1
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Policarpi C, Munafò M, Tsagkris S, Carlini V, Hackett JA. Systematic epigenome editing captures the context-dependent instructive function of chromatin modifications. Nat Genet 2024; 56:1168-1180. [PMID: 38724747 PMCID: PMC11176084 DOI: 10.1038/s41588-024-01706-w] [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: 09/02/2022] [Accepted: 03/05/2024] [Indexed: 05/22/2024]
Abstract
Chromatin modifications are linked with regulating patterns of gene expression, but their causal role and context-dependent impact on transcription remains unresolved. Here we develop a modular epigenome editing platform that programs nine key chromatin modifications, or combinations thereof, to precise loci in living cells. We couple this with single-cell readouts to systematically quantitate the magnitude and heterogeneity of transcriptional responses elicited by each specific chromatin modification. Among these, we show that installing histone H3 lysine 4 trimethylation (H3K4me3) at promoters can causally instruct transcription by hierarchically remodeling the chromatin landscape. We further dissect how DNA sequence motifs influence the transcriptional impact of chromatin marks, identifying switch-like and attenuative effects within distinct cis contexts. Finally, we examine the interplay of combinatorial modifications, revealing that co-targeted H3K27 trimethylation (H3K27me3) and H2AK119 monoubiquitination (H2AK119ub) maximizes silencing penetrance across single cells. Our precision-perturbation strategy unveils the causal principles of how chromatin modification(s) influence transcription and dissects how quantitative responses are calibrated by contextual interactions.
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Affiliation(s)
- Cristina Policarpi
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Marzia Munafò
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Stylianos Tsagkris
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Valentina Carlini
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
- Faculty of Biosciences, EMBL and Heidelberg University, Heidelberg, Germany
| | - Jamie A Hackett
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy.
- Genome Biology Unit, EMBL, Heidelberg, Germany.
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2
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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.
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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
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3
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Li Y, Mo Y, Chen C, He J, Guo Z. Research advances of polycomb group proteins in regulating mammalian development. Front Cell Dev Biol 2024; 12:1383200. [PMID: 38505258 PMCID: PMC10950033 DOI: 10.3389/fcell.2024.1383200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
Polycomb group (PcG) proteins are a subset of epigenetic factors that are highly conserved throughout evolution. In mammals, PcG proteins can be classified into two muti-proteins complexes: Polycomb repressive complex 1 (PRC1) and PRC2. Increasing evidence has demonstrated that PcG complexes play critical roles in the regulation of gene expression, genomic imprinting, chromosome X-inactivation, and chromatin structure. Accordingly, the dysfunction of PcG proteins is tightly orchestrated with abnormal developmental processes. Here, we summarized and discussed the current knowledge of the biochemical and molecular functions of PcG complexes, especially the PRC1 and PRC2 in mammalian development including embryonic development and tissue development, which will shed further light on the deep understanding of the basic knowledge of PcGs and their functions for reproductive health and developmental disorders.
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Affiliation(s)
| | | | | | - Jin He
- Department of Obstetrics and Gynecology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhiheng Guo
- Department of Obstetrics and Gynecology, The First Hospital of Jilin University, Changchun, Jilin, China
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4
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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.
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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.
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5
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Ke D, Guo HH, Jiang N, Shi RS, Fan TY. Inhibition of UFM1 expression suppresses cancer progression and is linked to the dismal prognosis and immune infiltration in oral squamous cell carcinoma. Aging (Albany NY) 2023; 15:13059-13076. [PMID: 37980168 DOI: 10.18632/aging.205219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 10/17/2023] [Indexed: 11/20/2023]
Abstract
BACKGROUND Ubiquitin fold modifier 1 (UFM1) overexpression is associated with cancer cell proliferation, migration and invasion. However, the roles and pathways of UFM1 in oral squamous cell carcinoma (OSCC) has remained undefined. METHODS The expression of UFM1 and the relationship between UFM1 expression and prognosis were investigated using data of OSCC patients from The Cancer Genome Atlas (TCGA) database. The UFM1 co-expressed genes, and the association between the UFM1 expression and immune cells and ubiquitination were explored. The effects of UFM1 expression on the growth and migration of OSCC cells were investigated by siRNA interference, Cell Counting Kit-8 (CCK-8), Transwell, Western blotting, and wound healing experiments. RESULTS UFM1 was highly expressed in OSCC. UFM1 overexpression was associated with short overall survival, disease-specific survival, and progression-free interval, and was an adverse factor for prognosis in OSCC. UFM1-related nomograms were significantly associated with poor prognosis in OSCC patients. Decreased UFM1 expression could inhibit the proliferation, migration, and invasion of OSCC cells. UFM1 was associated with the immune cells (such as the Th17 cells, T helper cells, and cytotoxic cells) and ubiquitination. CONCLUSION Elevated UFM1 expression was associated with poor prognosis, ubiquitination and immune infiltration in OSCC, and inhibition of UFM1 expression delayed OSCC progression, showing that UFM1 could be a biomarker for prognosis and treating OSCC patients.
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Affiliation(s)
- Di Ke
- Department of Radiology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Hao-Han Guo
- Department of Stomatology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Ni Jiang
- Department of Obstetrics and Gynecology, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Rong-Shu Shi
- Department of Radiology, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Teng-Yang Fan
- Department of General Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
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6
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Yakhou L, Azogui A, Gupta N, Richard Albert J, Miura F, Ferry L, Yamaguchi K, Battault S, Therizols P, Bonhomme F, Bethuel E, Sarkar A, Greenberg MC, Arimondo P, Cristofari G, Kirsh O, Ito T, Defossez PA. A genetic screen identifies BEND3 as a regulator of bivalent gene expression and global DNA methylation. Nucleic Acids Res 2023; 51:10292-10308. [PMID: 37650637 PMCID: PMC10602864 DOI: 10.1093/nar/gkad719] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/20/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023] Open
Abstract
Epigenetic mechanisms are essential to establish and safeguard cellular identities in mammals. They dynamically regulate the expression of genes, transposable elements and higher-order chromatin structures. Consequently, these chromatin marks are indispensable for mammalian development and alterations often lead to disease, such as cancer. Bivalent promoters are especially important during differentiation and development. Here we used a genetic screen to identify new regulators of a bivalent repressed gene. We identify BEND3 as a regulator of hundreds of bivalent promoters, some of which it represses, and some of which it activates. We show that BEND3 is recruited to a CpG-containg consensus site that is present in multiple copies in many bivalent promoters. Besides having direct effect on the promoters it binds, the loss of BEND3 leads to genome-wide gains of DNA methylation, which are especially marked at regions normally protected by the TET enzymes. DNA hydroxymethylation is reduced in Bend3 mutant cells, possibly as consequence of altered gene expression leading to diminished alpha-ketoglutarate production, thus lowering TET activity. Our results clarify the direct and indirect roles of an important chromatin regulator, BEND3, and, more broadly, they shed light on the regulation of bivalent promoters.
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Affiliation(s)
- Lounis Yakhou
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | - Anaelle Azogui
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | - Nikhil Gupta
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | | | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka 812-8582, Japan
| | - Laure Ferry
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | - Kosuke Yamaguchi
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | - Sarah Battault
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | - Pierre Therizols
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | - Frédéric Bonhomme
- Institut Pasteur, Université Paris Cité, CNRS, Epigenetic Chemical Biology, UMR 3523, F-75724 Paris, France
| | - Elouan Bethuel
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | - Arpita Sarkar
- Université Côte d’Azur, Inserm, CNRS, IRCAN, Nice, France
| | | | - Paola B Arimondo
- Institut Pasteur, Université Paris Cité, CNRS, Epigenetic Chemical Biology, UMR 3523, F-75724 Paris, France
| | | | - Olivier Kirsh
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013 Paris, France
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka 812-8582, Japan
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7
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Hu M, Schultz RM, Namekawa SH. Epigenetic programming in the ovarian reserve. Bioessays 2023; 45:e2300069. [PMID: 37417392 PMCID: PMC10698196 DOI: 10.1002/bies.202300069] [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: 04/18/2023] [Revised: 06/02/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023]
Abstract
The ovarian reserve defines female reproductive lifespan, which in humans spans decades. The ovarian reserve consists of oocytes residing in primordial follicles arrested in meiotic prophase I and is maintained independent of DNA replication and cell proliferation, thereby lacking stem cell-based maintenance. Largely unknown is how cellular states of the ovarian reserve are established and maintained for decades. Our recent study revealed that a distinct chromatin state is established during ovarian reserve formation in mice, uncovering a novel window of epigenetic programming in female germline development. We showed that an epigenetic regulator, Polycomb Repressive Complex 1 (PRC1), establishes a repressive chromatin state in perinatal mouse oocytes that is essential for prophase I-arrested oocytes to form the ovarian reserve. Here we discuss the biological roles and mechanisms underlying epigenetic programming in ovarian reserve formation, highlighting current knowledge gaps and emerging research areas in female reproductive biology.
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Affiliation(s)
- Mengwen Hu
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA
| | - Richard M. Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Satoshi H. Namekawa
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA
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8
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Gupta N, Yakhou L, Albert JR, Azogui A, Ferry L, Kirsh O, Miura F, Battault S, Yamaguchi K, Laisné M, Domrane C, Bonhomme F, Sarkar A, Delagrange M, Ducos B, Cristofari G, Ito T, Greenberg MVC, Defossez PA. A genome-wide screen reveals new regulators of the 2-cell-like cell state. Nat Struct Mol Biol 2023; 30:1105-1118. [PMID: 37488355 DOI: 10.1038/s41594-023-01038-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/19/2023] [Indexed: 07/26/2023]
Abstract
In mammals, only the zygote and blastomeres of the early embryo are totipotent. This totipotency is mirrored in vitro by mouse '2-cell-like cells' (2CLCs), which appear at low frequency in cultures of embryonic stem cells (ESCs). Because totipotency is not completely understood, we carried out a genome-wide CRISPR knockout screen in mouse ESCs, searching for mutants that reactivate the expression of Dazl, a gene expressed in 2CLCs. Here we report the identification of four mutants that reactivate Dazl and a broader 2-cell-like signature: the E3 ubiquitin ligase adaptor SPOP, the Zinc-Finger transcription factor ZBTB14, MCM3AP, a component of the RNA processing complex TREX-2, and the lysine demethylase KDM5C. All four factors function upstream of DPPA2 and DUX, but not via p53. In addition, SPOP binds DPPA2, and KDM5C interacts with ncPRC1.6 and inhibits 2CLC gene expression in a catalytic-independent manner. These results extend our knowledge of totipotency, a key phase of organismal life.
