1
|
Shi TH, Sugishita H, Gotoh Y. Crosstalk within and beyond the Polycomb repressive system. J Cell Biol 2024; 223:e202311021. [PMID: 38506728 PMCID: PMC10955045 DOI: 10.1083/jcb.202311021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
The development of multicellular organisms depends on spatiotemporally controlled differentiation of numerous cell types and their maintenance. To generate such diversity based on the invariant genetic information stored in DNA, epigenetic mechanisms, which are heritable changes in gene function that do not involve alterations to the underlying DNA sequence, are required to establish and maintain unique gene expression programs. Polycomb repressive complexes represent a paradigm of epigenetic regulation of developmentally regulated genes, and the roles of these complexes as well as the epigenetic marks they deposit, namely H3K27me3 and H2AK119ub, have been extensively studied. However, an emerging theme from recent studies is that not only the autonomous functions of the Polycomb repressive system, but also crosstalks of Polycomb with other epigenetic modifications, are important for gene regulation. In this review, we summarize how these crosstalk mechanisms have improved our understanding of Polycomb biology and how such knowledge could help with the design of cancer treatments that target the dysregulated epigenome.
Collapse
Affiliation(s)
- Tianyi Hideyuki Shi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroki Sugishita
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- International Research Center for Neurointelligence, The University of Tokyo, Tokyo, Japan
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- International Research Center for Neurointelligence, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
2
|
Suzuki A, Uranishi K, Nishimoto M, Mizuno Y, Mizuno S, Takahashi S, Eisenman RN, Okuda A. MAX controls meiotic entry in sexually undifferentiated germ cells. Sci Rep 2024; 14:5236. [PMID: 38433229 PMCID: PMC10909893 DOI: 10.1038/s41598-024-55506-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/24/2024] [Indexed: 03/05/2024] Open
Abstract
Meiosis is a specialized type of cell division that occurs physiologically only in germ cells. We previously demonstrated that MYC-associated factor X (MAX) blocks the ectopic onset of meiosis in embryonic and germline stem cells in culture systems. Here, we investigated the Max gene's role in mouse primordial germ cells. Although Max is generally ubiquitously expressed, we revealed that sexually undifferentiated male and female germ cells had abundant MAX protein because of their higher Max gene expression than somatic cells. Moreover, our data revealed that this high MAX protein level in female germ cells declined significantly around physiological meiotic onset. Max disruption in sexually undifferentiated germ cells led to ectopic and precocious expression of meiosis-related genes, including Meiosin, the gatekeeper of meiotic onset, in both male and female germ cells. However, Max-null male and female germ cells did not complete the entire meiotic process, but stalled during its early stages and were eventually eliminated by apoptosis. Additionally, our meta-analyses identified a regulatory region that supports the high Max expression in sexually undifferentiated male and female germ cells. These results indicate the strong connection between the Max gene and physiological onset of meiosis in vivo through dynamic alteration of its expression.
Collapse
Affiliation(s)
- Ayumu Suzuki
- 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
| | - Masazumi Nishimoto
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan
| | - Yosuke Mizuno
- Division of Morphological Science, Biomedical Research Center, Saitama Medical University, 38 Morohongo, Moroyama, Iruma-gun, Saitama, 350-0495, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Robert N Eisenman
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Akihiko Okuda
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan.
| |
Collapse
|
3
|
Wei R, Zhang X, Li X, Wen J, Liu H, Fu J, Li L, Zhang W, Liu Z, Yang Y, Zou K. A rapid and stable spontaneous reprogramming system of Spermatogonial stem cells to Pluripotent State. Cell Biosci 2023; 13:222. [PMID: 38041111 PMCID: PMC10693117 DOI: 10.1186/s13578-023-01150-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/20/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND The scarcity of pluripotent stem cells poses a major challenge to the clinical application, given ethical and biosafety considerations. While germline stem cells commit to gamete differentiation throughout life, studies demonstrated the spontaneous acquisition of pluripotency by spermatogonial stem cells (SSCs) from neonatal testes at a low frequency (1 in 1.5 × 107). Notably, this process occurs without exogenous oncogenes or chemical supplementation. However, while knockout of the p53 gene accelerates the transformation of SSCs, it also increases risk and hampers their clinical use. RESULTS We report a transformation system that efficiently and stably convert SSCs into pluripotent stem cells around 10 passages with the morphology similar to that of epiblast stem cells, which convert to embryonic stem (ES) cell-like colonies after change with ES medium. Epidermal growth factor (EGF), leukemia inhibitory factor (LIF) and fresh mouse embryonic fibroblast feeder (MEF) are essential for transformation, and addition of 2i (CHIR99021 and PD0325901) further enhanced the pluripotency. Transcriptome analysis revealed that EGF activated the RAS signaling pathway and inhibited p38 to initiate transformation, and synergically cooperated with LIF to promote the transformation. CONCLUSION This system established an efficient and safe resource of pluripotent cells from autologous germline, and provide new avenues for regenerative medicine and animal cloning.
