia, Athens, Georgia 30602
| | - Aileen R Ferraro
- Department of Microbiology, University of Georgia, Athens, Georgia 30602
| | - Kexin Gai
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qun He
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shinji Honda
- Division of Chromosome Biology, Faculty of Medical Sciences, University of Fukui, 910-1193, Japan
| | - Zachary A Lewis
- Department of Microbiology, University of Georgia, Athens, Georgia 30602
| |
Collapse
|
75
|
The genetic basis for PRC1 complex diversity emerged early in animal evolution. Proc Natl Acad Sci U S A 2020; 117:22880-22889. [PMID: 32868440 DOI: 10.1073/pnas.2005136117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Polycomb group proteins are essential regulators of developmental processes across animals. Despite their importance, studies on Polycomb are often restricted to classical model systems and, as such, little is known about the evolution of these important chromatin regulators. Here we focus on Polycomb Repressive Complex 1 (PRC1) and trace the evolution of core components of canonical and non-canonical PRC1 complexes in animals. Previous work suggested that a major expansion in the number of PRC1 complexes occurred in the vertebrate lineage. We show that the expansion of the Polycomb Group RING Finger (PCGF) protein family, an essential step for the establishment of the large diversity of PRC1 complexes found in vertebrates, predates the bilaterian-cnidarian ancestor. This means that the genetic repertoire necessary to form all major vertebrate PRC1 complexes emerged early in animal evolution, over 550 million years ago. We further show that PCGF5, a gene conserved in cnidarians and vertebrates but lost in all other studied groups, is expressed in the nervous system in the sea anemone Nematostella vectensis, similar to its mammalian counterpart. Together this work provides a framework for understanding the evolution of PRC1 complex diversity and it establishes Nematostella as a promising model system in which the functional ramifications of this diversification can be further explored.
Collapse
|
76
|
Yan B, Lv Y, Zhao C, Wang X. Knowing When to Silence: Roles of Polycomb-Group Proteins in SAM Maintenance, Root Development, and Developmental Phase Transition. Int J Mol Sci 2020; 21:ijms21165871. [PMID: 32824274 PMCID: PMC7461556 DOI: 10.3390/ijms21165871] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/06/2020] [Accepted: 08/06/2020] [Indexed: 01/01/2023] Open
Abstract
Polycomb repressive complex 1 (PRC1) and PRC2 are the major complexes composed of polycomb-group (PcG) proteins in plants. PRC2 catalyzes trimethylation of lysine 27 on histone 3 to silence target genes. Like Heterochromatin Protein 1/Terminal Flower 2 (LHP1/TFL2) recognizes and binds to H3K27me3 generated by PRC2 activities and enrolls PRC1 complex to further silence the chromatin through depositing monoubiquitylation of lysine 119 on H2A. Mutations in PcG genes display diverse developmental defects during shoot apical meristem (SAM) maintenance and differentiation, seed development and germination, floral transition, and so on so forth. PcG proteins play essential roles in regulating plant development through repressing gene expression. In this review, we are focusing on recent discovery about the regulatory roles of PcG proteins in SAM maintenance, root development, embryo development to seedling phase transition, and vegetative to reproductive phase transition.
Collapse
|
77
|
Akerberg BN, Pu WT. Genetic and Epigenetic Control of Heart Development. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a036756. [PMID: 31818853 DOI: 10.1101/cshperspect.a036756] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A transcriptional program implemented by transcription factors and epigenetic regulators governs cardiac development and disease. Mutations in these factors are important causes of congenital heart disease. Here, we review selected recent advances in our understanding of the transcriptional and epigenetic control of heart development, including determinants of cardiac transcription factor chromatin occupancy, the gene regulatory network that regulates atrial septation, the chromatin landscape and cardiac gene regulation, and the role of Brg/Brahma-associated factor (BAF), nucleosome remodeling and histone deacetylation (NuRD), and Polycomb epigenetic regulatory complexes in heart development.
Collapse
Affiliation(s)
- Brynn N Akerberg
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| |
Collapse
|
78
|
Chen Z, Zhang Y. Maternal H3K27me3-dependent autosomal and X chromosome imprinting. Nat Rev Genet 2020; 21:555-571. [PMID: 32514155 DOI: 10.1038/s41576-020-0245-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2020] [Indexed: 12/19/2022]
Abstract
Genomic imprinting and X-chromosome inactivation (XCI) are classic epigenetic phenomena that involve transcriptional silencing of one parental allele. Germline-derived differential DNA methylation is the best-studied epigenetic mark that initiates imprinting, but evidence indicates that other mechanisms exist. Recent studies have revealed that maternal trimethylation of H3 on lysine 27 (H3K27me3) mediates autosomal maternal allele-specific gene silencing and has an important role in imprinted XCI through repression of maternal Xist. Furthermore, loss of H3K27me3-mediated imprinting contributes to the developmental defects observed in cloned embryos. This novel maternal H3K27me3-mediated non-canonical imprinting mechanism further emphasizes the important role of parental chromatin in development and could provide the basis for improving the efficiency of embryo cloning.