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Affiliation(s)
- Nikhil Gupta
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France.
- Joint AZ CRUK Functional Genomics Centre, The Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
| | - Lounis Yakhou
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | | | - Anaelle Azogui
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Laure Ferry
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Olivier Kirsh
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, Japan
| | - Sarah Battault
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Kosuke Yamaguchi
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Marthe Laisné
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Cécilia Domrane
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Frédéric Bonhomme
- Epigenetic Chemical Biology, UMR3523, Institut Pasteur, Université Paris Cité, CNRS, Paris, France
| | - Arpita Sarkar
- IRCAN, Université Côte d'Azur, Inserm, CNRS, Nice, France
| | - Marine Delagrange
- High Throughput qPCR Facility, Institut de Biologie de l'École Normale Supérieure (IBENS), Laboratoire de Physique de l'ENS CNRS UMR8023, PSL Research University, Paris, France
| | - Bertrand Ducos
- High Throughput qPCR Facility, Institut de Biologie de l'École Normale Supérieure (IBENS), Laboratoire de Physique de l'ENS CNRS UMR8023, PSL Research University, Paris, France
| | | | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, Japan
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9
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Aristodemou AEN, Rueda DS, Taylor GP, Bangham CRM. The transcriptome of HTLV-1-infected primary cells following reactivation reveals changes to host gene expression central to the proviral life cycle. PLoS Pathog 2023; 19:e1011494. [PMID: 37523412 PMCID: PMC10431621 DOI: 10.1371/journal.ppat.1011494] [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: 01/16/2023] [Revised: 08/16/2023] [Accepted: 06/19/2023] [Indexed: 08/02/2023] Open
Abstract
Infections by Human T cell Leukaemia Virus type 1 (HTLV-1) persist for the lifetime of the host by integrating into the genome of CD4+ T cells. Proviral gene expression is essential for proviral survival and the maintenance of the proviral load, through the pro-proliferative changes it induces in infected cells. Despite their role in HTLV-1 infection and a persistent cytotoxic T lymphocyte response raised against the virus, proviral transcripts from the sense-strand are rarely detected in fresh cells extracted from the peripheral blood, and have recently been found to be expressed intermittently by a small subset of cells at a given time. Ex vivo culture of infected cells prompts synchronised proviral expression in infected cells from peripheral blood, allowing the study of factors involved in reactivation in primary cells. Here, we used bulk RNA-seq to examine the host transcriptome over six days in vitro, following proviral reactivation in primary peripheral CD4+ T cells isolated from subjects with non-malignant HTLV-1 infection. Infected cells displayed a conserved response to reactivation, characterised by discrete stages of gene expression, cell division and subsequently horizontal transmission of the virus. We observed widespread changes in Polycomb gene expression following reactivation, including an increase in PRC2 transcript levels and diverse changes in the expression of PRC1 components. We hypothesize that these transcriptional changes constitute a negative feedback loop that maintains proviral latency by re-deposition of H2AK119ub1 following the end of proviral expression. Using RNAi, we found that certain deubiquitinases, BAP1, USP14 and OTUD5 each promote proviral transcription. These data demonstrate the detailed trajectory of HTLV-1 proviral reactivation in primary HTLV-1-carrier lymphocytes and the impact on the host cell.
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Affiliation(s)
- Aris E. N. Aristodemou
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - David S. Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, United Kingdom
| | - Graham P. Taylor
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Charles R. M. Bangham
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
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10
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Al Adhami H, Vallet J, Schaal C, Schumacher P, Bardet AF, Dumas M, Chicher J, Hammann P, Daujat S, Weber M. Systematic identification of factors involved in the silencing of germline genes in mouse embryonic stem cells. Nucleic Acids Res 2023; 51:3130-3149. [PMID: 36772830 PMCID: PMC10123117 DOI: 10.1093/nar/gkad071] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 12/29/2022] [Accepted: 01/23/2023] [Indexed: 02/12/2023] Open
Abstract
In mammals, many germline genes are epigenetically repressed to prevent their illegitimate expression in somatic cells. To advance our understanding of the mechanisms restricting the expression of germline genes, we analyzed their chromatin signature and performed a CRISPR-Cas9 knock-out screen for genes involved in germline gene repression using a Dazl-GFP reporter system in mouse embryonic stem cells (mESCs). We show that the repression of germline genes mainly depends on the polycomb complex PRC1.6 and DNA methylation, which function additively in mESCs. Furthermore, we validated novel genes involved in the repression of germline genes and characterized three of them: Usp7, Shfm1 (also known as Sem1) and Erh. Inactivation of Usp7, Shfm1 or Erh led to the upregulation of germline genes, as well as retrotransposons for Shfm1, in mESCs. Mechanistically, USP7 interacts with PRC1.6 components, promotes PRC1.6 stability and presence at germline genes, and facilitates DNA methylation deposition at germline gene promoters for long term repression. Our study provides a global view of the mechanisms and novel factors required for silencing germline genes in embryonic stem cells.
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Affiliation(s)
- Hala Al Adhami
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Judith Vallet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Celia Schaal
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Paul Schumacher
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France.,Karlsruhe Institute of Technology (KIT), IAB, Department of Food Chemistry and Toxicology, 76131 Karlsruhe, Germany
| | - Anaïs Flore Bardet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Michael Dumas
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg Esplanade, CNRS, University of Strasbourg, 67000 Strasbourg, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade, CNRS, University of Strasbourg, 67000 Strasbourg, France
| | - Sylvain Daujat
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Michael Weber
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
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11
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Hanot M, Raby L, Völkel P, Le Bourhis X, Angrand PO. The Contribution of the Zebrafish Model to the Understanding of Polycomb Repression in Vertebrates. Int J Mol Sci 2023; 24:ijms24032322. [PMID: 36768643 PMCID: PMC9916924 DOI: 10.3390/ijms24032322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/26/2023] Open
Abstract
Polycomb group (PcG) proteins are highly conserved proteins assembled into two major types of complexes, PRC1 and PRC2, involved in the epigenetic silencing of a wide range of gene expression programs regulating cell fate and tissue development. The crucial role of PRC1 and PRC2 in the fundamental cellular processes and their involvement in human pathologies such as cancer attracted intense attention over the last few decades. Here, we review recent advancements regarding PRC1 and PRC2 function using the zebrafish model. We point out that the unique characteristics of the zebrafish model provide an exceptional opportunity to increase our knowledge of the role of the PRC1 and PRC2 complexes in tissue development, in the maintenance of organ integrity and in pathology.
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Affiliation(s)
- Mariette Hanot
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Ludivine Raby
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Pamela Völkel
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Xuefen Le Bourhis
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Pierre-Olivier Angrand
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
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12
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Ahn HW, Worman ZF, Lechsinska A, Payer LM, Wang T, Malik N, Li W, Burns KH, Nath A, Levin HL. Retrotransposon insertions associated with risk of neurologic and psychiatric diseases. EMBO Rep 2023; 24:e55197. [PMID: 36367221 PMCID: PMC9827563 DOI: 10.15252/embr.202255197] [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: 04/08/2022] [Revised: 10/11/2022] [Accepted: 10/20/2022] [Indexed: 11/13/2022] Open
Abstract
Transposable elements (TEs) are active in neuronal cells raising the question whether TE insertions contribute to risk of neuropsychiatric disease. While genome-wide association studies (GWAS) serve as a tool to discover genetic loci associated with neuropsychiatric diseases, unfortunately GWAS do not directly detect structural variants such as TEs. To examine the role of TEs in psychiatric and neurologic disease, we evaluated 17,000 polymorphic TEs and find 76 are in linkage disequilibrium with disease haplotypes (P < 10-6 ) defined by GWAS. From these 76 polymorphic TEs, we identify potentially causal candidates based on having insertions in genomic regions of regulatory chromatin and on having associations with altered gene expression in brain tissues. We show that lead candidate insertions have regulatory effects on gene expression in human neural stem cells altering the activity of a minimal promoter. Taken together, we identify 10 polymorphic TE insertions that are potential candidates on par with other variants for having a causal role in neurologic and psychiatric disorders.
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Affiliation(s)
- Hyo Won Ahn
- Division of Molecular and Cellular BiologyEunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaMDUSA
| | - Zelia F Worman
- Division of Molecular and Cellular BiologyEunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaMDUSA
- Present address:
Seven BridgesCharlestownMAUSA
| | - Arianna Lechsinska
- Division of Molecular and Cellular BiologyEunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaMDUSA
| | - Lindsay M Payer
- Department of PathologyJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Tongguang Wang
- Translational Neuroscience CenterNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
| | - Nasir Malik
- Translational Neuroscience CenterNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
| | - Wenxue Li
- Section of Infections of the Nervous SystemNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
| | - Kathleen H Burns
- Department of Oncologic PathologyDana‐Farber Cancer InstituteBostonMAUSA
| | - Avindra Nath
- Translational Neuroscience CenterNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
- Section of Infections of the Nervous SystemNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
| | - Henry L Levin
- Division of Molecular and Cellular BiologyEunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaMDUSA
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13
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Ito T, Ohta M, Osada A, Nishiyama A, Ishiguro KI, Tamura T, Sekita Y, Kimura T. Switching defective/sucrose non-fermenting chromatin remodeling complex coordinates meiotic gene activation via promoter remodeling and Meiosin activation in female germline. Genes Cells 2023; 28:15-28. [PMID: 36371617 DOI: 10.1111/gtc.12990] [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: 09/26/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/15/2022]
Abstract
In mammals, primordial germ cells (PGCs) enter meiosis and differentiate into primary oocytes in embryonic ovaries. Previously, we demonstrated that meiotic gene induction and meiotic initiation were impaired in female germline cells of conditional knockout (CKO) mice lacking the Smarcb1 (Snf5) gene, which encodes a core subunit of the switching defective/sucrose non-fermenting (SWI/SNF) complex. In this study, we classified meiotic genes expressed at lower levels in Snf5 CKO females into two groups based on promoter accessibility. The promoters of 74% of these genes showed lower accessibility in mutant mice, whereas those of the remaining genes were opened without the SWI/SNF complex. Notably, the former genes included Meiosin, which encodes a transcriptional regulator essential for meiotic gene activation. The promoters of the former and the latter genes were mainly modified with H3K27me3/bivalent and H3K4me3 histone marks, respectively. A subset of the former genes was precociously activated in female PGCs deficient in polycomb repressive complexes (PRCs). Our results point to a mechanism through which the SWI/SNF complex coordinates meiotic gene activation via the remodeling of PRC-repressed genes, including Meiosin, in female germline cells.