Collapse
Affiliation(s)
- Rui Wei
- Germline Stem Cells and Microenvironment Lab, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Stem Cell Research and Translation Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoyu Zhang
- Germline Stem Cells and Microenvironment Lab, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Stem Cell Research and Translation Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoxiao Li
- Germline Stem Cells and Microenvironment Lab, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Stem Cell Research and Translation Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian Wen
- Germline Stem Cells and Microenvironment Lab, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Stem Cell Research and Translation Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongyang Liu
- Germline Stem Cells and Microenvironment Lab, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Stem Cell Research and Translation Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiqiang Fu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Li Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Wenyi Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China
| | - Zhen Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Yang Yang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, 211166, China.
| | - Kang Zou
- Germline Stem Cells and Microenvironment Lab, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
- Stem Cell Research and Translation Center, Nanjing Agricultural University, Nanjing, 210095, China.
| |
Collapse
|
4
|
Ong ALC, Kokaji T, Kishi A, Takihara Y, Shinozuka T, Shimamoto R, Isotani A, Shirai M, Sasai N. Acquisition of neural fate by combination of BMP blockade and chromatin modification. iScience 2023; 26:107887. [PMID: 37771660 PMCID: PMC10522999 DOI: 10.1016/j.isci.2023.107887] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/07/2023] [Accepted: 09/07/2023] [Indexed: 09/30/2023] Open
Abstract
Neural induction is a process where naive cells are converted into committed cells with neural characteristics, and it occurs at the earliest step during embryogenesis. Although the signaling molecules and chromatin remodeling for neural induction have been identified, the mutual relationships between these molecules are yet to be fully understood. By taking advantage of the neural differentiation system of mouse embryonic stem (ES) cells, we discovered that the BMP signal regulates the expression of several polycomb repressor complex (PRC) component genes. We particularly focused on Polyhomeotic Homolog 1 (Phc1) and established Phc1-knockout (Phc1-KO) ES cells. We found that Phc1-KO failed to acquire the neural fate, and the cells remained in pluripotent or primitive non-neural states. Chromatin accessibility analysis suggests that Phc1 is essential for chromatin packing. Aberrant upregulation of the BMP signal was confirmed in the Phc1 homozygotic mutant embryos. Taken together, Phc1 is required for neural differentiation through epigenetic modification.
Collapse
Affiliation(s)
- Agnes Lee Chen Ong
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Toshiya Kokaji
- Data-driven biology, NAIST Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Arisa Kishi
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Yoshihiro Takihara
- Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima 734-0037, Japan
| | - Takuma Shinozuka
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Ren Shimamoto
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Ayako Isotani
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Manabu Shirai
- Omics Research Center (ORC), National Cerebral and Cardiovascular Center, 6-1 Kishibe Shinmachi, Suita, Osaka 564-8565, Japan
| | - Noriaki Sasai
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| |
Collapse
|
5
|
Ruan Y, Wang J, Yu M, Wang F, Wang J, Xu Y, Liu L, Cheng Y, Yang R, Zhang C, Yang Y, Wang J, Wu W, Huang Y, Tian Y, Chen G, Zhang J, Jian R. A multi-omics integrative analysis based on CRISPR screens re-defines the pluripotency regulatory network in ESCs. Commun Biol 2023; 6:410. [PMID: 37059858 PMCID: PMC10104827 DOI: 10.1038/s42003-023-04700-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/13/2023] [Indexed: 04/16/2023] Open
Abstract
A comprehensive and precise definition of the pluripotency gene regulatory network (PGRN) is crucial for clarifying the regulatory mechanisms in embryonic stem cells (ESCs). Here, after a CRISPR/Cas9-based functional genomics screen and integrative analysis with other functional genomes, transcriptomes, proteomes and epigenome data, an expanded pluripotency-associated gene set is obtained, and a new PGRN with nine sub-classes is constructed. By integrating the DNA binding, epigenetic modification, chromatin conformation, and RNA expression profiles, the PGRN is resolved to six functionally independent transcriptional modules (CORE, MYC, PAF, PRC, PCGF and TBX). Spatiotemporal transcriptomics reveal activated CORE/MYC/PAF module activity and repressed PRC/PCGF/TBX module activity in both mouse ESCs (mESCs) and pluripotent cells of early embryos. Moreover, this module activity pattern is found to be shared by human ESCs (hESCs) and cancers. Thus, our results provide novel insights into elucidating the molecular basis of ESC pluripotency.
