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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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2
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Guan S, Tang J, Ma X, Miao R, Cheng B. CBX7C⋅PHC2 interaction facilitates PRC1 assembly and modulates its phase separation properties. iScience 2024; 27:109548. [PMID: 38600974 PMCID: PMC11004992 DOI: 10.1016/j.isci.2024.109548] [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: 08/06/2023] [Revised: 02/04/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
CBX7 is a key component of PRC1 complex. Cbx7C is an uncharacterized Cbx7 splicing isoform specifically expressed in mouse embryonic stem cells (mESCs). We demonstrate that CBX7C functions as an epigenetic repressor at the classic PRC1 targets in mESCs, and its preferential interaction to PHC2 facilitates PRC1 assembly. Both Cbx7C and Phc2 are significantly upregulated during cell differentiation, and knockdown of Cbx7C abolishes the differentiation of mESCs to embryoid bodies. Interestingly, CBX7C⋅PHC2 interaction at low levels efficiently undergoes the formation of functional Polycomb bodies with high mobility, whereas the coordination of the two factors at high doses results in the formation of large, low-mobility, chromatin-free aggregates. Overall, these findings uncover the unique roles and molecular basis of the CBX7C⋅PHC2 interaction in PRC1 assembly on chromatin and Pc body formation and open a new avenue of controlling PRC1 activities via modulation of its phase separation properties.
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Affiliation(s)
- Shanli Guan
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
| | - Jiajia Tang
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
| | - Xiaojun Ma
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
| | - Ruidong Miao
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
| | - Bo Cheng
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
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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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Zhang J, Wang T, Shi R, Zhao Y, Zhang Y, Zhang C, Xing Q, Zhou T, Shan Y, Yao H, Zhang X, Pan G. YTHDF1 facilitates PRC1-mediated H2AK119ub in human ES cells. J Cell Physiol 2024; 239:152-165. [PMID: 37991435 DOI: 10.1002/jcp.31152] [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: 06/03/2023] [Revised: 09/25/2023] [Accepted: 10/18/2023] [Indexed: 11/23/2023]
Abstract
Polycomb repressive complexes (PRCs) play critical roles in cell fate decisions during normal development as well as disease progression through mediating histone modifications such as H3K27me3 and H2AK119ub. How exactly PRCs recruited to chromatin remains to be fully illuminated. Here, we report that YTHDF1, the N6-methyladenine (m6 A) RNA reader that was previously known to be mainly cytoplasmic, associates with RNF2, a PRC1 protein that mediates H2AK119ub in human embryonic stem cells (hESCs). A portion of YTHDF1 localizes in the nuclei and associates with RNF2/H2AK119ub on a subset of gene loci related to neural development functions. Knock-down YTHDF1 attenuates H2AK119ub modification on these genes and promotes neural differentiation in hESCs. Our findings provide a noncanonical mechanism that YTHDF1 participates in PRC1 functions in hESCs.
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Affiliation(s)
- Jingyuan Zhang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Department of Basic Science Research, Guangzhou Laboratory, Guangzhou, China
| | - Tianyu Wang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ruona Shi
- University of Chinese Academy of Sciences, Beijing, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
| | - Yuan Zhao
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yanqi Zhang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Cong Zhang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qi Xing
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Tiancheng Zhou
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yongli Shan
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Hongjie Yao
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Department of Basic Science Research, Guangzhou Laboratory, Guangzhou, China
| | - Xiaofei Zhang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Guangjin Pan
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
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Miller A, Dasen JS. Establishing and maintaining Hox profiles during spinal cord development. Semin Cell Dev Biol 2024; 152-153:44-57. [PMID: 37029058 PMCID: PMC10524138 DOI: 10.1016/j.semcdb.2023.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/18/2023] [Accepted: 03/30/2023] [Indexed: 04/09/2023]
Abstract
The chromosomally-arrayed Hox gene family plays central roles in embryonic patterning and the specification of cell identities throughout the animal kingdom. In vertebrates, the relatively large number of Hox genes and pervasive expression throughout the body has hindered understanding of their biological roles during differentiation. Studies on the subtype diversification of spinal motor neurons (MNs) have provided a tractable system to explore the function of Hox genes during differentiation, and have provided an entry point to explore how neuronal fate determinants contribute to motor circuit assembly. Recent work, using both in vitro and in vivo models of MN subtype differentiation, have revealed how patterning morphogens and regulation of chromatin structure determine cell-type specific programs of gene expression. These studies have not only shed light on basic mechanisms of rostrocaudal patterning in vertebrates, but also have illuminated mechanistic principles of gene regulation that likely operate in the development and maintenance of terminal fates in other systems.
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Affiliation(s)
- Alexander Miller
- NYU Neuroscience Institute and Developmental Genetics Programs, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA.
| | - Jeremy S Dasen
- NYU Neuroscience Institute and Developmental Genetics Programs, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA.
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Lomeli C. S, Kristin B. A. Epigenetic regulation of craniofacial development and disease. Birth Defects Res 2024; 116:e2271. [PMID: 37964651 PMCID: PMC10872612 DOI: 10.1002/bdr2.2271] [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: 06/29/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND The formation of the craniofacial complex relies on proper neural crest development. The gene regulatory networks (GRNs) and signaling pathways orchestrating this process have been extensively studied. These GRNs and signaling cascades are tightly regulated as alterations to any stage of neural crest development can lead to common congenital birth defects, including multiple syndromes affecting facial morphology as well as nonsyndromic facial defects, such as cleft lip with or without cleft palate. Epigenetic factors add a hierarchy to the regulation of transcriptional networks and influence the spatiotemporal activation or repression of specific gene regulatory cascades; however less is known about their exact mechanisms in controlling precise gene regulation. AIMS In this review, we discuss the role of epigenetic factors during neural crest development, specifically during craniofacial development and how compromised activities of these regulators contribute to congenital defects that affect the craniofacial complex.
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Affiliation(s)
- Shull Lomeli C.
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Artinger Kristin B.
- Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN, USA
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7
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Barrasa JI, Kahn TG, Lundkvist MJ, Schwartz YB. DNA elements tether canonical Polycomb Repressive Complex 1 to human genes. Nucleic Acids Res 2023; 51:11613-11633. [PMID: 37855680 PMCID: PMC10681801 DOI: 10.1093/nar/gkad889] [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: 03/08/2023] [Revised: 09/25/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023] Open
Abstract
Development of multicellular animals requires epigenetic repression by Polycomb group proteins. The latter assemble in multi-subunit complexes, of which two kinds, Polycomb Repressive Complex 1 (PRC1) and Polycomb Repressive Complex 2 (PRC2), act together to repress key developmental genes. How PRC1 and PRC2 recognize specific genes remains an open question. Here we report the identification of several hundreds of DNA elements that tether canonical PRC1 to human developmental genes. We use the term tether to describe a process leading to a prominent presence of canonical PRC1 at certain genomic sites, although the complex is unlikely to interact with DNA directly. Detailed analysis indicates that sequence features associated with PRC1 tethering differ from those that favour PRC2 binding. Throughout the genome, the two kinds of sequence features mix in different proportions to yield a gamut of DNA elements that range from those tethering predominantly PRC1 or PRC2 to ones capable of tethering both complexes. The emerging picture is similar to the paradigmatic targeting of Polycomb complexes by Polycomb Response Elements (PREs) of Drosophila but providing for greater plasticity.