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Affiliation(s)
- Toshiaki Ito
- Laboratory of Stem Cell Biology, Department of Biosciences, Graduate School of Science, School of Science, Kitasato University, Sagamihara, Kanagawa, Japan
- Chitose Laboratory Corp., Biotechnology Research Center, Kawasaki, Kanagawa, Japan
| | - Masami Ohta
- Laboratory of Stem Cell Biology, Department of Biosciences, Graduate School of Science, School of Science, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Atsuki Osada
- Laboratory of Stem Cell Biology, Department of Biosciences, Graduate School of Science, School of Science, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Akira Nishiyama
- Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Kei-Ichiro Ishiguro
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Tomohiko Tamura
- Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
- Advanced Medical Research Center, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Yoichi Sekita
- Laboratory of Stem Cell Biology, Department of Biosciences, Graduate School of Science, School of Science, Kitasato University, Sagamihara, Kanagawa, Japan
| | - Tohru Kimura
- Laboratory of Stem Cell Biology, Department of Biosciences, Graduate School of Science, School of Science, Kitasato University, Sagamihara, Kanagawa, Japan
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14
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Huang Y, Roig I. Genetic control of meiosis surveillance mechanisms in mammals. Front Cell Dev Biol 2023; 11:1127440. [PMID: 36910159 PMCID: PMC9996228 DOI: 10.3389/fcell.2023.1127440] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
Meiosis is a specialized cell division that generates haploid gametes and is critical for successful sexual reproduction. During the extended meiotic prophase I, homologous chromosomes progressively pair, synapse and desynapse. These chromosomal dynamics are tightly integrated with meiotic recombination (MR), during which programmed DNA double-strand breaks (DSBs) are formed and subsequently repaired. Consequently, parental chromosome arms reciprocally exchange, ultimately ensuring accurate homolog segregation and genetic diversity in the offspring. Surveillance mechanisms carefully monitor the MR and homologous chromosome synapsis during meiotic prophase I to avoid producing aberrant chromosomes and defective gametes. Errors in these critical processes would lead to aneuploidy and/or genetic instability. Studies of mutation in mouse models, coupled with advances in genomic technologies, lead us to more clearly understand how meiosis is controlled and how meiotic errors are linked to mammalian infertility. Here, we review the genetic regulations of these major meiotic events in mice and highlight our current understanding of their surveillance mechanisms. Furthermore, we summarize meiotic prophase genes, the mutations that activate the surveillance system leading to meiotic prophase arrest in mouse models, and their corresponding genetic variants identified in human infertile patients. Finally, we discuss their value for the diagnosis of causes of meiosis-based infertility in humans.
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Affiliation(s)
- Yan Huang
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Histology Unit, Department of Cell Biology, Physiology, and Immunology, Cytology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ignasi Roig
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Histology Unit, Department of Cell Biology, Physiology, and Immunology, Cytology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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15
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Roles of Polycomb Complexes in the Reconstruction of 3D Genome Architecture during Preimplantation Embryonic Development. Genes (Basel) 2022; 13:genes13122382. [PMID: 36553649 PMCID: PMC9778514 DOI: 10.3390/genes13122382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/29/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
The appropriate deployment of developmental programs depends on complex genetic information encoded by genomic DNA sequences and their positioning and contacts in the three-dimensional (3D) space within the nucleus. Current studies using novel techniques including, but not limited to, Hi-C, ChIA-PET, and Hi-ChIP reveal that regulatory elements (Res), such as enhancers and promoters, may participate in the precise regulation of expression of tissue-specific genes important for both embryogenesis and organogenesis by recruiting Polycomb Group (PcG) complexes. PcG complexes usually poise the transcription of developmental genes by forming Polycomb bodies to compact poised enhancers and promoters marked by H3K27me3 in the 3D space. Additionally, recent studies have also uncovered their roles in transcriptional activation. To better understand the full complexities in the mechanisms of how PcG complexes regulate transcription and long-range 3D contacts of enhancers and promoters during developmental programs, we outline novel insights regarding PcG-associated dramatic changes in the 3D chromatin conformation in developmental programs of early embryos and naïve-ground-state transitions of pluripotent embryonic stem cells (ESCs), and highlight the distinct roles of unique and common subunits of canonical and non-canonical PcG complexes in shaping genome architectures and transcriptional programs.
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16
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RINGs, DUBs and Abnormal Brain Growth-Histone H2A Ubiquitination in Brain Development and Disease. EPIGENOMES 2022; 6:epigenomes6040042. [PMID: 36547251 PMCID: PMC9778336 DOI: 10.3390/epigenomes6040042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
During mammalian neurodevelopment, signaling pathways converge upon transcription factors (TFs) to establish appropriate gene expression programmes leading to the production of distinct neural and glial cell types. This process is partially regulated by the dynamic modulation of chromatin states by epigenetic systems, including the polycomb group (PcG) family of co-repressors. PcG proteins form multi-subunit assemblies that sub-divide into distinct, yet functionally related families. Polycomb repressive complexes 1 and 2 (PRC1 and 2) modify the chemical properties of chromatin by covalently modifying histone tails via H2A ubiquitination (H2AK119ub1) and H3 methylation, respectively. In contrast to the PRCs, the Polycomb repressive deubiquitinase (PR-DUB) complex removes H2AK119ub1 from chromatin through the action of the C-terminal hydrolase BAP1. Genetic screening has identified several PcG mutations that are causally associated with a range of congenital neuropathologies associated with both localised and/or systemic growth abnormalities. As PRC1 and PR-DUB hold opposing functions to control H2AK119ub1 levels across the genome, it is plausible that such neurodevelopmental disorders arise through a common mechanism. In this review, we will focus on advancements regarding the composition and opposing molecular functions of mammalian PRC1 and PR-DUB, and explore how their dysfunction contributes to the emergence of neurodevelopmental disorders.
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17
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Li L, Li P, Chen J, Li L, Shen Y, Zhu Y, Liu J, Lv L, Mao S, Chen F, Hu G, Yuan K. Rif1 interacts with non-canonical polycomb repressive complex PRC1.6 to regulate mouse embryonic stem cells fate potential. CELL REGENERATION 2022; 11:25. [PMID: 35915272 PMCID: PMC9343540 DOI: 10.1186/s13619-022-00124-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 07/05/2022] [Indexed: 11/10/2022]
Abstract
Mouse embryonic stem cells (mESCs) cycle in and out of a transient 2-cell (2C)-like totipotent state, driven by a complex genetic circuit involves both the coding and repetitive sections of the genome. While a vast array of regulators, including the multi-functional protein Rif1, has been reported to influence the switch of fate potential, how they act in concert to achieve this cellular plasticity remains elusive. Here, by modularizing the known totipotency regulatory factors, we identify an unprecedented functional connection between Rif1 and the non-canonical polycomb repressive complex PRC1.6. Downregulation of the expression of either Rif1 or PRC1.6 subunits imposes similar impacts on the transcriptome of mESCs. The LacO-LacI induced ectopic colocalization assay detects a specific interaction between Rif1 and Pcgf6, bolstering the intactness of the PRC1.6 complex. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis further reveals that Rif1 is required for the accurate targeting of Pcgf6 to a group of genomic loci encompassing many genes involved in the regulation of the 2C-like state. Depletion of Rif1 or Pcgf6 not only activates 2C genes such as Zscan4 and Zfp352, but also derepresses a group of the endogenous retroviral element MERVL, a key marker for totipotency. Collectively, our findings discover that Rif1 can serve as a novel auxiliary component in the PRC1.6 complex to restrain the genetic circuit underlying totipotent fate potential, shedding new mechanistic insights into its function in regulating the cellular plasticity of embryonic stem cells.
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18
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van Gelderen TA, Montfort J, Álvarez-Dios JA, Thermes V, Piferrer F, Bobe J, Ribas L. Deciphering sex-specific miRNAs as heat-recorders in zebrafish. Sci Rep 2022; 12:18722. [PMID: 36333360 PMCID: PMC9636255 DOI: 10.1038/s41598-022-21864-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
In the last decade, a plethora of microRNAs (miRNAs) has been reported in a wide variety of physiological processes, including reproduction, in many aquatic organisms. However, miRNAome alterations occurred by environmental cues due to water temperature increment have not yet been elucidated. With the aim to identify epigenetic regulations mediated by miRNAs in the gonads in a climate change scenario, the animal model zebrafish (Danio rerio) were subjected to high temperatures during sex differentiation, a treatment that results in male-skewed sex ratios in the adulthood. Once the fish reached adulthood, gonads were sequenced by high-throughput technologies and a total of 23 and 1 differentially expressed miRNAs in ovaries and testes, respectively, were identified two months after the heat treatment. Most of these heat-recorder miRNAs were involved in human sex-related cancer and about 400 predicted-target genes were obtained, some with reproduction-related functions. Their synteny in the zebrafish genome was, for more than half of the predicted target genes, in the chromosomes 7, 2, 4, 3 and 11 in the ovaries, chromosome 4 being the place where the sex-associated-region (sar) is localized in wild zebrafish. Further, spatial localization in the gonads of two selected heat-recorder miRNAs (miR-122-5p and miR-146-5p) showed exclusive expression in the ovarian germ cells. The present study expands the catalog of sex-specific miRNAs and deciphers, for the first time, thermosensitive miRNAs in the zebrafish gonads that might be used as potential epimarkers to predict environmental past events.