Collapse
Affiliation(s)
- Zhiyuan Chen
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA. .,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. .,Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Harvard Stem Cell Institute, Boston, MA, USA.
| |
Collapse
|
79
|
Boyle S, Flyamer IM, Williamson I, Sengupta D, Bickmore WA, Illingworth RS. A central role for canonical PRC1 in shaping the 3D nuclear landscape. Genes Dev 2020; 34:931-949. [PMID: 32439634 PMCID: PMC7328521 DOI: 10.1101/gad.336487.120] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/13/2020] [Indexed: 02/04/2023]
Abstract
In this study from Boyle et al., the authors investigated the role of Polycomb-repressive complex 1 (PRC1) in shaping 3D genome organization in mouse embryonic stem cells. Using a combination of imaging and Hi-C analyses they show that PRC1-mediated long-range interactions are independent of CTCF and can bridge sites at a megabase scale, thus providing novel insights into the function of PRC1. Polycomb group (PcG) proteins silence gene expression by chemically and physically modifying chromatin. A subset of PcG target loci are compacted and cluster in the nucleus; a conformation that is thought to contribute to gene silencing. However, how these interactions influence gross nuclear organization and their relationship with transcription remains poorly understood. Here we examine the role of Polycomb-repressive complex 1 (PRC1) in shaping 3D genome organization in mouse embryonic stem cells (mESCs). Using a combination of imaging and Hi-C analyses, we show that PRC1-mediated long-range interactions are independent of CTCF and can bridge sites at a megabase scale. Impairment of PRC1 enzymatic activity does not directly disrupt these interactions. We demonstrate that PcG targets coalesce in vivo, and that developmentally induced expression of one of the target loci disrupts this spatial arrangement. Finally, we show that transcriptional activation and the loss of PRC1-mediated interactions are separable events. These findings provide important insights into the function of PRC1, while highlighting the complexity of this regulatory system.
Collapse
Affiliation(s)
- Shelagh Boyle
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Ilya M Flyamer
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Iain Williamson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Dipta Sengupta
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Robert S Illingworth
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| |
Collapse
|
80
|
Heenan PR, Wang X, Gooding AR, Cech TR, Perkins TT. Bending and looping of long DNA by Polycomb repressive complex 2 revealed by AFM imaging in liquid. Nucleic Acids Res 2020; 48:2969-2981. [PMID: 32043141 DOI: 10.1093/nar/gkaa073] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/20/2020] [Accepted: 01/25/2020] [Indexed: 12/12/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that methylates histone H3 at Lysine 27. PRC2 is critical for epigenetic gene silencing, cellular differentiation and the formation of facultative heterochromatin. It can also promote or inhibit oncogenesis. Despite this importance, the molecular mechanisms by which PRC2 compacts chromatin are relatively understudied. Here, we visualized the binding of PRC2 to naked DNA in liquid at the single-molecule level using atomic force microscopy. Analysis of the resulting images showed PRC2, consisting of five subunits (EZH2, EED, SUZ12, AEBP2 and RBBP4), bound to a 2.5-kb DNA with an apparent dissociation constant ($K_{\rm{D}}^{{\rm{app}}}$) of 150 ± 12 nM. PRC2 did not show sequence-specific binding to a region of high GC content (76%) derived from a CpG island embedded in such a long DNA substrate. At higher concentrations, PRC2 compacted DNA by forming DNA loops typically anchored by two or more PRC2 molecules. Additionally, PRC2 binding led to a 3-fold increase in the local bending of DNA's helical backbone without evidence of DNA wrapping around the protein. We suggest that the bending and looping of DNA by PRC2, independent of PRC2's methylation activity, may contribute to heterochromatin formation and therefore epigenetic gene silencing.
Collapse
Affiliation(s)
- Patrick R Heenan
- Department of Physics, University of Colorado, Boulder, CO 80309, USA.,JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA
| | - Xueyin Wang
- Department of Biochemistry & BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Anne R Gooding
- Department of Biochemistry & BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA.,Howard Hughes Medical Institute, University of Colorado, Boulder, CO, USA
| | - Thomas R Cech
- Department of Biochemistry & BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA.,Howard Hughes Medical Institute, University of Colorado, Boulder, CO, USA
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| |
Collapse
|
81
|
Cohen I, Bar C, Ezhkova E. Activity of PRC1 and Histone H2AK119 Monoubiquitination: Revising Popular Misconceptions. Bioessays 2020; 42:e1900192. [PMID: 32196702 PMCID: PMC7585675 DOI: 10.1002/bies.201900192] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/12/2020] [Indexed: 12/21/2022]
Abstract
Polycomb group proteins are evolutionary conserved chromatin-modifying complexes, essential for the regulation of developmental and cell-identity genes. Polycomb-mediated transcriptional regulation is provided by two multi-protein complexes known as Polycomb repressive complex 1 (PRC1) and 2 (PRC2). Recent studies positioned PRC1 as a foremost executer of Polycomb-mediated transcriptional control. Mammalian PRC1 complexes can form multiple sub-complexes that vary in their core and accessory subunit composition, leading to fascinating and diverse transcriptional regulatory mechanisms employed by PRC1 complexes. These mechanisms include PRC1-catalytic activity toward monoubiquitination of histone H2AK119, a well-established hallmark of PRC1 complexes, whose importance has been long debated. In this review, the central roles that PRC1-catalytic activity plays in transcriptional repression are emphasized and the recent evidence supporting a role for PRC1 complexes in gene activation is discussed.