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Affiliation(s)
- Juan I Barrasa
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Tatyana G Kahn
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Moa J Lundkvist
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Yuri B Schwartz
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
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8
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Wales-McGrath B, Mercer H, Piontkivska H. Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections. BMC Genomics 2023; 24:685. [PMID: 37968596 PMCID: PMC10652522 DOI: 10.1186/s12864-023-09778-4] [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: 06/18/2023] [Accepted: 10/31/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND RNA editing is a process that increases transcriptome diversity, often through Adenosine Deaminases Acting on RNA (ADARs) that catalyze the deamination of adenosine to inosine. ADAR editing plays an important role in regulating brain function and immune activation, and is dynamically regulated during brain development. Additionally, the ADAR1 p150 isoform is induced by interferons in viral infection and plays a role in antiviral immune response. However, the question of how virus-induced ADAR expression affects host transcriptome editing remains largely unanswered. This question is particularly relevant in the context of congenital infections, given the dynamic regulation of ADAR editing during brain development, the importance of this editing for brain function, and subsequent neurological symptoms of such infections, including microcephaly, sensory issues, and other neurodevelopmental abnormalities. Here, we begin to address this question, examining ADAR expression in publicly available datasets of congenital infections of human cytomegalovirus (HCMV) microarray expression data, as well as mouse cytomegalovirus (MCMV) and mouse/ human induced pluripotent neuroprogenitor stem cell (hiNPC) Zika virus (ZIKV) RNA-seq data. RESULTS We found that in all three datasets, ADAR1 was overexpressed in infected samples compared to uninfected samples. In the RNA-seq datasets, editing rates were also analyzed. In all mouse infections cases, the number of editing sites was significantly increased in infected samples, albeit this was not the case for hiNPC ZIKV samples. Mouse ZIKV samples showed altered editing of well-established protein-recoding sites such as Gria3, Grik5, and Nova1, as well as editing sites that may impact miRNA binding. CONCLUSIONS Our findings provide evidence for changes in ADAR expression and subsequent dysregulation of ADAR editing of host transcriptomes in congenital infections. These changes in editing patterns of key neural genes have potential significance in the development of neurological symptoms, thus contributing to neurodevelopmental abnormalities. Further experiments should be performed to explore the full range of editing changes that occur in different congenital infections, and to confirm the specific functional consequences of these editing changes.
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Affiliation(s)
- Benjamin Wales-McGrath
- University of Pennsylvania, Perelman School of Medicine, Department of Genetics, Philadelphia, PA, USA
- Children's Hospital of Philadelphia, Division of Cancer Pathobiology, Philadelphia, PA, USA
| | - Heather Mercer
- Department of Biological and Environmental Sciences, University of Mount Union, Alliance, OH, USA
| | - Helen Piontkivska
- Department of Biological Sciences, Kent State University, Kent, OH, USA.
- School of Biomedical Sciences, Kent State University, Kent, OH, USA.
- Brain Health Research Institute, Kent State University, Kent, OH, USA.
- Healthy Communities Research Institute, Kent State University, Kent, OH, USA.
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Ong ALC, Kokaji T, Kishi A, Takihara Y, Shinozuka T, Shimamoto R, Isotani A, Shirai M, Sasai N. Acquisition of neural fate by combination of BMP blockade and chromatin modification. iScience 2023; 26:107887. [PMID: 37771660 PMCID: PMC10522999 DOI: 10.1016/j.isci.2023.107887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/07/2023] [Accepted: 09/07/2023] [Indexed: 09/30/2023] Open
Abstract
Neural induction is a process where naive cells are converted into committed cells with neural characteristics, and it occurs at the earliest step during embryogenesis. Although the signaling molecules and chromatin remodeling for neural induction have been identified, the mutual relationships between these molecules are yet to be fully understood. By taking advantage of the neural differentiation system of mouse embryonic stem (ES) cells, we discovered that the BMP signal regulates the expression of several polycomb repressor complex (PRC) component genes. We particularly focused on Polyhomeotic Homolog 1 (Phc1) and established Phc1-knockout (Phc1-KO) ES cells. We found that Phc1-KO failed to acquire the neural fate, and the cells remained in pluripotent or primitive non-neural states. Chromatin accessibility analysis suggests that Phc1 is essential for chromatin packing. Aberrant upregulation of the BMP signal was confirmed in the Phc1 homozygotic mutant embryos. Taken together, Phc1 is required for neural differentiation through epigenetic modification.
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Affiliation(s)
- Agnes Lee Chen Ong
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Toshiya Kokaji
- Data-driven biology, NAIST Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Arisa Kishi
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Yoshihiro Takihara
- Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima 734-0037, Japan
| | - Takuma Shinozuka
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Ren Shimamoto
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Ayako Isotani
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Manabu Shirai
- Omics Research Center (ORC), National Cerebral and Cardiovascular Center, 6-1 Kishibe Shinmachi, Suita, Osaka 564-8565, Japan
| | - Noriaki Sasai
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
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Marc S, Mizeranschi AE, Paul C, Otavă G, Savici J, Sicoe B, Torda I, Huțu I, Mircu C, Ilie DE, Carabaș M, Boldura OM. Simultaneous Occurrence of Hypospadias and Bilateral Cleft Lip and Jaw in a Crossbred Calf: Clinical, Computer Tomographic, and Genomic Characterization. Animals (Basel) 2023; 13:ani13101709. [PMID: 37238140 DOI: 10.3390/ani13101709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/17/2023] [Accepted: 05/20/2023] [Indexed: 05/28/2023] Open
Abstract
Congenital abnormalities in animals, including abnormalities of the cleft lip and jaw and hypospadias have been reported in all domesticated species. They are a major concern for breeders due to the increased economic loss they entail. In this article, we described a congenital bilateral cheilognathoschisis (cleft lip and jaw) with campylognathia in association with penile hypospadias and preputial hypoplasia with failure of preputial fusion in a Bos taurus crossbred Piedmontese × Wagyu calf. Clinical examination, computed tomography, and whole genome sequencing were performed to describe and identify a possible cause of the abnormalities. Clinical examination revealed a bilateral cheilognathoschisis of approximately 4 cm in length and 3 cm in width in the widest part, with computer tomography analyses confirming the bilateral absence of the processus nasalis of the incisive bone and the lateral deviation of the processus palatinus towards the left side. Genomic data analyses identified 13 mutations with a high impact on the products of the following overlapped genes: ACVR1, ADGRA2, BHMT2, BMPR1B, CCDC8, CDH1, EGF, F13A1, GSTP1, IRF6, MMP14, MYBPHL, and PHC2 with ADGRA2, EGF, F13A1, GSTP1, and IRF6 having mutations in a homozygous state. The whole genome investigation indicates the involvement of multiple genes in the birth defects observed in this case.