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Affiliation(s)
- Tosca A van Gelderen
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (ICM-CSIC), 08003, Barcelona, Spain
- PhD Program in Genetics, Autonomous University of Barcelona, 08193, Bellaterra, Spain
| | - Jérôme Montfort
- Laboratoire de Physiologie et Génomique des Poissons, INRAE, Rennes, France
| | - José Antonio Álvarez-Dios
- Departamento de Matemática Aplicada, Facultad de Matemáticas, Universidad de Santiago de Compostela, 15781, Santiago de Compostela, Spain
| | - Violette Thermes
- Laboratoire de Physiologie et Génomique des Poissons, INRAE, Rennes, France
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (ICM-CSIC), 08003, Barcelona, Spain
| | - Julien Bobe
- Laboratoire de Physiologie et Génomique des Poissons, INRAE, Rennes, France
| | - Laia Ribas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (ICM-CSIC), 08003, Barcelona, Spain.
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19
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Sijm A, Atlasi Y, van der Knaap JA, Wolf van der Meer J, Chalkley GE, Bezstarosti K, Dekkers DHW, Doff WAS, Ozgur Z, van IJcken WFJ, Demmers JAA, Verrijzer CP. USP7 regulates the ncPRC1 Polycomb axis to stimulate genomic H2AK119ub1 deposition uncoupled from H3K27me3. SCIENCE ADVANCES 2022; 8:eabq7598. [PMID: 36332031 PMCID: PMC9635827 DOI: 10.1126/sciadv.abq7598] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/16/2022] [Indexed: 05/29/2023]
Abstract
Ubiquitin-specific protease 7 (USP7) has been implicated in cancer progression and neurodevelopment. However, its molecular targets remain poorly characterized. We combined quantitative proteomics, transcriptomics, and epigenomics to define the core USP7 network. Our multi-omics analysis reveals USP7 as a control hub that links genome regulation, tumor suppression, and histone H2A ubiquitylation (H2AK119ub1) by noncanonical Polycomb-repressive complexes (ncPRC1s). USP7 strongly stabilizes ncPRC1.6 and, to a lesser extent, ncPRC1.1. Moreover, USP7 represses expression of AUTS2, which suppresses H2A ubiquitylation by ncPRC1.3/5. Collectively, these USP7 activities promote the genomic deposition of H2AK119ub1 by ncPRC1, especially at transcriptionally repressed loci. Notably, USP7-dependent changes in H2AK119ub1 levels are uncoupled from H3K27me3. Even complete loss of the PRC1 catalytic core and H2AK119ub1 has only a limited effect on H3K27me3. Besides defining the USP7 regulome, our results reveal that H2AK119ub1 dosage is largely disconnected from H3K27me3.
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Affiliation(s)
- Ayestha Sijm
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Yaser Atlasi
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
| | - Jan A. van der Knaap
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Gillian E. Chalkley
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Karel Bezstarosti
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Proteomics Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Dick H. W. Dekkers
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Proteomics Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Wouter A. S. Doff
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Proteomics Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Zeliha Ozgur
- Center for Biomics, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Jeroen A. A. Demmers
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Proteomics Center, Erasmus University Medical Center, Rotterdam, Netherlands
| | - C. Peter Verrijzer
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
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20
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Kim JJ, Kingston RE. Context-specific Polycomb mechanisms in development. Nat Rev Genet 2022; 23:680-695. [PMID: 35681061 PMCID: PMC9933872 DOI: 10.1038/s41576-022-00499-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2022] [Indexed: 12/11/2022]
Abstract
Polycomb group (PcG) proteins are crucial chromatin regulators that maintain repression of lineage-inappropriate genes and are therefore required for stable cell fate. Recent advances show that PcG proteins form distinct multi-protein complexes in various cellular environments, such as in early development, adult tissue maintenance and cancer. This surprising compositional diversity provides the basis for mechanistic diversity. Understanding this complexity deepens and refines the principles of PcG complex recruitment, target-gene repression and inheritance of memory. We review how the core molecular mechanism of Polycomb complexes operates in diverse developmental settings and propose that context-dependent changes in composition and mechanism are essential for proper epigenetic regulation in development.
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Affiliation(s)
- Jongmin J. Kim
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Robert E. Kingston
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,
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21
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Doyle EJ, Morey L, Conway E. Know when to fold 'em: Polycomb complexes in oncogenic 3D genome regulation. Front Cell Dev Biol 2022; 10:986319. [PMID: 36105358 PMCID: PMC9464936 DOI: 10.3389/fcell.2022.986319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
Chromatin is spatially and temporally regulated through a series of orchestrated processes resulting in the formation of 3D chromatin structures such as topologically associating domains (TADs), loops and Polycomb Bodies. These structures are closely linked to transcriptional regulation, with loss of control of these processes a frequent feature of cancer and developmental syndromes. One such oncogenic disruption of the 3D genome is through recurrent dysregulation of Polycomb Group Complex (PcG) functions either through genetic mutations, amplification or deletion of genes that encode for PcG proteins. PcG complexes are evolutionarily conserved epigenetic complexes. They are key for early development and are essential transcriptional repressors. PcG complexes include PRC1, PRC2 and PR-DUB which are responsible for the control of the histone modifications H2AK119ub1 and H3K27me3. The spatial distribution of the complexes within the nuclear environment, and their associated modifications have profound effects on the regulation of gene transcription and the 3D genome. Nevertheless, how PcG complexes regulate 3D chromatin organization is still poorly understood. Here we glean insights into the role of PcG complexes in 3D genome regulation and compaction, how these processes go awry during tumorigenesis and the therapeutic implications that result from our insights into these mechanisms.
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Affiliation(s)
- Emma J. Doyle
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - Lluis Morey
- Sylvester Comprehensive Cancer Centre, Miami, FL, United States
- Department of Human Genetics, Biomedical Research Building, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Eric Conway
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
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22
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De Novo Polycomb Recruitment and Repressive Domain Formation. EPIGENOMES 2022; 6:epigenomes6030025. [PMID: 35997371 PMCID: PMC9397058 DOI: 10.3390/epigenomes6030025] [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: 07/18/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022] Open
Abstract
Every cell of an organism shares the same genome; even so, each cellular lineage owns a different transcriptome and proteome. The Polycomb group proteins (PcG) are essential regulators of gene repression patterning during development and homeostasis. However, it is unknown how the repressive complexes, PRC1 and PRC2, identify their targets and elicit new Polycomb domains during cell differentiation. Classical recruitment models consider the pre-existence of repressive histone marks; still, de novo target binding overcomes the absence of both H3K27me3 and H2AK119ub. The CpG islands (CGIs), non-core proteins, and RNA molecules are involved in Polycomb recruitment. Nonetheless, it is unclear how de novo targets are identified depending on the physiological context and developmental stage and which are the leading players stabilizing Polycomb complexes at domain nucleation sites. Here, we examine the features of de novo sites and the accessory elements bridging its recruitment and discuss the first steps of Polycomb domain formation and transcriptional regulation, comprehended by the experimental reconstruction of the repressive domains through time-resolved genomic analyses in mammals.
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23
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Kitamura Y, Suzuki A, Uranishi K, Nishimoto M, Mizuno S, Takahashi S, Okuda A. Alternative splicing for germ cell‐specific
Mga
transcript can be eliminated without compromising mouse viability or fertility. Dev Growth Differ 2022; 64:409-416. [DOI: 10.1111/dgd.12806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Yuka Kitamura
- Division of Biomedical Sciences, Research Center for Genomic Medicine Saitama Medical University, 1397‐1 Yamane, Hidaka Saitama Japan
| | - Ayumu Suzuki
- Division of Biomedical Sciences, Research Center for Genomic Medicine Saitama Medical University, 1397‐1 Yamane, Hidaka Saitama Japan
| | - Kousuke Uranishi
- Division of Biomedical Sciences, Research Center for Genomic Medicine Saitama Medical University, 1397‐1 Yamane, Hidaka Saitama Japan
| | - Masazumi Nishimoto
- Division of Biomedical Sciences, Research Center for Genomic Medicine Saitama Medical University, 1397‐1 Yamane, Hidaka Saitama Japan
- Biomedical Research Center Saitama Medical University, 1397‐1 Yamane, Hidaka Saitama Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center University of Tsukuba, 1‐1‐1 Tennodai Tsukuba Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center University of Tsukuba, 1‐1‐1 Tennodai Tsukuba Japan
| | - Akihiko Okuda
- Division of Biomedical Sciences, Research Center for Genomic Medicine Saitama Medical University, 1397‐1 Yamane, Hidaka Saitama Japan
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24
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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. Variant Polycomb complexes can have tissue-specific roles during development. Here they show that PCGF6 controls lineage-specification in human PSCs by promoting neuroectoderm differentiation and repressing mesendoderm differentiation via distinct downstream targets.
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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.
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25
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Oss-Ronen L, Sarusi T, Cohen I. Histone Mono-Ubiquitination in Transcriptional Regulation and Its Mark on Life: Emerging Roles in Tissue Development and Disease. Cells 2022; 11:cells11152404. [PMID: 35954248 PMCID: PMC9368181 DOI: 10.3390/cells11152404] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/26/2022] [Accepted: 08/02/2022] [Indexed: 02/06/2023] Open
Abstract
Epigenetic regulation plays an essential role in driving precise transcriptional programs during development and homeostasis. Among epigenetic mechanisms, histone mono-ubiquitination has emerged as an important post-transcriptional modification. Two major histone mono-ubiquitination events are the mono-ubiquitination of histone H2A at lysine 119 (H2AK119ub), placed by Polycomb repressive complex 1 (PRC1), and histone H2B lysine 120 mono-ubiquitination (H2BK120ub), placed by the heteromeric RNF20/RNF40 complex. Both of these events play fundamental roles in shaping the chromatin epigenetic landscape and cellular identity. In this review we summarize the current understandings of molecular concepts behind histone mono-ubiquitination, focusing on their recently identified roles in tissue development and pathologies.