Collapse
Affiliation(s)
- Yan Ruan
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Jiaqi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University, Chongqing, 400038, China
| | - Meng Yu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Joint Surgery, The First Affiliated Hospital, Army Medical University, Chongqing, 400038, China
| | - Fengsheng Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Jiangjun Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Cell Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yixiao Xu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Lianlian Liu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yuda Cheng
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Ran Yang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University, Chongqing, 400038, China
| | - Chen Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yi Yang
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - JiaLi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Wei Wu
- Thoracic Surgery Department, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, 400038, China
| | - Yi Huang
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China
| | - Yanping Tian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Guangxing Chen
- Department of Joint Surgery, The First Affiliated Hospital, Army Medical University, Chongqing, 400038, China.
| | - Junlei Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
| | - Rui Jian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
| |
Collapse
|
6
|
Lan X, Ding S, Zhang T, Yi Y, Li C, Jin W, Chen J, Liang K, Wang H, Jiang W. PCGF6 controls neuroectoderm specification of human pluripotent stem cells by activating SOX2 expression. Nat Commun 2022; 13:4601. [PMID: 35933409 PMCID: PMC9357003 DOI: 10.1038/s41467-022-32295-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 07/25/2022] [Indexed: 11/28/2022] Open
Abstract
Polycomb group (PcG) proteins are known to repress developmental genes during embryonic development and tissue homeostasis. Here, we report that PCGF6 controls neuroectoderm specification of human pluripotent stem cells (PSCs) by activating SOX2 gene. Human PSCs with PCGF6 depletion display impaired neuroectoderm differentiation coupled with increased mesendoderm outcomes. Transcriptome analysis reveals that de-repression of the WNT/β-catenin signaling pathway is responsible for the differentiation of PSC toward the mesendodermal lineage. Interestingly, PCGF6 and MYC directly interact and co-occupy a distal regulatory element of SOX2 to activate SOX2 expression, which likely accounts for the regulation in neuroectoderm differentiation. Supporting this notion, genomic deletion of the SOX2-regulatory element phenocopies the impaired neuroectoderm differentiation, while overexpressing SOX2 rescues the neuroectoderm phenotype caused by PCGF6-depletion. Together, our study reveals that PCGF6 can function as lineage switcher between mesendoderm and neuroectoderm in human PSCs by both suppression and activation mechanisms.
Collapse
Affiliation(s)
- Xianchun Lan
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Song Ding
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Tianzhe Zhang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Ying Yi
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Conghui Li
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wenwen Jin
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Jian Chen
- Chinese Institute for Brain Research (Beijing), Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, 102206, Beijing, China
| | - Kaiwei Liang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Hengbin Wang
- Department of Internal Medicine, Division of Hematology, Oncology, and Palliative Care, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Wei Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, RNA Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China.
- Human Genetics Resource Preservation Center of Wuhan University, Wuhan, China.
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, China.
| |
Collapse
|
7
|
Systematic identification of cell-fate regulatory programs using a single-cell atlas of mouse development. Nat Genet 2022; 54:1051-1061. [PMID: 35817981 DOI: 10.1038/s41588-022-01118-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 06/01/2022] [Indexed: 12/21/2022]
Abstract
Waddington's epigenetic landscape is a metaphor frequently used to illustrate cell differentiation. Recent advances in single-cell genomics are altering our understanding of the Waddington landscape, yet the molecular mechanisms of cell-fate decisions remain poorly understood. We constructed a cell landscape of mouse lineage differentiation during development at the single-cell level and described both lineage-common and lineage-specific regulatory programs during cell-type maturation. We also found lineage-common regulatory programs that are broadly active during the development of invertebrates and vertebrates. In particular, we identified Xbp1 as an evolutionarily conserved regulator of cell-fate determinations across different species. We demonstrated that Xbp1 transcriptional regulation is important for the stabilization of the gene-regulatory networks for a wide range of mouse cell types. Our results offer genetic and molecular insights into cellular gene-regulatory programs and will serve as a basis for further advancing the understanding of cell-fate decisions.