Collapse
Affiliation(s)
- Idan Cohen
- The Shraga Segal Department of Microbiology, Immunology and Genetics; Faculty of Health Science; Ben-Gurion University of the Negev; Beer Sheva 84105; Israel
- These authors contributed equally to this work
| | - Carmit Bar
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology; Icahn School of Medicine at Mount Sinai; 1 Gustave L. Levy Place, New York, NY 10029; USA
- These authors contributed equally to this work
| | - Elena Ezhkova
- The Shraga Segal Department of Microbiology, Immunology and Genetics; Faculty of Health Science; Ben-Gurion University of the Negev; Beer Sheva 84105; Israel
| |
Collapse
|
82
|
Zepeda-Martinez JA, Pribitzer C, Wang J, Bsteh D, Golumbeanu S, Zhao Q, Burkard TR, Reichholf B, Rhie SK, Jude J, Moussa HF, Zuber J, Bell O. Parallel PRC2/cPRC1 and vPRC1 pathways silence lineage-specific genes and maintain self-renewal in mouse embryonic stem cells. SCIENCE ADVANCES 2020; 6:eaax5692. [PMID: 32270030 PMCID: PMC7112768 DOI: 10.1126/sciadv.aax5692] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 01/09/2020] [Indexed: 05/29/2023]
Abstract
The transcriptional repressors Polycomb repressive complex 1 (PRC1) and PRC2 are required to maintain cell fate during embryonic development. PRC1 and PRC2 catalyze distinct histone modifications, establishing repressive chromatin at shared targets. How PRC1, which consists of canonical PRC1 (cPRC1) and variant PRC1 (vPRC1) complexes, and PRC2 cooperate to silence genes and support mouse embryonic stem cell (mESC) self-renewal is unclear. Using combinatorial genetic perturbations, we show that independent pathways of cPRC1 and vPRC1 are responsible for maintenance of H2A monoubiquitylation and silencing of shared target genes. Individual loss of PRC2-dependent cPRC1 or PRC2-independent vPRC1 disrupts only one pathway and does not impair mESC self-renewal capacity. However, loss of both pathways leads to mESC differentiation and activation of a subset of lineage-specific genes co-occupied by relatively high levels of PRC1/PRC2. Thus, parallel pathways explain the differential requirements for PRC1 and PRC2 and provide robust silencing of lineage-specific genes.
Collapse
Affiliation(s)
- J. A. Zepeda-Martinez
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - C. Pribitzer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - J. Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - D. Bsteh
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - S. Golumbeanu
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Q. Zhao
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - T. R. Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - B. Reichholf
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - S. K. Rhie
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - J. Jude
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - H. F. Moussa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - J. Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - O. Bell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
83
|
Dunican DS, Mjoseng HK, Duthie L, Flyamer IM, Bickmore WA, Meehan RR. Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cells. BMC Biol 2020; 18:25. [PMID: 32131813 PMCID: PMC7057567 DOI: 10.1186/s12915-020-0752-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/14/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Thousands of mammalian promoters are defined by co-enrichment of the histone tail modifications H3K27me3 (repressive) and H3K4me3 (activating) and are thus termed bivalent. It was previously observed that bivalent genes in human ES cells (hESC) are frequent targets for hypermethylation in human cancers, and depletion of DNA methylation in mouse embryonic stem cells has a marked impact on H3K27me3 distribution at bivalent promoters. However, only a fraction of bivalent genes in stem cells are targets of hypermethylation in cancer, and it is currently unclear whether all bivalent promoters are equally sensitive to DNA hypomethylation and whether H3K4me3 levels play a role in the interplay between DNA methylation and H3K27me3. RESULTS We report the sub-classification of bivalent promoters into two groups-promoters with a high H3K27me3:H3K4me3 (hiBiv) ratio or promoters with a low H3K27me3:H3K4me3 ratio (loBiv). HiBiv are enriched in canonical Polycomb components, show a higher degree of local intrachromosomal contacts and are highly sensitive to DNA hypomethylation in terms of H3K27me3 depletion from broad Polycomb domains. In contrast, loBiv promoters are enriched in non-canonical Polycomb components, show lower intrachromosomal contacts and are less sensitive to DNA hypomethylation at the same genomic resolution. Multiple systems reveal that hiBiv promoters are more depleted of Polycomb complexes than loBiv promoters following a reduction in DNA methylation, and we demonstrate that H3K27me3 re-accumulates at promoters when DNA methylation is restored. In human cancer, we show that hiBiv promoters lose H3K27me3 and are more susceptible to DNA hypermethylation than loBiv promoters. CONCLUSION We conclude that bivalency as a general term to describe mammalian promoters is an over-simplification and our sub-classification has revealed novel insights into the interplay between the largely antagonistic presence of DNA methylation and Polycomb systems at bivalent promoters. This approach redefines molecular pathologies underlying disease in which global DNA methylation is aberrant or where Polycomb mutations are present.
Collapse
Affiliation(s)
- Donnchadh S. Dunican
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
| | - Heidi K. Mjoseng
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
| | - Leanne Duthie
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
| | - Ilya M. Flyamer
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
| | - Wendy A. Bickmore
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
| | - Richard R. Meehan
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
| |
Collapse
|
84
|
Ghotbi E, Lackey K, Wong V, Thompson KT, Caston EG, Haddadi M, Benes J, Jones RS. Differential Contributions of DNA-Binding Proteins to Polycomb Response Element Activity at the Drosophila giant Gene. Genetics 2020; 214:623-634. [PMID: 31919108 PMCID: PMC7054010 DOI: 10.1534/genetics.119.302981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 01/06/2020] [Indexed: 11/18/2022] Open
Abstract
Polycomb-group (PcG) proteins are evolutionarily conserved epigenetic regulators whose primary function is to maintain the transcriptional repression of target genes. Recruitment of Drosophila melanogaster PcG proteins to target genes requires the presence of one or more Polycomb Response Elements (PREs). The functions or necessity for more than one PRE at a gene are not clear and individual PREs at some loci may have distinct regulatory roles. Various combinations of sequence-specific DNA-binding proteins are present at a given PRE, but only Pleiohomeotic (Pho) is present at all strong PREs. The giant (gt) locus has two PREs, a proximal PRE1 and a distal PRE2. During early embryonic development, Pho binds to PRE1 ∼30-min prior to stable binding to PRE2. This observation indicated a possible dependence of PRE2 on PRE1 for PcG recruitment; however, we find here that PRE2 recruits PcG proteins and maintains transcriptional repression independently of Pho binding to PRE1. Pho-like (Phol) is partially redundant with Pho during larval development and binds to the same DNA sequences in vitro Although binding of Pho to PRE1 is dependent on the presence of consensus Pho-Phol-binding sites, Phol binding is less so and appears to play a minimal role in recruiting other PcG proteins to gt Another PRE-binding protein, Sp1/Kruppel-like factor, is dependent on the presence of Pho for PRE1 binding. Further, we show that, in addition to silencing gene expression, PcG proteins dampen transcription of an active gene.