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Affiliation(s)
- Simona Marc
- Faculty of Veterinary Medicine, University of Life Sciences ''King Mihai I'' from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania
- Research Institute for Biosecurity and Bioengineering, University of Life Sciences ''King Mihai I'' from Timisoara, 300645 Timișoara, Romania
| | - Alexandru Eugeniu Mizeranschi
- The Molecular Research Department, Research and Development Station for Bovine Arad, Bodrogului Street, 32, 310059 Arad, Romania
| | - Cristina Paul
- Department of Applied Chemistry and Engineering of Organic and Natural Compounds, Faculty of Industrial Chemistry and Environmental Engineering, Politehnica University Timisoara, Carol Telbisz 6, 300001 Timisoara, Romania
| | - Gabriel Otavă
- Faculty of Veterinary Medicine, University of Life Sciences ''King Mihai I'' from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania
- Research Institute for Biosecurity and Bioengineering, University of Life Sciences ''King Mihai I'' from Timisoara, 300645 Timișoara, Romania
| | - Jelena Savici
- Faculty of Veterinary Medicine, University of Life Sciences ''King Mihai I'' from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania
| | - Bogdan Sicoe
- Faculty of Veterinary Medicine, University of Life Sciences ''King Mihai I'' from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania
| | - Iuliu Torda
- Faculty of Veterinary Medicine, University of Life Sciences ''King Mihai I'' from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania
- Research Institute for Biosecurity and Bioengineering, University of Life Sciences ''King Mihai I'' from Timisoara, 300645 Timișoara, Romania
| | - Ioan Huțu
- Faculty of Veterinary Medicine, University of Life Sciences ''King Mihai I'' from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania
- Research Institute for Biosecurity and Bioengineering, University of Life Sciences ''King Mihai I'' from Timisoara, 300645 Timișoara, Romania
| | - Călin Mircu
- Faculty of Veterinary Medicine, University of Life Sciences ''King Mihai I'' from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania
- Research Institute for Biosecurity and Bioengineering, University of Life Sciences ''King Mihai I'' from Timisoara, 300645 Timișoara, Romania
| | - Daniela Elena Ilie
- The Molecular Research Department, Research and Development Station for Bovine Arad, Bodrogului Street, 32, 310059 Arad, Romania
| | - Mihai Carabaș
- Faculty of Automatic Control and Computer Science, Politehnica University of Bucharest, Splaiul Independenţei 313, 060042 Bucharest, Romania
| | - Oana Maria Boldura
- Faculty of Veterinary Medicine, University of Life Sciences ''King Mihai I'' from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania
- Research Institute for Biosecurity and Bioengineering, University of Life Sciences ''King Mihai I'' from Timisoara, 300645 Timișoara, Romania
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11
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Ma Y, Liu L, Wei Z, Zhu M, Huang L, Wang S, Yi X, Ying F, Zhao S, Cai J, Wang Z, Sun S. Loss of CBX2 causes genomic instability and Wnt activation in high grade serous ovarian carcinoma cells. Mol Carcinog 2023; 62:479-492. [PMID: 36621979 DOI: 10.1002/mc.23500] [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: 09/01/2022] [Revised: 11/24/2022] [Accepted: 12/09/2022] [Indexed: 01/10/2023]
Abstract
High grade serous ovarian carcinoma (HGSOC) is lethal with insidious onset, rapid progression, poor prognosis, and limited treatment options. Polycomb repressor complexes (PRC) 1 and 2 are intimately involved in progression of many types of cancer including HGSOC. Unlike the consistent constitution of PRC2, PRC1 consists of diverse components whose clinical significance in HGSOC are not entirely clear. Here, prognosis-associated PRC1 components were identified through data-mining. CBX2 promoted proliferation and reduced apoptosis of HGSOC cell lines OVCAR4, OVCAR3, and CAOV3. Complete loss of CBX2 by CRISPR-cas9 editing (CBX2KO ) destabilized genome stability with increased spontaneous chromosomal breaks and tendency to polyploidy accompanied by disrupted cell cycle especially stalled G2/M transition and caused severe cell death. Wnt/β-catenin/LEF1/TCF7L1 was activated in surviving OVCAR4-CBX2KO clones to bypass the crisis caused by loss of CBX2. The relieve of TCF7L1 core-promoter region occupied by CBX2 might be one of the possible explanations to TCF7L1 increase in OVCAR4-CBX2KO clones. Subcutaneous tumor model further validated that depletion of CBX2 repressed HGSOC cell line derived tumor growth. High immunohistochemistry score of CBX2 in primary ovarian cancer tissue associated with advanced clinical stage (p = 0.033), poor overall survival (HR = 3.056, 95% CI: 1.024-9.123), and progression free survival (HR = 4.455, 95% CI: 1.513-13.118) in HGSOC. Overall, our results suggested that CBX2 was a promising prognostic factor and therapeutic target in HGSOC.
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Affiliation(s)
- Yujia Ma
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lin Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zheng Wei
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mengna Zhu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lin Huang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shan Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoqing Yi
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Feiquan Ying
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Simei Zhao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Cai
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zehua Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Si Sun
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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12
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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: 33] [Impact Index Per Article: 16.5] [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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13
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Dimitrova E, Feldmann A, van der Weide RH, Flach KD, Lastuvkova A, de Wit E, Klose RJ. Distinct roles for CKM-Mediator in controlling Polycomb-dependent chromosomal interactions and priming genes for induction. Nat Struct Mol Biol 2022; 29:1000-1010. [PMID: 36220895 PMCID: PMC9568430 DOI: 10.1038/s41594-022-00840-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 08/22/2022] [Indexed: 11/20/2022]
Abstract
Precise control of gene expression underpins normal development. This relies on mechanisms that enable communication between gene promoters and other regulatory elements. In embryonic stem cells (ESCs), the cyclin-dependent kinase module Mediator complex (CKM-Mediator) has been reported to physically link gene regulatory elements to enable gene expression and also prime genes for induction during differentiation. Here, we show that CKM-Mediator contributes little to three-dimensional genome organization in ESCs, but it has a specific and essential role in controlling interactions between inactive gene regulatory elements bound by Polycomb repressive complexes (PRCs). These interactions are established by the canonical PRC1 (cPRC1) complex but rely on CKM-Mediator, which facilitates binding of cPRC1 to its target sites. Importantly, through separation-of-function experiments, we reveal that this collaboration between CKM-Mediator and cPRC1 in creating long-range interactions does not function to prime genes for induction during differentiation. Instead, we discover that priming relies on an interaction-independent mechanism whereby the CKM supports core Mediator engagement with gene promoters during differentiation to enable gene activation.
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Affiliation(s)
| | - Angelika Feldmann
- Department of Biochemistry, University of Oxford, Oxford, UK
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Robin H van der Weide
- Division of Gene Regulation, Oncode Institute and The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Hubrecht Institute KNAW, Utrecht, The Netherlands
| | - Koen D Flach
- Division of Gene Regulation, Oncode Institute and The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anna Lastuvkova
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Elzo de Wit
- Division of Gene Regulation, Oncode Institute and The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK.
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14
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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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15
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The Role of Polycomb Proteins in Cell Lineage Commitment and Embryonic Development. EPIGENOMES 2022; 6:epigenomes6030023. [PMID: 35997369 PMCID: PMC9397020 DOI: 10.3390/epigenomes6030023] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
Embryonic development is a highly intricate and complex process. Different regulatory mechanisms cooperatively dictate the fate of cells as they progress from pluripotent stem cells to terminally differentiated cell types in tissues. A crucial regulator of these processes is the Polycomb Repressive Complex 2 (PRC2). By catalyzing the mono-, di-, and tri-methylation of lysine residues on histone H3 tails (H3K27me3), PRC2 compacts chromatin by cooperating with Polycomb Repressive Complex 1 (PRC1) and represses transcription of target genes. Proteomic and biochemical studies have revealed two variant complexes of PRC2, namely PRC2.1 which consists of the core proteins (EZH2, SUZ12, EED, and RBBP4/7) interacting with one of the Polycomb-like proteins (MTF2, PHF1, PHF19), and EPOP or PALI1/2, and PRC2.2 which contains JARID2 and AEBP2 proteins. MTF2 and JARID2 have been discovered to have crucial roles in directing and recruiting PRC2 to target genes for repression in embryonic stem cells (ESCs). Following these findings, recent work in the field has begun to explore the roles of different PRC2 variant complexes during different stages of embryonic development, by examining molecular phenotypes of PRC2 mutants in both in vitro (2D and 3D differentiation) and in vivo (knock-out mice) assays, analyzed with modern single-cell omics and biochemical assays. In this review, we discuss the latest findings that uncovered the roles of different PRC2 proteins during cell-fate and lineage specification and extrapolate these findings to define a developmental roadmap for different flavors of PRC2 regulation during mammalian embryonic development.