Collapse
|
8
|
Owen BM, Davidovich C. DNA binding by polycomb-group proteins: searching for the link to CpG islands. Nucleic Acids Res 2022; 50:4813-4839. [PMID: 35489059 PMCID: PMC9122586 DOI: 10.1093/nar/gkac290] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/25/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Polycomb group proteins predominantly exist in polycomb repressive complexes (PRCs) that cooperate to maintain the repressed state of thousands of cell-type-specific genes. Targeting PRCs to the correct sites in chromatin is essential for their function. However, the mechanisms by which PRCs are recruited to their target genes in mammals are multifactorial and complex. Here we review DNA binding by polycomb group proteins. There is strong evidence that the DNA-binding subunits of PRCs and their DNA-binding activities are required for chromatin binding and CpG targeting in cells. In vitro, CpG-specific binding was observed for truncated proteins externally to the context of their PRCs. Yet, the mere DNA sequence cannot fully explain the subset of CpG islands that are targeted by PRCs in any given cell type. At this time we find very little structural and biophysical evidence to support a model where sequence-specific DNA-binding activity is required or sufficient for the targeting of CpG-dinucleotide sequences by polycomb group proteins while they are within the context of their respective PRCs, either PRC1 or PRC2. We discuss the current knowledge and open questions on how the DNA-binding activities of polycomb group proteins facilitate the targeting of PRCs to chromatin.
Collapse
Affiliation(s)
- Brady M Owen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia.,EMBL-Australia, Clayton, VIC, Australia
| |
Collapse
|
9
|
Mochizuki K, Sharif J, Shirane K, Uranishi K, Bogutz AB, Janssen SM, Suzuki A, Okuda A, Koseki H, Lorincz MC. Repression of germline genes by PRC1.6 and SETDB1 in the early embryo precedes DNA methylation-mediated silencing. Nat Commun 2021; 12:7020. [PMID: 34857746 PMCID: PMC8639735 DOI: 10.1038/s41467-021-27345-x] [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: 04/07/2021] [Accepted: 11/08/2021] [Indexed: 01/10/2023] Open
Abstract
Silencing of a subset of germline genes is dependent upon DNA methylation (DNAme) post-implantation. However, these genes are generally hypomethylated in the blastocyst, implicating alternative repressive pathways before implantation. Indeed, in embryonic stem cells (ESCs), an overlapping set of genes, including germline "genome-defence" (GGD) genes, are upregulated following deletion of the H3K9 methyltransferase SETDB1 or subunits of the non-canonical PRC1 complex PRC1.6. Here, we show that in pre-implantation embryos and naïve ESCs (nESCs), hypomethylated promoters of germline genes bound by the PRC1.6 DNA-binding subunits MGA/MAX/E2F6 are enriched for RING1B-dependent H2AK119ub1 and H3K9me3. Accordingly, repression of these genes in nESCs shows a greater dependence on PRC1.6 than DNAme. In contrast, GGD genes are hypermethylated in epiblast-like cells (EpiLCs) and their silencing is dependent upon SETDB1, PRC1.6/RING1B and DNAme, with H3K9me3 and DNAme establishment dependent upon MGA binding. Thus, GGD genes are initially repressed by PRC1.6, with DNAme subsequently engaged in post-implantation embryos.
Collapse
Affiliation(s)
- Kentaro Mochizuki
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jafar Sharif
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Kenjiro Shirane
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Kousuke Uranishi
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Aaron B Bogutz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sanne M Janssen
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ayumu Suzuki
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Akihiko Okuda
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo ward, Chiba, Japan
| | - Matthew C Lorincz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
10
|
Ji G, Zhou W, Du J, Zhou J, Wu D, Zhao M, Yang L, Hao A. PCGF1 promotes epigenetic activation of stemness markers and colorectal cancer stem cell enrichment. Cell Death Dis 2021; 12:633. [PMID: 34148069 PMCID: PMC8214626 DOI: 10.1038/s41419-021-03914-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 12/23/2022]
Abstract
Colorectal cancer (CRC) stem cells are resistant to cancer therapy and are therefore responsible for tumour progression after conventional therapy fails. However, the molecular mechanisms underlying the maintenance of stemness are poorly understood. In this study, we identified PCGF1 as a crucial epigenetic regulator that sustains the stem cell-like phenotype of CRC. PCGF1 expression was increased in CRC and was significantly correlated with cancer progression and poor prognosis in CRC patients. PCGF1 knockdown inhibited CRC stem cell proliferation and CRC stem cell enrichment. Importantly, PCGF1 silencing impaired tumour growth in vivo. Mechanistically, PCGF1 bound to the promoters of CRC stem cell markers and activated their transcription by increasing the H3K4 histone trimethylation (H3K4me3) marks and decreasing the H3K27 histone trimethylation (H3K27me3) marks on their promoters by increasing expression of the H3K4me3 methyltransferase KMT2A and the H3K27me3 demethylase KDM6A. Our findings suggest that PCGF1 is a potential therapeutic target for CRC treatment.