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Affiliation(s)
| | | | - Idan Cohen
- Correspondence: ; Tel.: +972-8-6477593; Fax: +972-8-6477626
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26
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Chen J, Zhao Y, Zhang F, Li J, Boland JA, Cheng NC, Liu K, Tiffen JC, Bertolino P, Bowen DG, Krueger A, Lisowski L, Alexander IE, Vadas MA, El-Omar E, Gamble JR, McCaughan GW. Liver-specific deletion of miR-181ab1 reduces liver tumour progression via upregulation of CBX7. Cell Mol Life Sci 2022; 79:443. [PMID: 35867177 PMCID: PMC9307539 DOI: 10.1007/s00018-022-04452-6] [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: 03/24/2022] [Revised: 06/23/2022] [Accepted: 06/26/2022] [Indexed: 11/30/2022]
Abstract
MiR-181 expression levels increased in hepatocellular carcinoma (HCC) compared to non-cancerous tissues. MiR-181 has been widely reported as a possible driver of tumourigenesis but also acts as a tumour suppressor. In addition, the miR-181 family regulates the development and function of immune and vascular cells, which play vital roles in the progression of tumours. More complicatedly, many genes have been identified as miR-181 targets to mediate the effects of miR-181. However, the role of miR-181 in the development of primary tumours remains largely unexplored. We aimed to examine the function of miR-181 and its vital mediators in the progression of diethylnitrosamine-induced primary liver cancers in mice. The size of liver tumours was significantly reduced by 90% in global (GKO) or liver-specific (LKO) 181ab1 knockout mice but not in hematopoietic and endothelial lineage-specific knockout mice, compared to WT mice. In addition, the number of tumours was significantly reduced by 50% in GKO mice. Whole-genome RNA-seq analysis and immunohistochemistry showed that epithelial-mesenchymal transition was partially reversed in GKO tumours compared to WT tumours. The expression of CBX7, a confirmed miR-181 target, was up-regulated in GKO compared to WT tumours. Stable CBX7 expression was achieved with an AAV/Transposase Hybrid-Vector System and up-regulated CBX7 expression inhibited liver tumour progression in WT mice. Hepatic CBX7 deletion restored the progression of LKO liver tumours. MiR-181a expression was the lowest and CBX7 expression the highest in iClust2 and 3 subclasses of human HCC compared to iClust1. Gene expression profiles of GKO tumours overlapped with low-proliferative peri-portal-type HCCs. Liver-specific loss of miR-181ab1 inhibited primary liver tumour progression via up-regulating CBX7 expression, but tumour induction requires both hepatic and non-hepatic miR-181. Also, miR-181ab1-deficient liver tumours may resemble low-proliferative periportal-type human HCC.
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Affiliation(s)
- Jinbiao Chen
- Liver Injury and Cancer Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Yang Zhao
- Vascular Biology Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia.,School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Fan Zhang
- UNSW Microbiome Research Centre, School of Clinical Medicine, UNSW Medicine and Health, St George and Sutherland Clinical Campuses, Kogarah, NSW, 2217, Australia
| | - Jia Li
- Vascular Biology Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia.,Centre for Motor Neuron Disease, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Jade A Boland
- Liver Injury and Cancer Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Ngan Ching Cheng
- Liver Injury and Cancer Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia.,Vascular Biology Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Ken Liu
- Liver Injury and Cancer Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia.,Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW, 2050, Australia
| | - Jessamy C Tiffen
- Melanoma Epigenetics Lab Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Patrick Bertolino
- Liver Immunology Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - David G Bowen
- Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW, 2050, Australia.,Liver Immunology Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Andreas Krueger
- Molecular Immunology, Faculty of Biology and Chemistry, Justus Liebig University Gießen, Schubertstr 81, 35392, Giessen, Germany.,Institute for Molecular Medicine, Frankfurt Cancer Institute, Goethe-University, Frankfurt, Germany
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, 2145, Australia.,Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, Warsaw, Poland
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW, 2145, Australia
| | - Mathew A Vadas
- Vascular Biology Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Emad El-Omar
- UNSW Microbiome Research Centre, School of Clinical Medicine, UNSW Medicine and Health, St George and Sutherland Clinical Campuses, Kogarah, NSW, 2217, Australia
| | - Jennifer R Gamble
- Vascular Biology Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Geoffrey W McCaughan
- Liver Injury and Cancer Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia. .,Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW, 2050, Australia.
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27
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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: 14] [Impact Index Per Article: 7.0] [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.
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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
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28
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Tanaskovic N, Dalsass M, Filipuzzi M, Ceccotti G, Verrecchia A, Nicoli P, Doni M, Olivero D, Pasini D, Koseki H, Sabò A, Bisso A, Amati B. Polycomb group ring finger protein 6 suppresses Myc-induced lymphomagenesis. Life Sci Alliance 2022; 5:5/8/e202101344. [PMID: 35422437 PMCID: PMC9012912 DOI: 10.26508/lsa.202101344] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 12/15/2022] Open
Abstract
Max dimerizes with Mga to form the repressive complex PRC1.6; another PRC1.6 subunit, Pcgf6, suppresses Myc-induced lymphomagenesis but, unexpectedly, does so in a Mga- and PRC1.6-independent manner. Max is an obligate dimerization partner for the Myc transcription factors and for several repressors, such as Mnt, Mxd1-4, and Mga, collectively thought to antagonize Myc function in transcription and oncogenesis. Mga, in particular, is part of the variant Polycomb group repressive complex PRC1.6. Here, we show that ablation of the distinct PRC1.6 subunit Pcgf6–but not Mga–accelerates Myc-induced lymphomagenesis in Eµ-myc transgenic mice. Unexpectedly, however, Pcgf6 loss shows no significant impact on transcriptional profiles, in neither pre-tumoral B-cells, nor lymphomas. Altogether, these data unravel an unforeseen, Mga- and PRC1.6-independent tumor suppressor activity of Pcgf6.
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Affiliation(s)
| | - Mattia Dalsass
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | | | | | | | - Paola Nicoli
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Mirko Doni
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Daniela Olivero
- Laboratorio Analisi Veterinarie BiEsseA, A Company of Scil Animal Care Company Srl, Milan, Italy
| | - Diego Pasini
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
- Department of Health Sciences, University of Milan, Milan, Italy
| | - Haruhiko Koseki
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Cellular and Molecular Medicine, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Arianna Sabò
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Andrea Bisso
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Bruno Amati
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
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29
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Bonefas KM, Iwase S. Soma-to-germline transformation in chromatin-linked neurodevelopmental disorders? FEBS J 2022; 289:2301-2317. [PMID: 34514717 PMCID: PMC8918023 DOI: 10.1111/febs.16196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/16/2021] [Accepted: 09/10/2021] [Indexed: 01/22/2023]
Abstract
Mutations in numerous chromatin regulators cause neurodevelopmental disorders (NDDs) with unknown mechanisms. Understandably, most research has focused on how chromatin regulators control gene expression that is directly relevant to brain development and function, such as synaptic genes. However, some NDD models surprisingly show ectopic expression of germline genes in the brain. These germline genes are usually expressed only in the primordial germ cells, testis, and ovaries for germ cell development and sexual reproduction. Such ectopic germline gene expression has been reported in several NDDs, including immunodeficiency, centromeric instability, facial anomalies syndrome 1; Kleefstra syndrome 1; MeCP2 duplication syndrome; and mental retardation, X-linked syndromic, Claes-Jensen type. The responsible genes, DNMT3B, G9A/GLP, MECP2, and KDM5C, all encode chromatin regulators for gene silencing. These mutations may therefore lead to germline gene derepression and, in turn, a severe identity crisis of brain cells-potentially interfering with normal brain development. Thus, the ectopic expression of germline genes is a unique hallmark defining this NDD subset and further implicates the importance of germline gene silencing during brain development. The functional impact of germline gene expression on brain development, however, remains undetermined. This perspective article explores how this apparent soma-to-germline transformation arises and how it may interfere with neurodevelopment through genomic instability and impaired sensory cilium formation. Furthermore, we also discuss how to test these hypotheses experimentally to ultimately determine the contribution of ectopic germline transcripts to chromatin-linked NDDs.
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Affiliation(s)
- Katherine M. Bonefas
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109,The University of Michigan Neuroscience Graduate Program,Corresponding authors: Please address correspondence to: , and
| | - Shigeki Iwase
- Department of Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109,The University of Michigan Neuroscience Graduate Program,Corresponding authors: Please address correspondence to: , and
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30
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Functional redundancy among Polycomb complexes in maintaining the pluripotent state of embryonic stem cells. Stem Cell Reports 2022; 17:1198-1214. [PMID: 35364009 PMCID: PMC9120860 DOI: 10.1016/j.stemcr.2022.02.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 12/23/2022] Open
Abstract
Polycomb group proteins assemble into multi-protein complexes, known as Polycomb repressive complexes 1 and 2 (PRC1 and PRC2), that guide cell fate decisions during embryonic development. PRC1 forms an array of biochemically distinct canonical PRC1 (cPRC1) or non-canonical PRC1 (ncPRC1) complexes characterized by the mutually exclusive presence of PCGF (PCGF1-PCGF6) paralog subunit; however, whether each one of these subcomplexes fulfills a distinct role remains largely controversial. Here, by performing a CRISPR-based loss-of-function screen in embryonic stem cells (ESCs), we uncovered a previously unappreciated functional redundancy among PRC1 subcomplexes. Disruption of ncPRC1, but not cPRC1, displayed severe defects in ESC pluripotency. Remarkably, coablation of non-canonical and canonical PRC1 in ESCs resulted in exacerbation of the phenotype observed in the non-canonical PRC1-null ESCs, highlighting the importance of functional redundancy among PRC1 subcomplexes. Together, our studies demonstrate that PRC1 subcomplexes act redundantly to silence lineage-specific genes and ensure robust maintenance of ESC identity. cPRC1 complexes are not the key determinant of self-renewal and pluripotency in ESCs ncPRC1 complexes play a fundamental and redundant role in maintaining pluripotency in ESCs cPRC1 and ncPRC1 act redundantly to suppress lineage-specific genes and preserve ESC identity
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31
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Yakushiji-Kaminatsui N, Kondo T, Ohinata Y, Takano J, Koseki H. Genetic, Genomic, and Imaging Approaches to Dissect the Role of Polycomb Group Epigenetic Regulators in Mice. Methods Mol Biol 2022; 2529:207-228. [PMID: 35733017 DOI: 10.1007/978-1-0716-2481-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Among the most important histone methyltransferases for metazoan development are EZH1/2 and their homologs, which methylate histone H3 lysine 27 and act as part of a highly conserved set of chromatin regulators called Polycomb Group (PcG) proteins. Reaching a precise understanding of the roles of PcG proteins in the orchestration of differentiation and the maintenance of cell identity requires a variety of genetic and molecular approaches. Here, we present a full suite of methods for the study of PcG proteins in early murine development, including mutant strain generation, embryonic stem cell derivation, epigenomic profiling, and immunofluorescence and in situ hybridization.