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16
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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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17
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Yaghmaeian Salmani B, Balderson B, Bauer S, Ekman H, Starkenberg A, Perlmann T, Piper M, Bodén M, Thor S. Selective requirement for polycomb repressor complex 2 in the generation of specific hypothalamic neuronal subtypes. Development 2022; 149:274592. [PMID: 35245348 PMCID: PMC8959139 DOI: 10.1242/dev.200076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/18/2022] [Indexed: 11/20/2022]
Abstract
The hypothalamus displays staggering cellular diversity, chiefly established during embryogenesis by the interplay of several signalling pathways and a battery of transcription factors. However, the contribution of epigenetic cues to hypothalamus development remains unclear. We mutated the polycomb repressor complex 2 gene Eed in the developing mouse hypothalamus, which resulted in the loss of H3K27me3, a fundamental epigenetic repressor mark. This triggered ectopic expression of posteriorly expressed regulators (e.g. Hox homeotic genes), upregulation of cell cycle inhibitors and reduced proliferation. Surprisingly, despite these effects, single cell transcriptomic analysis revealed that most neuronal subtypes were still generated in Eed mutants. However, we observed an increase in glutamatergic/GABAergic double-positive cells, as well as loss/reduction of dopamine, hypocretin and Tac2-Pax6 neurons. These findings indicate that many aspects of the hypothalamic gene regulatory flow can proceed without the key H3K27me3 epigenetic repressor mark, but points to a unique sensitivity of particular neuronal subtypes to a disrupted epigenomic landscape. Summary: Polycomb repressor complex 2 inactivation results in selective effects on mouse hypothalamic development, increasing glutamatergic/GABA cells, while reducing dopamine, Hcrt and Tac2-Pax6 cells.
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Affiliation(s)
- Behzad Yaghmaeian Salmani
- Department of Clinical and Experimental Medicine, Linkoping University, SE-58185 Linkoping, Sweden
- Department of Cell and Molecular Biology, Karolinska Institute, SE-17177 Stockholm, Sweden
| | - Brad Balderson
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Susanne Bauer
- Department of Clinical and Experimental Medicine, Linkoping University, SE-58185 Linkoping, Sweden
| | - Helen Ekman
- Department of Clinical and Experimental Medicine, Linkoping University, SE-58185 Linkoping, Sweden
| | - Annika Starkenberg
- Department of Clinical and Experimental Medicine, Linkoping University, SE-58185 Linkoping, Sweden
| | - Thomas Perlmann
- Department of Cell and Molecular Biology, Karolinska Institute, SE-17177 Stockholm, Sweden
| | - Michael Piper
- School of Biomedical Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Stefan Thor
- Department of Clinical and Experimental Medicine, Linkoping University, SE-58185 Linkoping, Sweden
- School of Biomedical Sciences, University of Queensland, St Lucia, QLD 4072, Australia
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18
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Wang R, Sun J, Han H, Huang Y, Chen T, Yang M, Wei Q, Wan H, Liao Y. Whole-genome resequencing reveals genetic characteristics of different duck breeds from the Guangxi region in China. G3-GENES GENOMES GENETICS 2021; 11:6156632. [PMID: 33677537 PMCID: PMC8759808 DOI: 10.1093/g3journal/jkab054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/17/2021] [Indexed: 11/15/2022]
Abstract
Distinctive indigenous duck (Anas platyrhynchos) populations of Guangxi, China, evolved due to the geographical, cultural, and environmental variability of this region. To investigate the genetic diversity and population structure of the indigenous ducks of Guangxi, 78 individuals from eight populations were collected and sequenced by whole-genome resequencing with an average depth of ∼9.40×. The eight indigenous duck populations included four breeds and four resource populations. Moreover, the genome data of 47 individuals from two typical meat-type breeds and two native egg-type breeds were obtained from a public database. Calculation of heterozygosity, nucleotide diversity (π), Tajima’s D, and FST indicated that the Guangxi populations were characterized by higher genetic diversity and lower differentiation than meat-type breeds. The highest diversity was observed in the Xilin-Ma ducks. Principal component, structure, and phylogenetic tree analyses revealed the relationship between the indigenous duck populations of Guangxi. A mild degree of differentiation was observed among the Guangxi populations, although three populations were closer to the meat or egg breeds. Indigenous populations are famous for their special flavor, small body size, and slow growth rates. Selective sweep analysis revealed the candidate genes and pathways associated with these growth traits. Our findings provide a valuable source of information regarding genetic diversity, population conservation, and genome-associated breeding of ducks.
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Affiliation(s)
- Ran Wang
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, Guangdong 518120, China.,ShenZhen Engineering Laboratory for Genomics-Assisted Animal Breeding, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Junli Sun
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530001, China
| | - Hu Han
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, Guangdong 518120, China.,ShenZhen Engineering Laboratory for Genomics-Assisted Animal Breeding, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yingfei Huang
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530001, China
| | - Tao Chen
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, Guangdong 518120, China.,ShenZhen Engineering Laboratory for Genomics-Assisted Animal Breeding, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Manman Yang
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, Guangdong 518120, China.,ShenZhen Engineering Laboratory for Genomics-Assisted Animal Breeding, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Qiang Wei
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, Guangdong 518120, China.,ShenZhen Engineering Laboratory for Genomics-Assisted Animal Breeding, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Huofu Wan
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530001, China
| | - Yuying Liao
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530001, China.,Guangxi Veterinary Research Institute, Nanning, Guangxi 530001, China
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19
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PHC1 maintains pluripotency by organizing genome-wide chromatin interactions of the Nanog locus. Nat Commun 2021; 12:2829. [PMID: 33990559 PMCID: PMC8121881 DOI: 10.1038/s41467-021-22871-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/03/2021] [Indexed: 12/13/2022] Open
Abstract
Polycomb group (PcG) proteins maintain cell identity by repressing gene expression during development. Surprisingly, emerging studies have recently reported that a number of PcG proteins directly activate gene expression during cell fate determination process. However, the mechanisms by which they direct gene activation in pluripotency remain poorly understood. Here, we show that Phc1, a subunit of canonical polycomb repressive complex 1 (cPRC1), can exert its function in pluripotency maintenance via a PRC1-independent activation of Nanog. Ablation of Phc1 reduces the expression of Nanog and overexpression of Nanog partially rescues impaired pluripotency caused by Phc1 depletion. We find that Phc1 interacts with Nanog and activates Nanog transcription by stabilizing the genome-wide chromatin interactions of the Nanog locus. This adds to the already known canonical function of PRC1 in pluripotency maintenance via a PRC1-dependent repression of differentiation genes. Overall, our study reveals a function of Phc1 to activate Nanog transcription through regulating chromatin architecture and proposes a paradigm for PcG proteins to maintain pluripotency. Phc1 is a subunit of the polycomb repressive complex 1 (PRC1), which represses gene expression during development. Here the authors show that Phc1 acts independently from PRC1 to activate Nanog transcription by stabilizing genome-wide chromatin interactions of the Nanog locus, and in turn stabilize pluripotency.
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20
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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: 186] [Impact Index Per Article: 62.0] [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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21
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Genomic profiling of the transcription factor Zfp148 and its impact on the p53 pathway. Sci Rep 2020; 10:14156. [PMID: 32843651 PMCID: PMC7447789 DOI: 10.1038/s41598-020-70824-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 08/04/2020] [Indexed: 12/12/2022] Open
Abstract
Recent data suggest that the transcription factor Zfp148 represses activation of the tumor suppressor p53 in mice and that therapeutic targeting of the human orthologue ZNF148 could activate the p53 pathway without causing detrimental side effects. We have previously shown that Zfp148 deficiency promotes p53-dependent proliferation arrest of mouse embryonic fibroblasts (MEFs), but the underlying mechanism is not clear. Here, we showed that Zfp148 deficiency downregulated cell cycle genes in MEFs in a p53-dependent manner. Proliferation arrest of Zfp148-deficient cells required increased expression of ARF, a potent activator of the p53 pathway. Chromatin immunoprecipitation showed that Zfp148 bound to the ARF promoter, suggesting that Zfp148 represses ARF transcription. However, Zfp148 preferentially bound to promoters of other transcription factors, indicating that deletion of Zfp148 may have pleiotropic effects that activate ARF and p53 indirectly. In line with this, we found no evidence of genetic interaction between TP53 and ZNF148 in CRISPR and siRNA screen data from hundreds of human cancer cell lines. We conclude that Zfp148 deficiency, by increasing ARF transcription, downregulates cell cycle genes and cell proliferation in a p53-dependent manner. However, the lack of genetic interaction between ZNF148 and TP53 in human cancer cells suggests that therapeutic targeting of ZNF148 may not increase p53 activity in humans.