Collapse
Affiliation(s)
- 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, Shandong, 250012, 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, Shandong, 250012, 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, Shandong, 250012, 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, Shandong, 250012, China
| | - Dong Wu
- 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, Shandong, 250012, China
| | - Man Zhao
- 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, Shandong, 250012, China
| | - Liping Yang
- 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, Shandong, 250012, 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, Shandong, 250012, China.
| |
Collapse
|
11
|
Whiteley SL, Holleley CE, Wagner S, Blackburn J, Deveson IW, Marshall Graves JA, Georges A. Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination. PLoS Genet 2021; 17:e1009465. [PMID: 33857129 PMCID: PMC8049264 DOI: 10.1371/journal.pgen.1009465] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/03/2021] [Indexed: 12/19/2022] Open
Abstract
How temperature determines sex remains unknown. A recent hypothesis proposes that conserved cellular mechanisms (calcium and redox; 'CaRe' status) sense temperature and identify genes and regulatory pathways likely to be involved in driving sexual development. We take advantage of the unique sex determining system of the model organism, Pogona vitticeps, to assess predictions of this hypothesis. P. vitticeps has ZZ male: ZW female sex chromosomes whose influence can be overridden in genetic males by high temperatures, causing male-to-female sex reversal. We compare a developmental transcriptome series of ZWf females and temperature sex reversed ZZf females. We demonstrate that early developmental cascades differ dramatically between genetically driven and thermally driven females, later converging to produce a common outcome (ovaries). We show that genes proposed as regulators of thermosensitive sex determination play a role in temperature sex reversal. Our study greatly advances the search for the mechanisms by which temperature determines sex.
Collapse
Affiliation(s)
- Sarah L. Whiteley
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
- Australian National Wildlife Collection CSIRO National Research Collections Australia, Canberra, Australia
| | - Clare E. Holleley
- Australian National Wildlife Collection CSIRO National Research Collections Australia, Canberra, Australia
| | - Susan Wagner
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - James Blackburn
- Garvan Institute of Medical Research, Sydney, Australia
- St. Vincent’s Clinical School, UNSW, Sydney, Australia
| | - Ira W. Deveson
- Garvan Institute of Medical Research, Sydney, Australia
- St. Vincent’s Clinical School, UNSW, Sydney, Australia
| | - Jennifer A. Marshall Graves
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
- Latrobe University, Melbourne, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| |
Collapse
|
12
|
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: 7] [Impact Index Per Article: 1.8] [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
|
13
|
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: 1.2] [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
|
14
|
Huang X, Wei C, Li F, Jia L, Zeng P, Li J, Tan J, Sun T, Jiang S, Wang J, Tang X, Zhao Q, Liu B, Rong L, Li C, Ding J. PCGF6 regulates stem cell pluripotency as a transcription activator via super-enhancer dependent chromatin interactions. Protein Cell 2019; 10:709-725. [PMID: 31041782 PMCID: PMC6776568 DOI: 10.1007/s13238-019-0629-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/15/2019] [Indexed: 02/04/2023] Open
Abstract
Polycomb group (PcG) ring finger protein 6 (PCGF6), though known as a member of the transcription-repressing complexes, PcG, also has activation function in regulating pluripotency gene expression. However, the mechanism underlying the activation function of PCGF6 is poorly understood. Here, we found that PCGF6 co-localizes to gene activation regions along with pluripotency factors such as OCT4. In addition, PCGF6 was recruited to a subset of the super-enhancer (SE) regions upstream of cell cycle-associated genes by OCT4, and increased their expression. By combining with promoter capture Hi-C data, we found that PCGF6 activates cell cycle genes by regulating SE-promoter interactions via 3D chromatin. Our findings highlight a novel mechanism of PcG protein in regulating pluripotency, and provide a research basis for the therapeutic application of pluripotent stem cells.