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Affiliation(s)
- Nayuta Yakushiji-Kaminatsui
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), Yokohama, Kanagawa, Japan.
| | - Takashi Kondo
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), Yokohama, Kanagawa, Japan
| | - Yasuhide Ohinata
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
| | - Junichiro Takano
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), Yokohama, Kanagawa, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), Yokohama, Kanagawa, Japan.
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan.
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32
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p53 inactivation unmasks histone methylation-independent WDR5 functions that drive self-renewal and differentiation of pluripotent stem cells. Stem Cell Reports 2021; 16:2642-2658. [PMID: 34715053 PMCID: PMC8581203 DOI: 10.1016/j.stemcr.2021.10.002] [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: 09/15/2020] [Revised: 10/03/2021] [Accepted: 10/04/2021] [Indexed: 11/23/2022] Open
Abstract
p53 alterations occur during culture of pluripotent stem cells (PSCs), but the significance of these events on epigenetic control of PSC fate determination remains poorly understood. Wdr5 deletion in p53-null (DKO) mouse ESCs (mESCs) leads to impaired self-renewal, defective retinal neuroectoderm differentiation, and de-repression of germ cell/meiosis (GCM)-specific genes. Re-introduction of a WDR5 mutant with defective H3K4 methylation activity into DKO ESCs restored self-renewal and suppressed GCM gene expression but failed to induce retinal neuroectoderm differentiation. Mechanistically, mutant WDR5 targets chromatin that is largely devoid of H3K4me3 and regulates gene expression in p53-null mESCs. Furthermore, MAX and WDR5 co-target lineage-specifying chromatin and regulate chromatin accessibility of GCM-related genes. Importantly, MAX and WDR5 are core subunits of a non-canonical polycomb repressor complex 1 responsible for gene silencing. This function, together with canonical, pro-transcriptional WDR5-dependent MLL complex H3K4 methyltransferase activity, highlight how WDR5 mediates crosstalk between transcription and repression during mESC fate choice. H3K4me defective WDR5 supports self-renewal and GCM differentiation in p53-null mESCs WDR5 regulates H3K4me-independent stemness and GCM gene expression in p53-null mESCs MAX and WDR5 repress GCM-related gene chromatin accessibility upon differentiation
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33
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Flora P, Dalal G, Cohen I, Ezhkova E. Polycomb Repressive Complex(es) and Their Role in Adult Stem Cells. Genes (Basel) 2021; 12:1485. [PMID: 34680880 PMCID: PMC8535826 DOI: 10.3390/genes12101485] [Citation(s) in RCA: 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: 08/19/2021] [Revised: 09/13/2021] [Accepted: 09/22/2021] [Indexed: 12/31/2022] Open
Abstract
Populations of resident stem cells (SCs) are responsible for maintaining, repairing, and regenerating adult tissues. In addition to having the capacity to generate all the differentiated cell types of the tissue, adult SCs undergo long periods of quiescence within the niche to maintain themselves. The process of SC renewal and differentiation is tightly regulated for proper tissue regeneration throughout an organisms' lifetime. Epigenetic regulators, such as the polycomb group (PcG) of proteins have been implicated in modulating gene expression in adult SCs to maintain homeostatic and regenerative balances in adult tissues. In this review, we summarize the recent findings that elucidate the composition and function of the polycomb repressive complex machinery and highlight their role in diverse adult stem cell compartments.
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Affiliation(s)
- Pooja Flora
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA;
| | - Gil Dalal
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Idan Cohen
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
| | - Elena Ezhkova
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA;
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34
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Llabata P, Torres-Diz M, Gomez A, Tomas-Daza L, Romero OA, Grego-Bessa J, Llinas-Arias P, Valencia A, Esteller M, Javierre BM, Zhang X, Sanchez-Cespedes M. MAX mutant small-cell lung cancers exhibit impaired activities of MGA-dependent noncanonical polycomb repressive complex. Proc Natl Acad Sci U S A 2021; 118:e2024824118. [PMID: 34493659 PMCID: PMC8449313 DOI: 10.1073/pnas.2024824118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 07/08/2021] [Indexed: 12/17/2022] Open
Abstract
The MYC axis is disrupted in cancer, predominantly through activation of the MYC family oncogenes but also through inactivation of the MYC partner MAX or of the MAX partner MGA. MGA and MAX are also members of the polycomb repressive complex, ncPRC1.6. Here, we use genetically modified MAX-deficient small-cell lung cancer (SCLC) cells and carry out genome-wide and proteomics analyses to study the tumor suppressor function of MAX. We find that MAX mutant SCLCs have ASCL1 or NEUROD1 or combined ASCL1/NEUROD1 characteristics and lack MYC transcriptional activity. MAX restitution triggers prodifferentiation expression profiles that shift when MAX and oncogenic MYC are coexpressed. Although ncPRC1.6 can be formed, the lack of MAX restricts global MGA occupancy, selectively driving its recruitment toward E2F6-binding motifs. Conversely, MAX restitution enhances MGA occupancy to repress genes involved in different functions, including stem cell and DNA repair/replication. Collectively, these findings reveal that MAX mutant SCLCs have either ASCL1 or NEUROD1 or combined characteristics and are MYC independent and exhibit deficient ncPRC1.6-mediated gene repression.
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Affiliation(s)
- Paula Llabata
- Cancer Genetics Group, Josep Carreras Leukaemia Research Institute, 08916 Barcelona, Spain
| | - Manuel Torres-Diz
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 Barcelona, Spain
| | - Antonio Gomez
- Rheumatology Research Group, Vall d'Hebron Research Institute, 08035 Barcelona, Spain
| | - Laureano Tomas-Daza
- 3D Chromatin Organization Group, Josep Carreras Leukaemia Research Institute, 08916 Barcelona, Spain
| | - Octavio A Romero
- Cancer Genetics Group, Josep Carreras Leukaemia Research Institute, 08916 Barcelona, Spain
| | - Joaquim Grego-Bessa
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 Barcelona, Spain
| | - Pere Llinas-Arias
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, 08916 Barcelona, Spain
| | - Alfonso Valencia
- Computational Biology Life Sciences Group, Barcelona Supercomputing Centre, 08034 Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, 08916 Barcelona, Spain
- Centro de Investigacion Biomedica en Red Cancer, 28029 Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, 08907 Barcelona, Spain
| | - Biola M Javierre
- Rheumatology Research Group, Vall d'Hebron Research Institute, 08035 Barcelona, Spain
| | - Xiaoyang Zhang
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112
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35
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Sugishita H, Kondo T, Ito S, Nakayama M, Yakushiji-Kaminatsui N, Kawakami E, Koseki Y, Ohinata Y, Sharif J, Harachi M, Blackledge NP, Klose RJ, Koseki H. Variant PCGF1-PRC1 links PRC2 recruitment with differentiation-associated transcriptional inactivation at target genes. Nat Commun 2021; 12:5341. [PMID: 34504070 PMCID: PMC8429492 DOI: 10.1038/s41467-021-24894-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/23/2021] [Indexed: 12/21/2022] Open
Abstract
Polycomb repressive complexes-1 and -2 (PRC1 and 2) silence developmental genes in a spatiotemporal manner during embryogenesis. How Polycomb group (PcG) proteins orchestrate down-regulation of target genes upon differentiation, however, remains elusive. Here, by differentiating embryonic stem cells into embryoid bodies, we reveal a crucial role for the PCGF1-containing variant PRC1 complex (PCGF1-PRC1) to mediate differentiation-associated down-regulation of a group of genes. Upon differentiation cues, transcription is down-regulated at these genes, in association with PCGF1-PRC1-mediated deposition of histone H2AK119 mono-ubiquitination (H2AK119ub1) and PRC2 recruitment. In the absence of PCGF1-PRC1, both H2AK119ub1 deposition and PRC2 recruitment are disrupted, leading to aberrant expression of target genes. PCGF1-PRC1 is, therefore, required for initiation and consolidation of PcG-mediated gene repression during differentiation. Polycomb repressive complexes (PRC1 and PRC2) repress genes that are crucial for development via epigenetic modifications; however, their role in differentiation is not well known. Here the authors reveal that a PCGF1-containing PRC1 variant facilitates exit from pluripotency by downregulating target genes and recruiting PRC2.
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Affiliation(s)
- Hiroki Sugishita
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Cellular and Molecular Medicine, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba, Japan.,International Research Center for Neurointelligence (IRCN), Institutes for Advanced Study, The University of Tokyo, Bunkyo-ku, Japan
| | - Takashi Kondo
- 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
| | - Manabu Nakayama
- Laboratory of Medical Omics Research, Kazusa DNA Research Institute, Kisarazu, Japan
| | | | - Eiryo Kawakami
- Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.,Healthcare and Medical Data Driven AI based Predictive Reasoning Development Unit, RIKEN Medical Sciences Innovation Hub Program, Yokohama, Japan
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Cellular and Molecular Medicine, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yasuhide Ohinata
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Cellular and Molecular Medicine, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Jafar Sharif
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mio Harachi
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan. .,Cellular and Molecular Medicine, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba, Japan.