Collapse
Affiliation(s)
- Elnaz Ghotbi
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Kristina Lackey
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Vicki Wong
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Katie T Thompson
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Evan G Caston
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Minna Haddadi
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Judith Benes
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| | - Richard S Jones
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376
| |
Collapse
|
85
|
Blackledge NP, Fursova NA, Kelley JR, Huseyin MK, Feldmann A, Klose RJ. PRC1 Catalytic Activity Is Central to Polycomb System Function. Mol Cell 2020; 77:857-874.e9. [PMID: 31883950 PMCID: PMC7033600 DOI: 10.1016/j.molcel.2019.12.001] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/21/2019] [Accepted: 12/02/2019] [Indexed: 01/01/2023]
Abstract
The Polycomb repressive system is an essential chromatin-based regulator of gene expression. Despite being extensively studied, how the Polycomb system selects its target genes is poorly understood, and whether its histone-modifying activities are required for transcriptional repression remains controversial. Here, we directly test the requirement for PRC1 catalytic activity in Polycomb system function. To achieve this, we develop a conditional mutation system in embryonic stem cells that completely removes PRC1 catalytic activity. Using this system, we demonstrate that catalysis by PRC1 drives Polycomb chromatin domain formation and long-range chromatin interactions. Furthermore, we show that variant PRC1 complexes with DNA-binding activities occupy target sites independently of PRC1 catalytic activity, providing a putative mechanism for Polycomb target site selection. Finally, we discover that Polycomb-mediated gene repression requires PRC1 catalytic activity. Together these discoveries provide compelling evidence that PRC1 catalysis is central to Polycomb system function and gene regulation.
Collapse
Affiliation(s)
- Neil P Blackledge
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Nadezda A Fursova
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Jessica R Kelley
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Miles K Huseyin
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Angelika Feldmann
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK.
| |
Collapse
|
86
|
Wang XF, Tian Q, Qin WB, Yin Y, Zeng L, Tang YG, Su P, Zhou LQ. Histone H3 methylation orchestrates transcriptional program in mouse spermatogenic cell line. J Reprod Dev 2020; 66:223-230. [PMID: 32051348 PMCID: PMC7297638 DOI: 10.1262/jrd.2019-139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Changes in histone modifications always correlate with altered transcriptional activities of genes. Recent studies have shown that the mutation of certain lysine residues to
methionine in the histone variant H3.3 can act as a valuable tool to reduce specific H3 methylation levels. In our study, we used the mouse spermatogenic cell line GC-2 as a model
to generate cells stably expressing H3.3 K4, H3.3 K9, H3.3 K27, and H3.3 K36M. The expression of these H3.3 K-to-M mutants influenced the expression of different subsets of genes,
and a total of 891 differentially expressed genes were identified through global gene expression profiling. Moreover, the H3.3 K-to-M transgenes, especially H3.3 K36M, impacted the
expression of endogenous retrovirus ERVK. This study gives a global view of how different H3 modifications regulate transcriptomes in spermatogenic cell lines, and identifies
potential targets of H3 modifications in male germ line.
Collapse
Affiliation(s)
- Xiao-Fei Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei 430030, China
| | - Qing Tian
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei 430030, China
| | - Wei-Bing Qin
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, Guangzhou 510600, China
| | - Ying Yin
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Hubei 430030, China
| | - Ling Zeng
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei 430030, China
| | - Yun-Ge Tang
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, Guangzhou 510600, China
| | - Ping Su
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei 430030, China
| | - Li-Quan Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei 430030, China
| |
Collapse
|
87
|
Fujino T, Kitamura T. ASXL1 mutation in clonal hematopoiesis. Exp Hematol 2020; 83:74-84. [PMID: 31945396 DOI: 10.1016/j.exphem.2020.01.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/04/2020] [Accepted: 01/06/2020] [Indexed: 12/13/2022]
Abstract
Recent advances in DNA sequencing technologies have enhanced our knowledge about several diseases. Coupled with easy accessibility to blood samples, hematology plays a leading role in understanding the process of carcinogenesis. Clonal hematopoiesis (CH) with somatic mutations is observed in at least 10% of people over 65 years of age, without apparent hematologic disorders. CH is associated with increased risk of hematologic malignancies, which is indicative of a pre-malignant condition. Therefore, a better understanding of CH will help elucidate the mechanism of multi-step tumorigenesis in the hematopoietic system. Somatic mutations of ASXL1 are frequently detected in CH and myeloid malignancies. Although ASXL1 does not have any catalytic activity, it is involved in multiple histone modifications including H3K4me3, H3K27me3, and H2AK119Ub, suggesting its function as a scaffolding protein. Most ASXL1 mutations detected in CH and myeloid malignancies are frameshift or nonsense mutations of the last exon, generating a C-terminally truncated protein. Deletion of Asxl1 or expression of mutant ASXL1 in mice alters histone modifications and facilitates aberrant gene expression, resulting in myeloid transformation. On the contrary, these mice exhibit impaired functioning of hematopoietic stem cells (HSCs), suggesting the negative effects of ASXL1 mutations on stem cell function. Thus, how ASXL1 mutations induce a clonal advantage of hematopoietic cells and subsequent CH development has not been elucidated. Here, we have reviewed the current literature that enhances our understanding of ASXL1, including its mutational landscape, function, and involvement of its mutation in pathogenesis of CH and myeloid malignancies. Finally, we discuss the potential causes of CH harboring ASXL1 mutations with our latest knowledge.