Collapse
Affiliation(s)
- Xiaona Huang
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China.,Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.,Program in Stem Cell and Regenerative Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Chao Wei
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China.,Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.,Program in Stem Cell and Regenerative Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Fenjie Li
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China.,Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.,Program in Stem Cell and Regenerative Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Lumeng Jia
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Pengguihang Zeng
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China.,Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jiahe Li
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China.,Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jin Tan
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China.,Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Tuanfeng Sun
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China.,Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Shaoshuai Jiang
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China.,Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jia Wang
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China.,Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xiuxiao Tang
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China.,Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Qingquan Zhao
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China.,Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Bin Liu
- Department of Spine Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Limin Rong
- Department of Spine Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Junjun Ding
- RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China. .,Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, 510080, China. .,Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,Program in Stem Cell and Regenerative Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China. .,Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
| |
Collapse
|
15
|
Scelfo A, Fernández-Pérez D, Tamburri S, Zanotti M, Lavarone E, Soldi M, Bonaldi T, Ferrari KJ, Pasini D. Functional Landscape of PCGF Proteins Reveals Both RING1A/B-Dependent-and RING1A/B-Independent-Specific Activities. Mol Cell 2019; 74:1037-1052.e7. [PMID: 31029542 PMCID: PMC6561742 DOI: 10.1016/j.molcel.2019.04.002] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/22/2019] [Accepted: 03/28/2019] [Indexed: 01/24/2023]
Abstract
Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) control cell identity by establishing facultative heterochromatin repressive domains at common sets of target genes. PRC1, which deposits H2Aub1 through the E3 ligases RING1A/B, forms six biochemically distinct subcomplexes depending on the assembled PCGF protein (PCGF1–PCGF6); however, it is yet unclear whether these subcomplexes have also specific activities. Here we show that PCGF1 and PCGF2 largely compensate for each other, while other PCGF proteins have high levels of specificity for distinct target genes. PCGF2 associates with transcription repression, whereas PCGF3 and PCGF6 associate with actively transcribed genes. Notably, PCGF3 and PCGF6 complexes can assemble and be recruited to several active sites independently of RING1A/B activity (therefore, of PRC1). For chromatin recruitment, the PCGF6 complex requires the combinatorial activities of its MGA-MAX and E2F6-DP1 subunits, while PCGF3 requires an interaction with the USF1 DNA binding transcription factor. PRC1 complexes retain high target specificity with little compensatory functions PCGF2 defines repressive signatures and PCGF3 and PCGF6 transcription active states RING1A/B is dispensable for the assembly and recruitment of PCGF3 and PCGF6 complexes PCGF3 and PCGF6 complexes bind target genes through specific DNA binding activities
Collapse
Affiliation(s)
- Andrea Scelfo
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Daniel Fernández-Pérez
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via A. di Rudinì, 8, 20142 Milan, Italy
| | - Simone Tamburri
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Marika Zanotti
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Elisa Lavarone
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Monica Soldi
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Karin Johanna Ferrari
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy.
| | - Diego Pasini
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via A. di Rudinì, 8, 20142 Milan, Italy.
| |
Collapse
|
16
|
Loubiere V, Martinez AM, Cavalli G. Cell Fate and Developmental Regulation Dynamics by Polycomb Proteins and 3D Genome Architecture. Bioessays 2019; 41:e1800222. [PMID: 30793782 DOI: 10.1002/bies.201800222] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/22/2018] [Indexed: 12/14/2022]
Abstract
Targeted transitions in chromatin states at thousands of genes are essential drivers of eukaryotic development. Therefore, understanding the in vivo dynamics of epigenetic regulators is crucial for deciphering the mechanisms underpinning cell fate decisions. This review illustrates how, in addition to its cell memory function, the Polycomb group of transcriptional regulators orchestrates temporal, cell and tissue-specific expression of master genes during development. These highly sophisticated developmental transitions are dependent on the context- and tissue-specific assembly of the different types of Polycomb Group (PcG) complexes, which regulates their targeting and/or activities on chromatin. Here, an overview is provided of how PcG complexes function at multiple scales to regulate transcription, local chromatin environment, and higher order structures that support normal differentiation and are perturbed in tumorigenesis.
Collapse
Affiliation(s)