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36
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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.
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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
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37
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Nguyen P, Pease NA, Kueh HY. Scalable control of developmental timetables by epigenetic switching networks. J R Soc Interface 2021; 18:20210109. [PMID: 34283940 DOI: 10.1098/rsif.2021.0109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
During development, progenitor cells follow timetables for differentiation that span many cell generations. These developmental timetables are robustly encoded by the embryo, yet scalably adjustable by evolution, facilitating variation in organism size and form. Epigenetic switches, involving rate-limiting activation steps at regulatory gene loci, control gene activation timing in diverse contexts, and could profoundly impact the dynamics of gene regulatory networks controlling developmental lineage specification. Here, we develop a mathematical framework to model regulatory networks with genes controlled by epigenetic switches. Using this framework, we show that such epigenetic switching networks uphold developmental timetables that robustly span many cell generations, and enable the generation of differentiated cells in precisely defined numbers and fractions. Changes to epigenetic switching networks can readily alter the timing of developmental events within a timetable, or alter the overall speed at which timetables unfold, enabling scalable control over differentiated population sizes. With their robust, yet flexibly adjustable nature, epigenetic switching networks could represent central targets on which evolution acts to manufacture diversity in organism size and form.
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Affiliation(s)
- Phuc Nguyen
- Molecular Engineering and Sciences Program, University of Washington, Seattle, WA, USA
| | - Nicholas A Pease
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington, Seattle, WA, USA.,Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
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38
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Uranishi K, Hirasaki M, Kitamura Y, Mizuno Y, Nishimoto M, Suzuki A, Okuda A. Two DNA binding domains of MGA act in combination to suppress ectopic activation of meiosis-related genes in mouse embryonic stem cells. STEM CELLS (DAYTON, OHIO) 2021; 39:1435-1446. [PMID: 34224650 DOI: 10.1002/stem.3433] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 06/25/2021] [Indexed: 11/10/2022]
Abstract
Although the physiological meaning of the high potential of mouse embryonic stem cells (ESCs) for meiotic entry is not understood, a rigid safeguarding system is required to prevent ectopic onset of meiosis. PRC1.6, a non-canonical PRC1, is known for its suppression of precocious and ectopic meiotic onset in germ cells and ESCs, respectively. MGA, a scaffolding component of PRC1.6, bears two distinct DNA-binding domains termed bHLHZ and T-box. However, it is unclear how this feature contributes to the functions of PRC1.6. Here, we demonstrated that both domains repress distinct sets of genes in murine ESCs, but substantial numbers of meiosis-related genes are included in both gene sets. In addition, our data demonstrated that bHLHZ is crucially involved in repressing the expression of Meiosin, which plays essential roles in meiotic entry with Stra8, revealing at least part of the molecular mechanisms that link negative and positive regulation of meiotic onset.
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Affiliation(s)
- Kousuke Uranishi
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama, Japan
| | - Masataka Hirasaki
- Department of Clinical Cancer Genomics, International Medical Center, Saitama Medical University, Yamane Hidaka, Saitama, Japan
| | - Yuka Kitamura
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama, Japan
| | - Yosuke Mizuno
- Biomedical Research Center, Saitama Medical University, Yamane Hidaka, Saitama, Japan
| | - Masazumi Nishimoto
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama, Japan.,Biomedical Research Center, Saitama Medical University, Yamane Hidaka, Saitama, Japan
| | - Ayumu Suzuki
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama, Japan
| | - Akihiko Okuda
- Division of Biomedical Sciences, Research Center for Genomic Medicine, Saitama Medical University, Yamane Hidaka, Saitama, Japan
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39
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Dahlet T, Truss M, Frede U, Al Adhami H, Bardet AF, Dumas M, Vallet J, Chicher J, Hammann P, Kottnik S, Hansen P, Luz U, Alvarez G, Auclair G, Hecht J, Robinson PN, Hagemeier C, Weber M. E2F6 initiates stable epigenetic silencing of germline genes during embryonic development. Nat Commun 2021; 12:3582. [PMID: 34117224 PMCID: PMC8195999 DOI: 10.1038/s41467-021-23596-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 05/04/2021] [Indexed: 11/24/2022] Open
Abstract
In mouse development, long-term silencing by CpG island DNA methylation is specifically targeted to germline genes; however, the molecular mechanisms of this specificity remain unclear. Here, we demonstrate that the transcription factor E2F6, a member of the polycomb repressive complex 1.6 (PRC1.6), is critical to target and initiate epigenetic silencing at germline genes in early embryogenesis. Genome-wide, E2F6 binds preferentially to CpG islands in embryonic cells. E2F6 cooperates with MGA to silence a subgroup of germline genes in mouse embryonic stem cells and in embryos, a function that critically depends on the E2F6 marked box domain. Inactivation of E2f6 leads to a failure to deposit CpG island DNA methylation at these genes during implantation. Furthermore, E2F6 is required to initiate epigenetic silencing in early embryonic cells but becomes dispensable for the maintenance in differentiated cells. Our findings elucidate the mechanisms of epigenetic targeting of germline genes and provide a paradigm for how transient repression signals by DNA-binding factors in early embryonic cells are translated into long-term epigenetic silencing during mouse development. DNA methylation targets CpG island promoters of germline genes to repress their expression in mouse somatic cells. Here the authors show that a transcription factor E2F6 is required to target CpG island DNA methylation and epigenetic silencing to germline genes during early mouse development.
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Affiliation(s)
- Thomas Dahlet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Matthias Truss
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany.
| | - Ute Frede
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Hala Al Adhami
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Anaïs F Bardet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Michael Dumas
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Judith Vallet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg Esplanade, CNRS, University of Strasbourg, Strasbourg, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade, CNRS, University of Strasbourg, Strasbourg, France
| | - Sarah Kottnik
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Hansen
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Uschi Luz
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Gonzalo Alvarez
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ghislain Auclair
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France
| | - Jochen Hecht
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, Germany.,Centre for Genomic Regulation, Barcelona, Spain
| | - Peter N Robinson
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, Germany.,Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Christian Hagemeier
- Pediatric Oncology, Labor für Pädiatrische Molekularbiologie, Charité - Universitätsmedizin Berlin, Berlin, Germany.
| | - Michael Weber
- University of Strasbourg, Strasbourg, France. .,CNRS UMR7242, Biotechnology and Cell Signaling, Illkirch, France.
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40
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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.
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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.
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41
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H2AK119ub1 guides maternal inheritance and zygotic deposition of H3K27me3 in mouse embryos. Nat Genet 2021; 53:539-550. [PMID: 33821003 DOI: 10.1038/s41588-021-00820-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/17/2021] [Indexed: 02/01/2023]
Abstract
Parental epigenomes are established during gametogenesis. While they are largely reset after fertilization, broad domains of Polycomb repressive complex 2 (PRC2)-mediated formation of lysine 27-trimethylated histone H3 (H3K27me3) are inherited from oocytes in mice. How maternal H3K27me3 is established and inherited by embryos remains elusive. Here, we show that PRC1-mediated formation of lysine 119-monoubiquititinated histone H2A (H2AK119ub1) confers maternally heritable H3K27me3. Temporal profiling of H2AK119ub1 dynamics revealed that atypically broad H2AK119ub1 domains are established, along with H3K27me3, during oocyte growth. From the two-cell stage, H2AK119ub1 is progressively deposited at typical Polycomb targets and precedes H3K27me3. Reduction of H2AK119ub1 by depletion of Polycomb group ring finger 1 (PCGF1) and PCGF6-essential components of variant PRC1 (vPRC1)-leads to H3K27me3 loss at a subset of genes in oocytes. The gene-selective H3K27me3 deficiency is irreversibly inherited by embryos, causing loss of maternal H3K27me3-dependent imprinting, embryonic sublethality and placental enlargement at term. Collectively, our study unveils preceding dynamics of H2AK119ub1 over H3K27me3 at the maternal-to-zygotic transition, and identifies PCGF1/6-vPRC1 as an essential player in maternal epigenetic inheritance.
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42
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Hanna R, Flamier A, Barabino A, Bernier G. G-quadruplexes originating from evolutionary conserved L1 elements interfere with neuronal gene expression in Alzheimer's disease. Nat Commun 2021; 12:1828. [PMID: 33758195 PMCID: PMC7987966 DOI: 10.1038/s41467-021-22129-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/03/2021] [Indexed: 02/06/2023] Open
Abstract
DNA sequences containing consecutive guanines organized in 4-interspaced tandem repeats can form stable single-stranded secondary structures, called G-quadruplexes (G4). Herein, we report that the Polycomb group protein BMI1 is enriched at heterochromatin regions containing putative G4 DNA sequences, and that G4 structures accumulate in cells with reduced BMI1 expression and/or relaxed chromatin, including sporadic Alzheimer's disease (AD) neurons. In AD neurons, G4 structures preferentially accumulate in lamina-associated domains, and this is rescued by re-establishing chromatin compaction. ChIP-seq analyses reveal that G4 peaks correspond to evolutionary conserved Long Interspersed Element-1 (L1) sequences predicted to be transcriptionally active. Hence, G4 structures co-localize with RNAPII, and inhibition of transcription can reverse the G4 phenotype without affecting chromatin's state, thus uncoupling both components. Intragenic G4 structures affecting splicing events are furthermore associated with reduced neuronal gene expression in AD. Active L1 sequences are thus at the origin of most G4 structures observed in human neurons.
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Affiliation(s)
- Roy Hanna
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
| | - Anthony Flamier
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
- Whitehead Institute of Biomedical Research, Cambridge, MA, USA
| | - Andrea Barabino
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
| | - Gilbert Bernier
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada.