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22
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Żylicz JJ, Heard E. Molecular Mechanisms of Facultative Heterochromatin Formation: An X-Chromosome Perspective. Annu Rev Biochem 2020; 89:255-282. [PMID: 32259458 DOI: 10.1146/annurev-biochem-062917-012655] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Facultative heterochromatin (fHC) concerns the developmentally regulated heterochromatinization of different regions of the genome and, in the case of the mammalian X chromosome and imprinted loci, of only one allele of a homologous pair. The formation of fHC participates in the timely repression of genes, by resisting strong trans activators. In this review, we discuss the molecular mechanisms underlying the establishment and maintenance of fHC in mammals using a mouse model. We focus on X-chromosome inactivation (XCI) as a paradigm for fHC but also relate it to genomic imprinting and homeobox (Hox) gene cluster repression. A vital role for noncoding transcription and/or transcripts emerges as the general principle of triggering XCI and canonical imprinting. However, other types of fHC are established through an unknown mechanism, independent of noncoding transcription (Hox clusters and noncanonical imprinting). We also extensively discuss polycomb-group repressive complexes (PRCs), which frequently play a vital role in fHC maintenance.
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Affiliation(s)
- Jan J Żylicz
- Mammalian Developmental Epigenetics Group, Institut Curie, CNRS UMR 3215, INSERM U934, PSL University, 75248 Paris Cedex 05, France.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, United Kingdom
| | - Edith Heard
- Directors' Research, EMBL Heidelberg, 69117 Heidelberg, Germany;
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23
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Guo CC, Majewski T, Zhang L, Yao H, Bondaruk J, Wang Y, Zhang S, Wang Z, Lee JG, Lee S, Cogdell D, Zhang M, Wei P, Grossman HB, Kamat A, Duplisea JJ, Ferguson JE, Huang H, Dadhania V, Gao J, Dinney C, Weinstein JN, Baggerly K, McConkey D, Czerniak B. Dysregulation of EMT Drives the Progression to Clinically Aggressive Sarcomatoid Bladder Cancer. Cell Rep 2020; 27:1781-1793.e4. [PMID: 31067463 DOI: 10.1016/j.celrep.2019.04.048] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/28/2019] [Accepted: 04/10/2019] [Indexed: 12/17/2022] Open
Abstract
Sarcomatoid urothelial bladder cancer (SARC) displays a high propensity for distant metastasis and is associated with short survival. We report a comprehensive genomic analysis of 28 cases of SARC and 84 cases of conventional urothelial carcinoma (UC), with the TCGA cohort of 408 muscle-invasive bladder cancers serving as the reference. SARCs show a distinct mutational landscape, with enrichment of TP53, RB1, and PIK3CA mutations. They are related to the basal molecular subtype of conventional UCs and could be divided into epithelial-basal and more clinically aggressive mesenchymal subsets on the basis of TP63 and its target gene expression levels. Other analyses reveal that SARCs are driven by downregulation of homotypic adherence genes and dysregulation of the EMT network, and nearly half exhibit a heavily infiltrated immune phenotype. Our observations have important implications for prognostication and the development of more effective therapies for this highly lethal variant of bladder cancer.
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Affiliation(s)
- Charles C Guo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tadeusz Majewski
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Li Zhang
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Hui Yao
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jolanta Bondaruk
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yan Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shizhen Zhang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ziqiao Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - June Goo Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sangkyou Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David Cogdell
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Miao Zhang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - H Barton Grossman
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashish Kamat
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - James Edward Ferguson
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - He Huang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vipulkumar Dadhania
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianjun Gao
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Colin Dinney
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John N Weinstein
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keith Baggerly
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Bogdan Czerniak
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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24
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Muñoz-Leija MA, Ordóñez Rivas FO, Barrera-Flores FJ, Treviño-González JL, Pinales-Razo R, Guzmán-López S, Elizondo-Omaña RE, Quiroga-Garza A. A proposed extension to the elongated styloid process definition: A morphological study with high-resolution tomography computer. Morphologie 2020; 104:117-124. [PMID: 32070640 DOI: 10.1016/j.morpho.2020.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
The objective of the present study was to evaluate the morphology and angulation of the styloid process (SP), analyzing results stratified by gender, side and age on asymptomatic patients. We retrospectively analyzed 99 high-resolution computed tomography study images from asymptomatic patients. The images were assessed intra-observatory by a head and neck expert radiologist. Data for length, morphology, and angulation in a coronal and sagittal plane were recorded and stratified by age and gender. Morphology was classified according to the Langlais modified by Guimares classification. The mean lengths were 31.67±0.97mm and 31.64±0.90mm for the right and left sides respectively. Using the Langlais modified by Guimares classification, the normal type was the most prevalent and without a statistically significant difference when comparing between genders. A total of 27.6% presented a morphologically elongated SP (>25mm of continuous process), 49.5% presented a radiologically elongated SP (>30mm), and a total of 9.59% had a longer length than the proposed≤45mm. The right transverse angle was greater in men than women, and a statistically significant difference was found (P=0.010). We show the morphological variability of the SP. Although our results are reported with the traditional definition, the high prevalence supports the need for a new definition of elongated SP and a normal angulation ranges.
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Affiliation(s)
- M A Muñoz-Leija
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Human Anatomy Department, Monterrey, Nuevo León, Mexico
| | - F O Ordóñez Rivas
- Universidad Autónoma de Nuevo León, Facultad de Medicina y Hospital Universitario "Dr. José Eleuterio González" Department of Radiology and Imaging, Monterrey, Nuevo León, Mexico
| | - F J Barrera-Flores
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Human Anatomy Department, Monterrey, Nuevo León, Mexico
| | - J L Treviño-González
- Universidad Autónoma de Nuevo León, Facultad de Medicina y Hospital Universitario "Dr. José Eleuterio González", Department of Othorinolaringology, Monterrey, Nuevo León, Mexico
| | - R Pinales-Razo
- Universidad Autónoma de Nuevo León, Facultad de Medicina y Hospital Universitario "Dr. José Eleuterio González" Department of Radiology and Imaging, Monterrey, Nuevo León, Mexico
| | - S Guzmán-López
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Human Anatomy Department, Monterrey, Nuevo León, Mexico
| | - R E Elizondo-Omaña
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Human Anatomy Department, Monterrey, Nuevo León, Mexico
| | - A Quiroga-Garza
- Universidad Autónoma de Nuevo León, Facultad de Medicina, Human Anatomy Department, Monterrey, Nuevo León, Mexico.
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25
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Phc2 controls hematopoietic stem and progenitor cell mobilization from bone marrow by repressing Vcam1 expression. Nat Commun 2019; 10:3496. [PMID: 31375680 PMCID: PMC6677815 DOI: 10.1038/s41467-019-11386-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/12/2019] [Indexed: 01/04/2023] Open
Abstract
The timely mobilization of hematopoietic stem and progenitor cells (HSPCs) is essential for maintaining hematopoietic and tissue leukocyte homeostasis. Understanding how HSPCs migrate between bone marrow (BM) and peripheral tissues is of great significance in the clinical setting, where therapeutic strategies for modulating their migration capacity determine the clinical outcome. Here, we identify an epigenetic regulator, Phc2, as a critical modulator of HSPC trafficking. The genetic ablation of Phc2 in mice causes a severe defect in HSPC mobilization through the derepression of Vcam1 in bone marrow stromal cells (BMSCs), ultimately leading to a systemic immunodeficiency. Moreover, the pharmacological inhibition of VCAM-1 in Phc2-deficient mice reverses the symptoms. We further determine that Phc2-dependent Vcam1 repression in BMSCs is mediated by the epigenetic regulation of H3K27me3 and H2AK119ub. Together, our data demonstrate a cell-extrinsic role for Phc2 in controlling the mobilization of HSPCs by finely tuning their bone marrow niche. Mobilization of hematopoietic stem and progenitor cells (HSPCs) into the circulation is essential for maintaining homeostasis. Here, the authors show that Phc2 in bone marrow stromal cells represses the cell adhesion molecule Vcam1 and facilitates mobilization of HSPCs through regulation of epigenetic marks.