- Vincent Loubiere
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, 34396, Montpellier, France
| | - Anne-Marie Martinez
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, 34396, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, 34396, Montpellier, France
| |
Collapse
|
17
|
Isshiki Y, Iwama A. Emerging role of noncanonical polycomb repressive complexes in normal and malignant hematopoiesis. Exp Hematol 2018; 68:10-14. [DOI: 10.1016/j.exphem.2018.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/17/2018] [Accepted: 10/19/2018] [Indexed: 12/09/2022]
|
18
|
From Flies to Mice: The Emerging Role of Non-Canonical PRC1 Members in Mammalian Development. EPIGENOMES 2018. [DOI: 10.3390/epigenomes2010004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
|
19
|
Stielow B, Finkernagel F, Stiewe T, Nist A, Suske G. MGA, L3MBTL2 and E2F6 determine genomic binding of the non-canonical Polycomb repressive complex PRC1.6. PLoS Genet 2018; 14:e1007193. [PMID: 29381691 PMCID: PMC5806899 DOI: 10.1371/journal.pgen.1007193] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/09/2018] [Accepted: 01/09/2018] [Indexed: 02/02/2023] Open
Abstract
Diverse Polycomb repressive complexes 1 (PRC1) play essential roles in gene regulation, differentiation and development. Six major groups of PRC1 complexes that differ in their subunit composition have been identified in mammals. How the different PRC1 complexes are recruited to specific genomic sites is poorly understood. The Polycomb Ring finger protein PCGF6, the transcription factors MGA and E2F6, and the histone-binding protein L3MBTL2 are specific components of the non-canonical PRC1.6 complex. In this study, we have investigated their role in genomic targeting of PRC1.6. ChIP-seq analysis revealed colocalization of MGA, L3MBTL2, E2F6 and PCGF6 genome-wide. Ablation of MGA in a human cell line by CRISPR/Cas resulted in complete loss of PRC1.6 binding. Rescue experiments revealed that MGA recruits PRC1.6 to specific loci both by DNA binding-dependent and by DNA binding-independent mechanisms. Depletion of L3MBTL2 and E2F6 but not of PCGF6 resulted in differential, locus-specific loss of PRC1.6 binding illustrating that different subunits mediate PRC1.6 loading to distinct sets of promoters. Mga, L3mbtl2 and Pcgf6 colocalize also in mouse embryonic stem cells, where PRC1.6 has been linked to repression of germ cell-related genes. Our findings unveil strikingly different genomic recruitment mechanisms of the non-canonical PRC1.6 complex, which specify its cell type- and context-specific regulatory functions. Polycomb group proteins assemble in two major repressive multi-subunit complexes (PRC1 and PRC2), which play important roles in many physiological processes, including stem cell maintenance, differentiation, cell cycle control and cancer. In mammals, six different groups of PRC1 complexes exist (PRC1.1 to PRC1.6), which differ in their subunit composition. The mechanisms that target the different PRC1 complexes to specific genomic sites appear diverse and are poorly understood. In this study, we have investigated the genomic targeting mechanisms of the non-canonical PRC1.6 complex. In PRC1.6, the defining subunit PCGF6 is specifically associated with several proteins including the transcription factors MGA and E2F6, and the histone-binding protein L3MBTL2. We found that MGA is absolutely essential for targeting PRC1.6. MGA executes recruitment of PRC1.6 to its target sites through two distinct functions. On the one hand it acts as a sequence-specific DNA-binding factor; on the other hand it has a scaffolding function, which is independent of its DNA binding capacity. E2F6 and L3MBTL2 are also important in genomic targeting of PRC1.6 as they promote binding of PRC1.6 to different sets of genes associated with distinct functions. Our finding that different components specify loading of PRC1.6 to distinct sets of genes could establish a paradigm for other chromatin-associated complexes.
Collapse
Affiliation(s)
- Bastian Stielow
- Institute of Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, Marburg, Germany
| | - Florian Finkernagel
- Institute of Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Center for Tumor Biology and Immunology (ZTI), Philipps-University of Marburg, Marburg, Germany
| | - Andrea Nist
- Genomics Core Facility, Center for Tumor Biology and Immunology (ZTI), Philipps-University of Marburg, Marburg, Germany
| | - Guntram Suske
- Institute of Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, Marburg, Germany
- * E-mail:
| |
Collapse
|
20
|
Endoh M, Endo TA, Shinga J, Hayashi K, Farcas A, Ma KW, Ito S, Sharif J, Endoh T, Onaga N, Nakayama M, Ishikura T, Masui O, Kessler BM, Suda T, Ohara O, Okuda A, Klose R, Koseki H. PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germ cell-related genes. eLife 2017; 6:21064. [PMID: 28304275 PMCID: PMC5375644 DOI: 10.7554/elife.21064] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 03/15/2017] [Indexed: 12/22/2022] Open
Abstract
The ring finger protein PCGF6 (polycomb group ring finger 6) interacts with RING1A/B and E2F6 associated factors to form a non-canonical PRC1 (polycomb repressive complex 1) known as PCGF6-PRC1. Here, we demonstrate that PCGF6-PRC1 plays a role in repressing a subset of PRC1 target genes by recruiting RING1B and mediating downstream mono-ubiquitination of histone H2A. PCGF6-PRC1 bound loci are highly enriched for promoters of germ cell-related genes in mouse embryonic stem cells (ESCs). Conditional ablation of Pcgf6 in ESCs leads to robust de-repression of such germ cell-related genes, in turn affecting cell growth and viability. We also find a role for PCGF6 in pre- and peri-implantation mouse embryonic development. We further show that a heterodimer of the transcription factors MAX and MGA recruits PCGF6 to target loci. PCGF6 thus links sequence specific target recognition by the MAX/MGA complex to PRC1-dependent transcriptional silencing of germ cell-specific genes in pluripotent stem cells.