- Department of Neurosciences, University of Montreal, Montreal, QC, Canada.
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43
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Piunti A, Shilatifard A. The roles of Polycomb repressive complexes in mammalian development and cancer. Nat Rev Mol Cell Biol 2021; 22:326-345. [PMID: 33723438 DOI: 10.1038/s41580-021-00341-1] [Citation(s) in RCA: 189] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
More than 80 years ago, the first Polycomb-related phenotype was identified in Drosophila melanogaster. Later, a group of diverse genes collectively called Polycomb group (PcG) genes were identified based on common mutant phenotypes. PcG proteins, which are well-conserved in animals, were originally characterized as negative regulators of gene transcription during development and subsequently shown to function in various biological processes; their deregulation is associated with diverse phenotypes in development and in disease, especially cancer. PcG proteins function on chromatin and can form two distinct complexes with different enzymatic activities: Polycomb repressive complex 1 (PRC1) is a histone ubiquitin ligase and PRC2 is a histone methyltransferase. Recent studies have revealed the existence of various mutually exclusive PRC1 and PRC2 variants. In this Review, we discuss new concepts concerning the biochemical and molecular functions of these new PcG complex variants, and how their epigenetic activities are involved in mammalian development and cancer.
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Affiliation(s)
- Andrea Piunti
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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44
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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.
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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
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45
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Qin J, Wang C, Zhu Y, Su T, Dong L, Huang Y, Hao K. Mga safeguards embryonic stem cells from acquiring extraembryonic endoderm fates. SCIENCE ADVANCES 2021; 7:7/4/eabe5689. [PMID: 33523934 PMCID: PMC7821913 DOI: 10.1126/sciadv.abe5689] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/24/2020] [Indexed: 05/17/2023]
Abstract
Polycomb group (PcG) proteins form multiprotein complexes that affect stem cell identity and fate decisions by still largely unexplored mechanisms. Here, by performing a CRISPR-based loss-of-function screen in embryonic stem cells (ESCs), we identify PcG gene Mga involved in the repression of endodermal transcription factor Gata6 We report that deletion of Mga results in peri-implantation embryonic lethality in mice. We further demonstrate that Mga-null ESCs exhibit impaired self-renewal and spontaneous differentiation to primitive endoderm (PE). Our data support a model in which Mga might serve as a scaffold for PRC1.6 assembly and guide this multimeric complex to specific genomic targets including genes that encode endodermal factors Gata4, Gata6, and Sox17. Our findings uncover an unexpected function of Mga in ESCs, where it functions as a gatekeeper to prevent ESCs from entering into the PE lineage by directly repressing expression of a set of endoderm differentiation master genes.
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Affiliation(s)
- Jinzhong Qin
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China.
| | - Congcong Wang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
| | - Yaru Zhu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
| | - Ting Su
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
| | - Lixia Dong
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
| | - Yikai Huang
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
| | - Kunying Hao
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, School of Medicine, Nanjing University, Nanjing, China
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Tsusaka T, Fukuda K, Shimura C, Kato M, Shinkai Y. The fibronectin type-III (FNIII) domain of ATF7IP contributes to efficient transcriptional silencing mediated by the SETDB1 complex. Epigenetics Chromatin 2020; 13:52. [PMID: 33256805 PMCID: PMC7706265 DOI: 10.1186/s13072-020-00374-4] [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: 07/17/2020] [Accepted: 11/13/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The histone methyltransferase SETDB1 (also known as ESET) represses genes and various types of transposable elements, such as endogenous retroviruses (ERVs) and integrated exogenous retroviruses, through a deposition of trimethylation on lysine 9 of histone H3 (H3K9me3) in mouse embryonic stem cells (mESCs). ATF7IP (also known as MCAF1 or AM), a binding partner of SETDB1, regulates the nuclear localization and enzymatic activities of SETDB1 and plays a crucial role in SETDB1-mediated transcriptional silencing. In this study, we further dissected the ATF7IP function with its truncated mutants in Atf7ip knockout (KO) mESCs. RESULTS We demonstrated that the SETDB1-interaction region within ATF7IP is essential for ATF7IP-dependent SETDB1 nuclear localization and silencing of both ERVs and integrated retroviral transgenes, whereas its C-terminal fibronectin type-III (FNIII) domain is dispensable for both these functions; rather, it has a role in efficient silencing mediated by the SETDB1 complex. Proteomic analysis identified a number of FNIII domain-interacting proteins, some of which have a consensus binding motif. We showed that one of the FNIII domain-binding proteins, ZMYM2, was involved in the efficient silencing of a transgene by ATF7IP. RNA-seq analysis of Atf7ip KO and WT or the FNIII domain mutant of ATF7IP-rescued Atf7ip KO mESCs showed that the FNIII domain mutant re-silenced most de-repressed SETDB1/ATF7IP-targeted ERVs compared to the WT. However, the silencing activity of the FNIII domain mutant was weaker than that of the ATF7IP WT, and some of the de-repressed germ cell-related genes in Atf7ip KO mESCs were not silenced by the FNIII domain mutant. Such germ cell-related genes are targeted and silenced by the MAX/MGA complex, and MGA was also identified as another potential binding molecule of the ATF7IP FNIII domain in the proteomic analysis. This suggests that the FNIII domain of ATF7IP acts as a binding hub of ATF7IP-interacting molecules possessing a specific interacting motif we named FAM and contributes to one layer of the SETDB1/ATF7IP complex-mediated silencing mechanisms. CONCLUSIONS Our findings contributed to further understanding the function of ATF7IP in the SETDB1 complex, revealed the role of the FNIII domain of ATF7IP in transcriptional silencing, and suggested a potential underlying molecular mechanism for it.
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Affiliation(s)
- Takeshi Tsusaka
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Orthopedic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Kei Fukuda
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan
| | - Chikako Shimura
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan
| | - Masaki Kato
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan. .,Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, 230-0045, Japan.
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan.
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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.
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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
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Maternal DNMT3A-dependent de novo methylation of the paternal genome inhibits gene expression in the early embryo. Nat Commun 2020; 11:5417. [PMID: 33110091 PMCID: PMC7591512 DOI: 10.1038/s41467-020-19279-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 10/01/2020] [Indexed: 12/20/2022] Open
Abstract
De novo DNA methylation (DNAme) during mammalian spermatogenesis yields a densely methylated genome, with the exception of CpG islands (CGIs), which are hypomethylated in sperm. While the paternal genome undergoes widespread DNAme loss before the first S-phase following fertilization, recent mass spectrometry analysis revealed that the zygotic paternal genome is paradoxically also subject to a low level of de novo DNAme. However, the loci involved, and impact on transcription were not addressed. Here, we employ allele-specific analysis of whole-genome bisulphite sequencing data and show that a number of genomic regions, including several dozen CGI promoters, are de novo methylated on the paternal genome by the 2-cell stage. A subset of these promoters maintains DNAme through development to the blastocyst stage. Consistent with paternal DNAme acquisition, many of these loci are hypermethylated in androgenetic blastocysts but hypomethylated in parthenogenetic blastocysts. Paternal DNAme acquisition is lost following maternal deletion of Dnmt3a, with a subset of promoters, which are normally transcribed from the paternal allele in blastocysts, being prematurely transcribed at the 4-cell stage in maternal Dnmt3a knockout embryos. These observations uncover a role for maternal DNMT3A activity in post-fertilization epigenetic reprogramming and transcriptional silencing of the paternal genome. The paternal genome in mice undergoes widespread DNA methylation loss post-fertilization. Here, the authors apply allele-specific analysis of WGBS data to show that a number of genomic regions are simultaneously de novo methylated on the paternal genome dependent on maternal DNMT3A activity, which induces transcriptional silencing of this allele in the early embryo.
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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.
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Bar C, Cohen I, Zhao D, Pothula V, Litskevitch A, Koseki H, Zheng D, Ezhkova E. Polycomb Repressive Complex 1 Controls Maintenance of Fungiform Papillae by Repressing Sonic Hedgehog Expression. Cell Rep 2020; 28:257-266.e5. [PMID: 31269445 PMCID: PMC6921245 DOI: 10.1016/j.celrep.2019.06.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 04/22/2019] [Accepted: 06/03/2019] [Indexed: 12/28/2022] Open
Abstract
How tissue patterns are formed and maintained are fundamental questions. The murine tongue epithelium, a paradigm for tissue patterning, consists of an array of specialized fungiform papillae structures that harbor taste cells. The formation of fungiform papillae is preceded by pronounced spatial changes in gene expression, in which taste cell genes such as Shh, initially diffused in lingual epithelial progenitors, become restricted to taste cells when their specification progresses. However, the requirement of spatial restriction of taste cell gene expression for patterning and formation of fungiform papillae is unknown. Here, we show that a chromatin regulator, Polycomb repressive complex (PRC) 1, is required for proper maintenance of fungiform papillae by repressing Shh and preventing ectopic SHH signaling in non-taste cells. Ablation of SHH signaling in PRC1-null non-taste cells rescues the maintenance of taste cells. Altogether, our studies exemplify how epigenetic regulation establishes spatial gene expression patterns necessary for specialized niche structures. Formation and maintenance of patterns are critical for tissue development. Bar et al. show that PRC1, an epigenetic regulator, is critical for lingual papillae development. Specifically, PRC1 regulates maintenance of the developing fungiform papillae, harboring taste cells, by repressing Shh expression in the non-gustatory epithelium surrounding taste cells.
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Affiliation(s)
- Carmit Bar
- Black Family Stem Cell Institute, The Tisch Cancer 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
| | - Idan Cohen
- Black Family Stem Cell Institute, The Tisch Cancer 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
| | - Dejian Zhao
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Venu Pothula
- Black Family Stem Cell Institute, The Tisch Cancer 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
| | - Anna Litskevitch
- Department of Molecular & Cell Biology, University of California, Berkeley, 142 Life Sciences Addition, Berkeley, CA 94720, USA
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; AMED-CREST, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Elena Ezhkova
- Black Family Stem Cell Institute, The Tisch Cancer 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.
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