Collapse
Affiliation(s)
- Takeshi Fujino
- Division of Cellular Therapy, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Toshio Kitamura
- Division of Cellular Therapy, The Institute of Medical Science, University of Tokyo, Tokyo, Japan.
| |
Collapse
|
88
|
Abstract
Comprehensive cataloguing of the acute myeloid leukaemia (AML) genome has revealed a high frequency of mutations and deletions in epigenetic factors that are frequently linked to treatment resistance and poor patient outcome. In this review, we discuss how the epigenetic mechanisms that underpin normal haematopoiesis are subverted in AML, and in particular how these processes are altered in childhood and adolescent leukaemias. We also provide a brief summary of the burgeoning field of epigenetic-based therapies, and how AML treatment might be improved through provision of better conceptual frameworks for understanding the pleiotropic molecular effects of epigenetic disruption.
Collapse
Affiliation(s)
- Luke Jones
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,National Children's Research Centre, Dublin, Ireland
| | - Peter McCarthy
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Jonathan Bond
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.,National Children's Research Centre, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
| |
Collapse
|
89
|
Evolving Role of RING1 and YY1 Binding Protein in the Regulation of Germ-Cell-Specific Transcription. Genes (Basel) 2019; 10:genes10110941. [PMID: 31752312 PMCID: PMC6895862 DOI: 10.3390/genes10110941] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/07/2019] [Accepted: 11/14/2019] [Indexed: 12/11/2022] Open
Abstract
Separation of germline cells from somatic lineages is one of the earliest decisions of embryogenesis. Genes expressed in germline cells include apoptotic and meiotic factors, which are not transcribed in the soma normally, but a number of testis-specific genes are active in numerous cancer types. During germ cell development, germ-cell-specific genes can be regulated by specific transcription factors, retinoic acid signaling and multimeric protein complexes. Non-canonical polycomb repressive complexes, like ncPRC1.6, play a critical role in the regulation of the activity of germ-cell-specific genes. RING1 and YY1 binding protein (RYBP) is one of the core members of the ncPRC1.6. Surprisingly, the role of Rybp in germ cell differentiation has not been defined yet. This review is focusing on the possible role of Rybp in this process. By analyzing whole-genome transcriptome alterations of the Rybp-/- embryonic stem (ES) cells and correlating this data with experimentally identified binding sites of ncPRC1.6 subunits and retinoic acid receptors in ES cells, we propose a model how germ-cell-specific transcription can be governed by an RYBP centered regulatory network, underlining the possible role of RYBP in germ cell differentiation and tumorigenesis.
Collapse
|
90
|
Zhao T, Zhan Z, Jiang D. Histone modifications and their regulatory roles in plant development and environmental memory. J Genet Genomics 2019; 46:467-476. [PMID: 31813758 DOI: 10.1016/j.jgg.2019.09.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/23/2019] [Accepted: 09/29/2019] [Indexed: 11/24/2022]
Abstract
Plants grow in dynamic environments where they receive diverse environmental signals. Swift and precise control of gene expression is essential for plants to align their development and metabolism with fluctuating surroundings. Modifications on histones serve as "histone code" to specify chromatin and gene activities. Different modifications execute distinct functions on the chromatin, promoting either active transcription or gene silencing. Histone writers, erasers, and readers mediate the regulation of histone modifications by catalyzing, removing, and recognizing modifications, respectively. Growing evidence indicates the important function of histone modifications in plant development and environmental responses. Histone modifications also serve as environmental memory for plants to adapt to environmental changes. Here we review recent progress on the regulation of histone modifications in plants, the impact of histone modifications on environment-controlled developmental transitions including germination and flowering, and the role of histone modifications in environmental memory.
Collapse
Affiliation(s)
- Ting Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenping Zhan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Danhua Jiang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
91
|
Gökbuget D, Blelloch R. Epigenetic control of transcriptional regulation in pluripotency and early differentiation. Development 2019; 146:dev164772. [PMID: 31554624 PMCID: PMC6803368 DOI: 10.1242/dev.164772] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pluripotent stem cells give rise to all cells of the adult organism, making them an invaluable tool in regenerative medicine. In response to differentiation cues, they can activate markedly distinct lineage-specific gene networks while turning off or rewiring pluripotency networks. Recent innovations in chromatin and nuclear structure analyses combined with classical genetics have led to novel insights into the transcriptional and epigenetic mechanisms underlying these networks. Here, we review these findings in relation to their impact on the maintenance of and exit from pluripotency and highlight the many factors that drive these processes, including histone modifying enzymes, DNA methylation and demethylation, nucleosome remodeling complexes and transcription factor-mediated enhancer switching.
Collapse
Affiliation(s)
- Deniz Gökbuget
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Robert Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94143, USA
| |
Collapse
|
92
|
Abstract
In mammals, dosage compensation of sex chromosomal genes between females (XX) and males (XY) is achieved through X-chromosome inactivation (XCI). The X-linked X-inactive-specific transcript (Xist) long noncoding RNA is indispensable for XCI and initiates the process early during development by spreading in cis across the X chromosome from which it is transcribed. During XCI, Xist RNA triggers gene silencing, recruits a plethora of chromatin modifying factors, and drives a major structural reorganization of the X chromosome. Here, we review our knowledge of the multitude of epigenetic events orchestrated by Xist RNA to allow female mammals to survive through embryonic development by establishing and maintaining proper dosage compensation. In particular, we focus on recent studies characterizing the interaction partners of Xist RNA, and we discuss how they have affected the field by addressing long-standing controversies or by giving rise to new research perspectives that are currently being explored. This review is dedicated to the memory of Denise Barlow, pioneer of genomic imprinting and functional long noncoding RNAs (lncRNAs), whose work has revolutionized the epigenetics field and continues to inspire generations of scientists.