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26
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Curt JR, Yaghmaeian Salmani B, Thor S. Anterior CNS expansion driven by brain transcription factors. eLife 2019; 8:45274. [PMID: 31271353 PMCID: PMC6634974 DOI: 10.7554/elife.45274] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/03/2019] [Indexed: 02/06/2023] Open
Abstract
During CNS development, there is prominent expansion of the anterior region, the brain. In Drosophila, anterior CNS expansion emerges from three rostral features: (1) increased progenitor cell generation, (2) extended progenitor cell proliferation, (3) more proliferative daughters. We find that tailless (mouse Nr2E1/Tlx), otp/Rx/hbn (Otp/Arx/Rax) and Doc1/2/3 (Tbx2/3/6) are important for brain progenitor generation. These genes, and earmuff (FezF1/2), are also important for subsequent progenitor and/or daughter cell proliferation in the brain. Brain TF co-misexpression can drive brain-profile proliferation in the nerve cord, and can reprogram developing wing discs into brain neural progenitors. Brain TF expression is promoted by the PRC2 complex, acting to keep the brain free of anti-proliferative and repressive action of Hox homeotic genes. Hence, anterior expansion of the Drosophila CNS is mediated by brain TF driven ‘super-generation’ of progenitors, as well as ‘hyper-proliferation’ of progenitor and daughter cells, promoted by PRC2-mediated repression of Hox activity.
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Affiliation(s)
- Jesús Rodriguez Curt
- Department of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden
| | | | - Stefan Thor
- Department of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden.,School of Biomedical Sciences, University of Queensland, Saint Lucia, Australia
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27
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Fursova NA, Blackledge NP, Nakayama M, Ito S, Koseki Y, Farcas AM, King HW, Koseki H, Klose RJ. Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene Repression. Mol Cell 2019; 74:1020-1036.e8. [PMID: 31029541 PMCID: PMC6561741 DOI: 10.1016/j.molcel.2019.03.024] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/04/2019] [Accepted: 03/21/2019] [Indexed: 01/30/2023]
Abstract
The Polycomb system modifies chromatin and plays an essential role in repressing gene expression to control normal mammalian development. However, the components and mechanisms that define how Polycomb protein complexes achieve this remain enigmatic. Here, we use combinatorial genetic perturbation coupled with quantitative genomics to discover the central determinants of Polycomb-mediated gene repression in mouse embryonic stem cells. We demonstrate that canonical Polycomb repressive complex 1 (PRC1), which mediates higher-order chromatin structures, contributes little to gene repression. Instead, we uncover an unexpectedly high degree of synergy between variant PRC1 complexes, which is fundamental to gene repression. We further demonstrate that variant PRC1 complexes are responsible for distinct pools of H2A monoubiquitylation that are associated with repression of Polycomb target genes and silencing during X chromosome inactivation. Together, these discoveries reveal a new variant PRC1-dependent logic for Polycomb-mediated gene repression.
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Affiliation(s)
- Nadezda A Fursova
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Neil P Blackledge
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Manabu Nakayama
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Anca M Farcas
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Hamish W King
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; AMED-CREST, Japanese Agency for Medical Research and Development, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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28
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Xu H, Cao L, Sun B, Wei Y, Liang M. Transcriptomic Analysis of Potential "lncRNA-mRNA" Interactions in Liver of the Marine Teleost Cynoglossus semilaevis Fed Diets With Different DHA/EPA Ratios. Front Physiol 2019; 10:331. [PMID: 31001132 PMCID: PMC6454198 DOI: 10.3389/fphys.2019.00331] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 03/11/2019] [Indexed: 01/22/2023] Open
Abstract
Long non-coding RNAs (lncRNA) have emerged as important regulators of lipid metabolism and have been shown to play multifaceted roles in controlling transcriptional gene regulation, but very little relevant information has been available in fish, especially in non-model fish species. With a feeding trial on a typical marine teleost tongue sole C. semilaevis followed by transcriptomic analysis, the present study investigated the possible involvement of lncRNA in hepatic mRNA expression in response to different levels of dietary DHA and EPA, which are two most important fatty acids for marine fish. An 80-day feeding trial was conducted in a flow-through seawater system, and in this trial three experimental diets differing basically in DHA/EPA ratio, i.e., 0.61 (D/E-0.61), 1.46 (D/E-1.46), and 2.75 (D/E-2.75), were randomly assigned to 9 tanks of experimental fish. A total of 124.04 G high quality genome-wide clean data about coding and non-coding transcripts was obtained in the analysis of hepatic transcriptome. Compared to diet D/E-0.61, D/E-1.46 up-regulated expression of 178 lncRNAs and 2629 mRNAs, and down-regulated that of 47 lncRNAs and 3059 mRNAs, while D/E-2.75 resulted in much less change in gene expression. The co-expression and co-localization analysis of differentially expressed (DE) lncRNA and mRNA among dietary groups were then conducted. The co-expressed DE lncRNA and mRNA were primarily enriched in GO terms such as Metabolic process, Intracellular organelle, Catalytic activity, and Oxidoreductase activity, as well as in KEGG pathways such as Ribosome and Oxidative phosphorylation. Overlap of co-expression and co-localization analysis, i.e., lncRNA–mRNA matches “XR_523541.1–solute carrier family 16, member 5 (slc16a5)” and “LNC_000285–bromodomain adjacent to zinc finger domain 2A (baz2a),” were observed in all inter-group comparisons, indicating that they might crucially mediate the effects of dietary DHA and EPA on hepatic gene expression in tongue sole. In conclusion, this was the first time in marine teleost to investigate the possible lncRNA–mRNA interactions in response to dietary fatty acids. The results provided novel knowledge of lncRNAs in non-model marine teleost, and will serve as important resources for future studies that further investigate the roles of lncRNAs in lipid metabolism of marine teleost.
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Affiliation(s)
- Houguo Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lin Cao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Beijing Institute of Feed Control, Beijing, China
| | - Bo Sun
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Yuliang Wei
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Mengqing Liang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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29
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Katoh-Fukui Y, Baba T, Sato T, Otake H, Nagakui-Noguchi Y, Shindo M, Suyama M, Ohkawa Y, Tsumura H, Morohashi KI, Fukami M. Mouse polycomb group gene Cbx2 promotes osteoblastic but suppresses adipogenic differentiation in postnatal long bones. Bone 2019; 120:219-231. [PMID: 30389610 DOI: 10.1016/j.bone.2018.10.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 12/29/2022]
Abstract
A set of key developmental genes is essential for skeletal growth from multipotent progenitor cells at weaning. Polycomb group proteins, which regulate such genes contributes to the cell lineage commitment and subsequent differentiation via epigenetic chromatin modification and remodeling. However, it is unclear which cell lineage and gene sets are targeted by polycomb proteins during skeletal growth. We now report that mice deficient in a polycomb group gene Cbx2cterm/cterm exhibited skeletal hypoplasia in the tibia, femur, and cranium. Long bone cavities in these mice contained fewer multipotent mesenchymal stromal cells. RNA-sequencing of bone marrow cells showed downregulation and upregulation of osteoblastic and adipogenic genes, respectively. Furthermore, the expression levels of genes specifically expressed in B-cell precursors were decreased. Forced expression of Cbx2 in Cbx2cterm/cterm bone marrow stromal cell recovered fibroblastic colony formation and suppressed adipogenic differentiation. Collectively, our results suggest that Cbx2 controls the maintenance and adipogenic differentiation of mesenchymal stromal cells in the bone marrow.