Collapse
Affiliation(s)
- Mitsuhiro Endoh
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan.,Centre for Translational Medicine,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan.,Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jun Shinga
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Katsuhiko Hayashi
- Department of Developmental Stem Cell Biology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Anca Farcas
- Department of Biochemistry, Oxford University, Oxford, United Kingdom
| | - Kit-Wan Ma
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan
| | - Jafar Sharif
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan
| | - Tamie Endoh
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Centre for Translational Medicine,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Naoko Onaga
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Manabu Nakayama
- Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Tomoyuki Ishikura
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Osamu Masui
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Benedikt M Kessler
- Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Toshio Suda
- Centre for Translational Medicine,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Akihiko Okuda
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| | - Robert Klose
- Department of Biochemistry, Oxford University, Oxford, United Kingdom
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan
| |
Collapse
|
21
|
Manna A, Banerjee S, Khan P, Bhattacharya A, Das T. Contribution of nuclear events in generation and maintenance of cancer stem cells: revisiting chemo-resistance. THE NUCLEUS 2017. [DOI: 10.1007/s13237-017-0193-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
|
22
|
Zhao W, Tong H, Huang Y, Yan Y, Teng H, Xia Y, Jiang Q, Qin J. Essential Role for Polycomb Group Protein Pcgf6 in Embryonic Stem Cell Maintenance and a Noncanonical Polycomb Repressive Complex 1 (PRC1) Integrity. J Biol Chem 2017; 292:2773-2784. [PMID: 28049731 DOI: 10.1074/jbc.m116.763961] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/29/2016] [Indexed: 11/06/2022] Open
Abstract
The Polycomb group (PcG) proteins have an important role in controlling the expression of key genes implicated in embryonic development, differentiation, and decision of cell fates. Emerging evidence suggests that Polycomb repressive complexes 1 (PRC1) is defined by the six Polycomb group RING finger protein (Pcgf) paralogs, and Pcgf proteins can assemble into noncanonical PRC1 complexes. However, little is known about the precise mechanisms of differently composed noncanonical PRC1 in the maintenance of the pluripotent cell state. Here we disrupt the Pcgf genes in mouse embryonic stem cells by CRISPR-Cas9 and find Pcgf6 null embryonic stem cells display severe defects in self-renewal and differentiation. Furthermore, Pcgf6 regulates genes mostly involved in differentiation and spermatogenesis by assembling a noncanonical PRC1 complex PRC1.6. Notably, Pcgf6 deletion causes a dramatic decrease in PRC1.6 binding to target genes and no loss of H2AK119ub1. Thus, Pcgf6 is essential for recruitment of PRC1.6 to chromatin. Our results reveal a previously uncharacterized, H2AK119ub1-independent chromatin assembly associated with PRC1.6 complex.
Collapse
Affiliation(s)
- Wukui Zhao
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing 210061, China
| | - Huan Tong
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing 210061, China
| | - Yikai Huang
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing 210061, China
| | - Yun Yan
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing 210061, China
| | - Huajian Teng
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing 210061, China
| | - Yin Xia
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China, and
| | - Qing Jiang
- Department of Sports Medicine and Adult Reconstructive Surgery, Nanjing Drum Tower Hospital Affiliated to Medical School of Nanjing University, Nanjing 210008, China
| | - Jinzhong Qin
- From the MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing Biomedical Research Institute, Nanjing University, Nanjing 210061, China,
| |
Collapse
|
23
|
The Transcriptional Repressor Polycomb Group Factor 6, PCGF6, Negatively Regulates Dendritic Cell Activation and Promotes Quiescence. Cell Rep 2016; 16:1829-37. [PMID: 27498878 DOI: 10.1016/j.celrep.2016.07.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 05/25/2016] [Accepted: 07/13/2016] [Indexed: 11/20/2022] Open
Abstract
Pro-inflammatory signals provided by the microenvironment are critical to activate dendritic cells (DCs), components of the innate immune system that shape both innate and adaptive immunity. However, to prevent inappropriate immune activation, mechanisms must be in place to restrain DC activation to ensure DCs are activated only once sufficient stimuli have been received. Here, we report that DC activation and immunogenicity are regulated by the transcriptional repressor Polycomb group factor 6 (PCGF6). Pcgf6 is rapidly downregulated upon stimulation, and this downregulation is necessary to permit full DC activation. Silencing PCGF6 expression enhanced both spontaneous and stimulated DC activation. We show that PCGF6 associates with the H3K4me3 demethylase JARID1c, and together, they negatively regulate H3K4me3 levels in DCs. Our results identify two key regulators, PCGF6 and JARID1c that temper DC activation and implicate active transcriptional silencing via histone demethylation as a previously unappreciated mechanism for regulating DC activation and quiescence.
Collapse
|