Collapse
|
93
|
Abstract
Though genetic data suggest that Polycomb group proteins (PcGs) are central chromatin modifiers and repressors that have been implicated in control of embryonic stem cell (ESC) pluripotency, the precise mechanism of PcG complex recruitment remains elusive, especially in mammals. We now report that the first and second MBT repeats of L3mbtl2 are important structural and functional features that are necessary and sufficient for L3mbtl2-mediated recruitment of PRC1.6 complex to target promoters. Interestingly, this region of L3mbtl2 harbors the evolutionarily conserved Pho-binding pocket also present in Drosophila Sfmbt, and mutation of the critical residues within this pocket completely abolishes its interaction with target promoters. Additionally, decreased PRC1.6 chromatin occupancy was observed following loss of individual components (L3mbtl2, Pcgf6, and Max) of the complex. Our findings suggest that the recruitment of noncanonical PRC1.6 complex in ESCs might be the result of L3mbtl2's interaction with multiple components of the complex.
Collapse
|
94
|
Dong H, Liu S, Zhang X, Chen S, Kang L, Chen Y, Ma S, Fu X, Liu Y, Zhang H, Zou B. An Allosteric PRC2 Inhibitor Targeting EED Suppresses Tumor Progression by Modulating the Immune Response. Cancer Res 2019; 79:5587-5596. [PMID: 31395608 DOI: 10.1158/0008-5472.can-19-0428] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 04/11/2019] [Accepted: 08/01/2019] [Indexed: 11/16/2022]
Abstract
Aberrant activity of polycomb repressive complex 2 (PRC2) is involved in a wide range of human cancer progression. The WD40 repeat-containing protein EED is a core component of PRC2 and enhances PRC2 activity through interaction with H3K27me3. In this study, we report the discovery of a class of pyrimidone compounds, represented by BR-001, as potent allosteric inhibitors of PRC2. X-ray co-crystallography showed that BR-001 directly binds EED in the H3K27me3-binding pocket. BR-001 displayed antitumor potency in vitro and in vivo. In Karpas422 and Pfeiffer xenograft mouse models, twice daily oral dosing with BR-001 resulted in robust antitumor activity. BR-001 was also efficacious in syngeneic CT26 colon tumor-bearing mice; oral dosing of 30 mg/kg of BR-001 led to 59.3% tumor growth suppression and increased frequency of effector CD8+ T-cell infiltrates in tumors. Pharmacodynamic analysis revealed that CXCL10 was highly upregulated, suggesting that CXCL10 triggers the trafficking of CD8+ T cells toward tumor sites. Our results demonstrate for the first time that inhibition of EED modulates the tumor immune microenvironment to induce regression of colon tumors and therefore has the potential to be used in combination with immune-oncology therapy. SIGNIFICANCE: BR-001, a potent inhibitor of the EED subunit of the PRC2 complex, suppresses tumor progression by modulating the tumor microenvironment.
Collapse
Affiliation(s)
- Hongping Dong
- Shanghai Blueray Biopharma Co. Ltd., Shanghai, China.
| | - Shaojun Liu
- Shanghai Blueray Biopharma Co. Ltd., Shanghai, China
| | - Xuejie Zhang
- Shanghai Blueray Biopharma Co. Ltd., Shanghai, China
| | - Sheng Chen
- Shanghai Blueray Biopharma Co. Ltd., Shanghai, China
| | - Lijing Kang
- Shanghai Blueray Biopharma Co. Ltd., Shanghai, China
| | - Yanni Chen
- Shanghai Blueray Biopharma Co. Ltd., Shanghai, China
| | - Shichao Ma
- Shanghai Blueray Biopharma Co. Ltd., Shanghai, China
| | - Xianlei Fu
- Shanghai Blueray Biopharma Co. Ltd., Shanghai, China
| | - Yanchao Liu
- Shanghai Blueray Biopharma Co. Ltd., Shanghai, China
| | - Hailong Zhang
- Shanghai Blueray Biopharma Co. Ltd., Shanghai, China
| | - Bin Zou
- Shanghai Blueray Biopharma Co. Ltd., Shanghai, China.
| |
Collapse
|
95
|
Ni J, Ma X, Feng Y, Tian Q, Wang Y, Xu N, Tang J, Wang G. Updating and interaction of polycomb repressive complex 2 components in maize (Zea mays). PLANTA 2019; 250:573-588. [PMID: 31127375 DOI: 10.1007/s00425-019-03193-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/16/2019] [Indexed: 06/09/2023]
Abstract
The information on core components in maize polycomb repressive complex 2 (PRC2) are updated at a genome-wide scale, and the protein-protein interaction networks of PRC2 components are further provided in maize. The evolutionarily conserved polycomb group (PcG) proteins form multi-subunits polycomb repressive complexes (PRCs) that repress gene expression via chromatin condensation. In Arabidopsis, three distinct PRC2s have been identified, each determining a specific developmental program with partly functional redundancy. However, the core components and biological functions of PRC2 in cereals remain obscure. Here, we updated the information on maize PRC2 components at a genome-wide scale. Maize PRC2 subunits are highly duplicated, with five MSI1, three E(z), two ESC and two Su(z)12 homologs. ZmFIE1 is preferentially expressed in the endosperm, whereas the remaining are broadly expressed in many tissues. ZmCLF/MEZ1 and ZmFIE1 are maternally expressed imprinted genes, in contrast to the paternal-dominantly expression of ZmFIE2 in the endosperm. In maize, E(z) members likely provide a scaffold for assembling PRC2 complexes, whereas Su(z)12 and p55/MSI1-like proteins together reinforce the complex; ESC members probably determine its specificity: FIE1-PRC2 regulates endosperm cell development, whereas FIE2-PRC2 controls other cell types. The duplicated Brassicaceae-specific MEA and FIS2 also directly interact with maize PRC2 members. Together, this study establishes a roadmap for protein-protein interactions of maize PRC2 components, providing new insights into their functions in the growth and development of cereals.