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Affiliation(s)
- Yuko Katoh-Fukui
- Department of Molecular Endocrinology, National Research Institute of Child Health and Development, Tokyo 157-8535, Japan.
| | - Takashi Baba
- Department of Molecular Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Sato
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan; Division of Bioinformatics, Kyushu University, Fukuoka, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Fukuoka, Japan
| | - Hiroyuki Otake
- Department of Molecular Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | | | - Miyuki Shindo
- Department of Experimental Animals, National Research Institute of Child Health and Development, Tokyo, Japan
| | - Mikita Suyama
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan; Division of Bioinformatics, Kyushu University, Fukuoka, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Fukuoka, Japan
| | - Yasuyuki Ohkawa
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Fukuoka, Japan; Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hideki Tsumura
- Department of Experimental Animals, National Research Institute of Child Health and Development, Tokyo, Japan
| | - Ken-Ichirou Morohashi
- Department of Molecular Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute of Child Health and Development, Tokyo 157-8535, Japan
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30
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Meyer SE, Muench DE, Rogers AM, Newkold TJ, Orr E, O'Brien E, Perentesis JP, Doench JG, Lal A, Morris PJ, Thomas CJ, Lieberman J, McGlinn E, Aronow BJ, Salomonis N, Grimes HL. miR-196b target screen reveals mechanisms maintaining leukemia stemness with therapeutic potential. J Exp Med 2018; 215:2115-2136. [PMID: 29997117 PMCID: PMC6080909 DOI: 10.1084/jem.20171312] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 04/30/2018] [Accepted: 06/26/2018] [Indexed: 01/02/2023] Open
Abstract
We have shown that antagomiR inhibition of miRNA miR-21 and miR-196b activity is sufficient to ablate MLL-AF9 leukemia stem cells (LSC) in vivo. Here, we used an shRNA screening approach to mimic miRNA activity on experimentally verified miR-196b targets to identify functionally important and therapeutically relevant pathways downstream of oncogenic miRNA in MLL-r AML. We found Cdkn1b (p27Kip1) is a direct miR-196b target whose repression enhanced an embryonic stem cell-like signature associated with decreased leukemia latency and increased numbers of leukemia stem cells in vivo. Conversely, elevation of p27Kip1 significantly reduced MLL-r leukemia self-renewal, promoted monocytic differentiation of leukemic blasts, and induced cell death. Antagonism of miR-196b activity or pharmacologic inhibition of the Cks1-Skp2-containing SCF E3-ubiquitin ligase complex increased p27Kip1 and inhibited human AML growth. This work illustrates that understanding oncogenic miRNA target pathways can identify actionable targets in leukemia.
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MESH Headings
- Animals
- Carcinogenesis/genetics
- Carcinogenesis/pathology
- Cell Differentiation/genetics
- Cell Line, Tumor
- Cell Proliferation/genetics
- Cell Survival/genetics
- Chromosomes, Human, Pair 11/genetics
- Cyclin-Dependent Kinase Inhibitor p27/metabolism
- Cyclin-Dependent Kinases/metabolism
- Cyclins/metabolism
- Embryonic Stem Cells/metabolism
- Gene Expression Regulation, Leukemic
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/therapy
- Mice, Inbred C57BL
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Oncogenes
- RNA, Small Interfering/metabolism
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Affiliation(s)
- Sara E Meyer
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - David E Muench
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Andrew M Rogers
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Tess J Newkold
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Emily Orr
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Eric O'Brien
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - John P Perentesis
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Patrick J Morris
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Edwina McGlinn
- EMBL Australia, Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - H Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
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31
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Cameron SR, Nandi S, Kahn TG, Barrasa JI, Stenberg P, Schwartz YB. PTE, a novel module to target Polycomb Repressive Complex 1 to the human cyclin D2 ( CCND2) oncogene. J Biol Chem 2018; 293:14342-14358. [PMID: 30068546 DOI: 10.1074/jbc.ra118.005010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Indexed: 11/06/2022] Open
Abstract
Polycomb group proteins are essential epigenetic repressors. They form multiple protein complexes of which two kinds, PRC1 and PRC2, are indispensable for repression. Although much is known about their biochemical properties, how mammalian PRC1 and PRC2 are targeted to specific genes is poorly understood. Here, we establish the cyclin D2 (CCND2) oncogene as a simple model to address this question. We provide the evidence that the targeting of PRC1 to CCND2 involves a dedicated PRC1-targeting element (PTE). The PTE appears to act in concert with an adjacent cytosine-phosphate-guanine (CpG) island to arrange for the robust binding of PRC1 and PRC2 to repressed CCND2 Our findings pave the way to identify sequence-specific DNA-binding proteins implicated in the targeting of mammalian PRC1 complexes and provide novel link between polycomb repression and cancer.
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Affiliation(s)
| | - Soumyadeep Nandi
- From the Department of Molecular Biology and.,the Computational Life Science Cluster (CLiC), Umeå University, 901 87 Umeå, Sweden and
| | | | | | - Per Stenberg
- From the Department of Molecular Biology and.,the Computational Life Science Cluster (CLiC), Umeå University, 901 87 Umeå, Sweden and.,the Division of Chemical, Biological, Radioactive and Nuclear (CBRN) Security and Defence, FOI-Swedish Defence Research Agency, 906 21 Umeå Sweden
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32
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Suzuki A, Jun G, Abdallah N, Gajera M, Iwata J. Gene datasets associated with mouse cleft palate. Data Brief 2018; 18:655-673. [PMID: 29896534 PMCID: PMC5996166 DOI: 10.1016/j.dib.2018.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 03/01/2018] [Indexed: 12/20/2022] Open
Abstract
This article presents data on genes associated with cleft palate (CP), retrieved through both a full-text systematic review and a mouse genome informatics (MGI) database search. In order to group CP-associated genes according to function, pathway, biological process, and cellular component, the genes were analyzed using category enrichment bioinformatics tools, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO). This approach provides invaluable opportunities for the identification of candidate pathways and genes in CP research.
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Affiliation(s)
- Akiko Suzuki
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Goo Jun
- Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Nada Abdallah
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Mona Gajera
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
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33
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From Flies to Mice: The Emerging Role of Non-Canonical PRC1 Members in Mammalian Development. EPIGENOMES 2018. [DOI: 10.3390/epigenomes2010004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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34
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Yaghmaeian Salmani B, Monedero Cobeta I, Rakar J, Bauer S, Curt JR, Starkenberg A, Thor S. Evolutionarily conserved anterior expansion of the central nervous system promoted by a common PcG-Hox program. Development 2018. [DOI: 10.1242/dev.160747] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A conserved feature of the central nervous system (CNS) is the prominent expansion of anterior regions (brain) when compared to posterior (nerve cord). The cellular and regulatory processes driving anterior CNS expansion are not well understood in any bilaterian species. Here, we address this expansion in Drosophila and mouse. We find that when compared to the nerve cord the brain, in both Drosophila and mouse, displays extended progenitor proliferation, more elaborate daughter cell proliferation and more rapid cell cycle speed. These features contribute to anterior CNS expansion in both species. With respect to genetic control, enhanced brain proliferation is severely reduced by ectopic Hox gene expression, by either Hox misexpression or by loss of Polycomb Group (PcG) function. Strikingly, in PcG mutants, early CNS proliferation appears unaffected, whereas subsequently, brain proliferation is severely reduced. Hence, a conserved PcG-Hox program promotes the anterior expansion of the CNS. The profound differences in proliferation and in the underlying genetic mechanisms between brain and nerve cord lend support to the emerging concept of separate evolutionary origins of these two CNS regions.