Collapse
Affiliation(s)
- Jiacheng Ni
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Xuexia Ma
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Yu Feng
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Qiuzhen Tian
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yongyan Wang
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ningkun Xu
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jihua Tang
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guifeng Wang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China.
- Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| |
Collapse
|
96
|
Hu T, Kitano A, Luu V, Dawson B, Hoegenauer KA, Lee BH, Nakada D. Bmi1 Suppresses Adipogenesis in the Hematopoietic Stem Cell Niche. Stem Cell Reports 2019; 13:545-558. [PMID: 31257132 PMCID: PMC6739622 DOI: 10.1016/j.stemcr.2019.05.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 05/28/2019] [Accepted: 05/29/2019] [Indexed: 12/11/2022] Open
Abstract
Bone marrow stromal cells (BMSCs) that express high levels of stem cell factor (SCF) and CXC chemokine ligand 12 (CXCL12) are one crucial component of the hematopoietic stem cell (HSC) niche. While the secreted factors produced by BMSCs to support HSCs have been well described, little is known regarding the transcriptional regulators controlling the cell fate of BMSCs and thus indirectly maintaining HSCs. BMI1 is a polycomb group protein that regulates HSCs both cell intrinsically and extrinsically, but it is unknown in which cell type and how BMI1 functions to maintain HSCs extrinsically. Here we show that Bmi1 maintains HSCs by preventing adipogenic differentiation of BMSCs. Bmi1 is highly expressed in BMSCs but becomes downregulated upon adipogenic differentiation and during aging. Deleting Bmi1 from BMSCs increased marrow adipocytes, induced HSC quiescence and depletion, and impaired hematopoiesis. We found that BMI1 repressed multiple developmental programs in BMSCs by safeguarding the repressive epigenetic marks histone H2A ubiquitylation and H3 lysine 27 trimethylation. We identified a novel adipogenic program governed by Pax3, which BMI1 repressed in BMSCs. Our results establish Bmi1 as a critical regulator of BMSC cell fate that suppresses marrow adipogenesis to create a supportive niche for HSCs.
Collapse
Affiliation(s)
- Tianyuan Hu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ayumi Kitano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Victor Luu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brian Dawson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin A Hoegenauer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brendan H Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daisuke Nakada
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
97
|
Fursova NA, Blackledge NP, Nakayama M, Ito S, Koseki Y, Farcas AM, King HW, Koseki H, Klose RJ. Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene Repression. Mol Cell 2019; 74:1020-1036.e8. [PMID: 31029541 PMCID: PMC6561741 DOI: 10.1016/j.molcel.2019.03.024] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/04/2019] [Accepted: 03/21/2019] [Indexed: 01/30/2023]
Abstract
The Polycomb system modifies chromatin and plays an essential role in repressing gene expression to control normal mammalian development. However, the components and mechanisms that define how Polycomb protein complexes achieve this remain enigmatic. Here, we use combinatorial genetic perturbation coupled with quantitative genomics to discover the central determinants of Polycomb-mediated gene repression in mouse embryonic stem cells. We demonstrate that canonical Polycomb repressive complex 1 (PRC1), which mediates higher-order chromatin structures, contributes little to gene repression. Instead, we uncover an unexpectedly high degree of synergy between variant PRC1 complexes, which is fundamental to gene repression. We further demonstrate that variant PRC1 complexes are responsible for distinct pools of H2A monoubiquitylation that are associated with repression of Polycomb target genes and silencing during X chromosome inactivation. Together, these discoveries reveal a new variant PRC1-dependent logic for Polycomb-mediated gene repression.
Collapse
Affiliation(s)
- Nadezda A Fursova
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Neil P Blackledge
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Manabu Nakayama
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Anca M Farcas
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Hamish W King
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; AMED-CREST, Japanese Agency for Medical Research and Development, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| |
Collapse
|
98
|
Kim JJ, Lee SY, Miller KM. Preserving genome integrity and function: the DNA damage response and histone modifications. Crit Rev Biochem Mol Biol 2019; 54:208-241. [PMID: 31164001 DOI: 10.1080/10409238.2019.1620676] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Modulation of chromatin templates in response to cellular cues, including DNA damage, relies heavily on the post-translation modification of histones. Numerous types of histone modifications including phosphorylation, methylation, acetylation, and ubiquitylation occur on specific histone residues in response to DNA damage. These histone marks regulate both the structure and function of chromatin, allowing for the transition between chromatin states that function in undamaged condition to those that occur in the presence of DNA damage. Histone modifications play well-recognized roles in sensing, processing, and repairing damaged DNA to ensure the integrity of genetic information and cellular homeostasis. This review highlights our current understanding of histone modifications as they relate to DNA damage responses (DDRs) and their involvement in genome maintenance, including the potential targeting of histone modification regulators in cancer, a disease that exhibits both epigenetic dysregulation and intrinsic DNA damage.
Collapse
Affiliation(s)
- Jae Jin Kim
- Department of Molecular Biosciences, LIVESTRONG Cancer Institute of the Dell Medical School, Institute for Cellular and Molecular Biology, The University of Texas at Austin , Austin , TX , USA
| | - Seo Yun Lee
- Department of Molecular Biosciences, LIVESTRONG Cancer Institute of the Dell Medical School, Institute for Cellular and Molecular Biology, The University of Texas at Austin , Austin , TX , USA
| | - Kyle M Miller
- Department of Molecular Biosciences, LIVESTRONG Cancer Institute of the Dell Medical School, Institute for Cellular and Molecular Biology, The University of Texas at Austin , Austin , TX , USA
| |
Collapse
|
99
|
Jia Y, Vong JSL, Asafova A, Garvalov BK, Caputo L, Cordero J, Singh A, Boettger T, Günther S, Fink L, Acker T, Barreto G, Seeger W, Braun T, Savai R, Dobreva G. Lamin B1 loss promotes lung cancer development and metastasis by epigenetic derepression of RET. J Exp Med 2019; 216:1377-1395. [PMID: 31015297 PMCID: PMC6547854 DOI: 10.1084/jem.20181394] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 02/13/2019] [Accepted: 03/20/2019] [Indexed: 12/12/2022] Open
Abstract
Although abnormal nuclear structure is an important criterion for cancer diagnostics, remarkably little is known about its relationship to tumor development. Here we report that loss of lamin B1, a determinant of nuclear architecture, plays a key role in lung cancer. We found that lamin B1 levels were reduced in lung cancer patients. Lamin B1 silencing in lung epithelial cells promoted epithelial-mesenchymal transition, cell migration, tumor growth, and metastasis. Mechanistically, we show that lamin B1 recruits the polycomb repressive complex 2 (PRC2) to alter the H3K27me3 landscape and repress genes involved in cell migration and signaling. In particular, epigenetic derepression of the RET proto-oncogene by loss of PRC2 recruitment, and activation of the RET/p38 signaling axis, play a crucial role in mediating the malignant phenotype upon lamin B1 disruption. Importantly, loss of a single lamin B1 allele induced spontaneous lung tumor formation and RET activation. Thus, lamin B1 acts as a tumor suppressor in lung cancer, linking aberrant nuclear structure and epigenetic patterning with malignancy.
Collapse
Affiliation(s)
- Yanhan Jia
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
- Anatomy and Developmental Biology, Centre for Biomedicine and Medical Technology Mannheim (CBTM) and European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Joaquim Si-Long Vong
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
| | - Alina Asafova
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
| | - Boyan K Garvalov
- Microvascular Biology and Pathobiology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Institute of Neuropathology, Justus Liebig University, Giessen, Germany
| | - Luca Caputo
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
| | - Julio Cordero
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
- Anatomy and Developmental Biology, Centre for Biomedicine and Medical Technology Mannheim (CBTM) and European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Anshu Singh
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
- Anatomy and Developmental Biology, Centre for Biomedicine and Medical Technology Mannheim (CBTM) and European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Boettger
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
| | - Stefan Günther
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
| | - Ludger Fink
- Institute of Pathology and Cytology, Überregionale Gemeinschaftspraxis für Pathologie (ÜGP), Wetzlar, Germany
| | - Till Acker
- Institute of Neuropathology, Justus Liebig University, Giessen, Germany
| | - Guillermo Barreto
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
| | - Werner Seeger
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
- Department of Internal Medicine, Justus Liebig University, Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
| | - Rajkumar Savai
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
- Department of Internal Medicine, Justus Liebig University, Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Gergana Dobreva
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research, Bad Nauheim, Germany
- Anatomy and Developmental Biology, Centre for Biomedicine and Medical Technology Mannheim (CBTM) and European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Medical Faculty, J.W. Goethe University Frankfurt, Frankfurt, Germany
| |
Collapse
|
100
|
Chou J, Ferris AC, Chen T, Seok R, Yoon D, Suzuki Y. Roles of Polycomb group proteins Enhancer of zeste (E(z)) and Polycomb (Pc) during metamorphosis and larval leg regeneration in the flour beetle Tribolium castaneum. Dev Biol 2019; 450:34-46. [PMID: 30851270 DOI: 10.1016/j.ydbio.2019.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/24/2019] [Accepted: 03/04/2019] [Indexed: 11/26/2022]
Abstract
Many organisms both undergo dramatic morphological changes during post-embryonic development and also regenerate lost structures, but the roles of epigenetic regulators in such processes are only beginning to be understood. In the present study, the functions of two histone modifiers were examined during metamorphosis and larval limb regeneration in the red flour beetle Tribolium castaneum. Polycomb (Pc), a member of Polycomb repressive complex 1 (PRC1), and Enhancer of zeste (E(z)), a member of Polycomb repressive complex 2 (PRC2), were silenced in larvae using RNA interference. In the absence of Pc, the head appendages of adults transformed into a leg-like morphology, and the legs and wings assumed a metathoracic identity, indicating that Pc acts to specify proper segmental identity. Similarly, silencing of E(z) led to homeotic transformation of legs and wings. Additional defects were also observed in limb patterning as well as eye morphogenesis, indicating that PcG proteins play critical roles in imaginal precursor cells. In addition, larval legs and antennae failed to re-differentiate when either Pc or E(z) was knocked down, indicating that histone modification is necessary for proper blastema growth and differentiation. These findings indicate that PcG proteins play extensive roles in postembryonic plasticity of imaginal precursor cells.
Collapse
Affiliation(s)
- Jacquelyn Chou
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA 02481, USA
| | - Alex C Ferris
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA 02481, USA
| | - Teresa Chen
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA 02481, USA
| | - Ruth Seok
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA 02481, USA
| | - Denise Yoon
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA 02481, USA
| | - Yuichiro Suzuki
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA 02481, USA.
| |
Collapse
|