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Affiliation(s)
| | - Ignacio Monedero Cobeta
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
| | - Jonathan Rakar
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
| | - Susanne Bauer
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
| | - Jesús Rodriguez Curt
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
| | - Annika Starkenberg
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
| | - Stefan Thor
- Dept. of Clinical and Experimental Medicine, Linkoping University, SE-58185, Linkoping, Sweden
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35
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Yakushiji-Kaminatsui N, Kondo T, Hironaka KI, Sharif J, Endo TA, Nakayama M, Masui O, Koseki Y, Kondo K, Ohara O, Vidal M, Morishita Y, Koseki H. Variant PRC1 competes with retinoic acid-related signals to repress Meis2 in distal forelimb bud. Development 2018; 145:dev.166348. [DOI: 10.1242/dev.166348] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/28/2018] [Indexed: 12/12/2022]
Abstract
Suppression of Meis genes in the distal limb bud is required for Proximal-Distal (PD) specification of the forelimb. Polycomb group (PcG) factors play a role in downregulation of retinoic acid (RA)-related signals in the distal forelimb bud, causing Meis repression. It is, however, not known if downregulation of RA-related signals and PcG-mediated proximal genes repression are functionally linked. Here, we reveal that PcG factors and RA-related signals antagonize each other to polarize Meis2 expression along the PD axis. With mathematical modeling and simulation, we propose that PcG factors are required to adjust the threshold for RA-related signaling to regulate Meis2 expression. Finally, we show that a variant Polycomb repressive complex 1 (PRC1), incorporating PCGF3 and PCGF5, represses Meis2 expression in the distal limb bud. Taken together, we reveal a previously unknown link between PcG proteins and downregulation of RA-related signals to mediate the phase transition of Meis2 transcriptional status during forelimb specification.
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Affiliation(s)
- Nayuta Yakushiji-Kaminatsui
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takashi Kondo
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- KAST, Project on Health and Anti-aging, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Ken-ichi Hironaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 113-0033, Japan
| | - Jafar Sharif
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takaho A. Endo
- Laboratory for Integrative Genomics, RIKEN-IMS, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Manabu Nakayama
- Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Osamu Masui
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kaori Kondo
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- KAST, Project on Health and Anti-aging, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN-IMS, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
- Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Miguel Vidal
- Centro de Investigaciones Biológicas, Department of Cellular and Molecular Biology, Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Yoshihiro Morishita
- Laboratory for Developmental Morphogeometry, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - 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
- CREST, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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36
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PRC1 Prevents Replication Stress during Chondrogenic Transit Amplification. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1030022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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37
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Samd7 is a cell type-specific PRC1 component essential for establishing retinal rod photoreceptor identity. Proc Natl Acad Sci U S A 2017; 114:E8264-E8273. [PMID: 28900001 DOI: 10.1073/pnas.1707021114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Precise transcriptional regulation controlled by a transcription factor network is known to be crucial for establishing correct neuronal cell identities and functions in the CNS. In the retina, the expression of various cone and rod photoreceptor cell genes is regulated by multiple transcription factors; however, the role of epigenetic regulation in photoreceptor cell gene expression has been poorly understood. Here, we found that Samd7, a rod-enriched sterile alpha domain (SAM) domain protein, is essential for silencing nonrod gene expression through H3K27me3 regulation in rod photoreceptor cells. Samd7-null mutant mice showed ectopic expression of nonrod genes including S-opsin in rod photoreceptor cells and rod photoreceptor cell dysfunction. Samd7 physically interacts with Polyhomeotic homologs (Phc proteins), components of the Polycomb repressive complex 1 (PRC1), and colocalizes with Phc2 and Ring1B in Polycomb bodies. ChIP assays showed a significant decrease of H3K27me3 in the genes up-regulated in the Samd7-deficient retina, showing that Samd7 deficiency causes the derepression of nonrod gene expression in rod photoreceptor cells. The current study suggests that Samd7 is a cell type-specific PRC1 component epigenetically defining rod photoreceptor cell identity.
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38
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Endoh M, Endo TA, Shinga J, Hayashi K, Farcas A, Ma KW, Ito S, Sharif J, Endoh T, Onaga N, Nakayama M, Ishikura T, Masui O, Kessler BM, Suda T, Ohara O, Okuda A, Klose R, Koseki H. PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germ cell-related genes. eLife 2017; 6:21064. [PMID: 28304275 PMCID: PMC5375644 DOI: 10.7554/elife.21064] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 03/15/2017] [Indexed: 12/22/2022] Open
Abstract
The ring finger protein PCGF6 (polycomb group ring finger 6) interacts with RING1A/B and E2F6 associated factors to form a non-canonical PRC1 (polycomb repressive complex 1) known as PCGF6-PRC1. Here, we demonstrate that PCGF6-PRC1 plays a role in repressing a subset of PRC1 target genes by recruiting RING1B and mediating downstream mono-ubiquitination of histone H2A. PCGF6-PRC1 bound loci are highly enriched for promoters of germ cell-related genes in mouse embryonic stem cells (ESCs). Conditional ablation of Pcgf6 in ESCs leads to robust de-repression of such germ cell-related genes, in turn affecting cell growth and viability. We also find a role for PCGF6 in pre- and peri-implantation mouse embryonic development. We further show that a heterodimer of the transcription factors MAX and MGA recruits PCGF6 to target loci. PCGF6 thus links sequence specific target recognition by the MAX/MGA complex to PRC1-dependent transcriptional silencing of germ cell-specific genes in pluripotent stem cells.
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Affiliation(s)
- Mitsuhiro Endoh
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan.,Centre for Translational Medicine,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan.,Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jun Shinga
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Katsuhiko Hayashi
- Department of Developmental Stem Cell Biology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Anca Farcas
- Department of Biochemistry, Oxford University, Oxford, United Kingdom
| | - Kit-Wan Ma
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan
| | - Jafar Sharif
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan
| | - Tamie Endoh
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Centre for Translational Medicine,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Naoko Onaga
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Manabu Nakayama
- Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Tomoyuki Ishikura
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Osamu Masui
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Benedikt M Kessler
- Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Toshio Suda
- Centre for Translational Medicine,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Osamu Ohara
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Akihiko Okuda
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan
| | - Robert Klose
- Department of Biochemistry, Oxford University, Oxford, United Kingdom
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Core Research for Evolutional Science and Technology, Yokohama, Japan
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39
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Modular transcriptional repertoire and MicroRNA target analyses characterize genomic dysregulation in the thymus of Down syndrome infants. Oncotarget 2016; 7:7497-533. [PMID: 26848775 PMCID: PMC4884935 DOI: 10.18632/oncotarget.7120] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/23/2016] [Indexed: 12/25/2022] Open
Abstract
Trisomy 21-driven transcriptional alterations in human thymus were characterized through gene coexpression network (GCN) and miRNA-target analyses. We used whole thymic tissue--obtained at heart surgery from Down syndrome (DS) and karyotipically normal subjects (CT)--and a network-based approach for GCN analysis that allows the identification of modular transcriptional repertoires (communities) and the interactions between all the system's constituents through community detection. Changes in the degree of connections observed for hierarchically important hubs/genes in CT and DS networks corresponded to community changes. Distinct communities of highly interconnected genes were topologically identified in these networks. The role of miRNAs in modulating the expression of highly connected genes in CT and DS was revealed through miRNA-target analysis. Trisomy 21 gene dysregulation in thymus may be depicted as the breakdown and altered reorganization of transcriptional modules. Leading networks acting in normal or disease states were identified. CT networks would depict the "canonical" way of thymus functioning. Conversely, DS networks represent a "non-canonical" way, i.e., thymic tissue adaptation under trisomy 21 genomic dysregulation. This adaptation is probably driven by epigenetic mechanisms acting at chromatin level and through the miRNA control of transcriptional programs involving the networks' high-hierarchy genes.
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40
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Connelly KE, Dykhuizen EC. Compositional and functional diversity of canonical PRC1 complexes in mammals. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:233-245. [PMID: 28007606 DOI: 10.1016/j.bbagrm.2016.12.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/12/2016] [Accepted: 12/15/2016] [Indexed: 12/17/2022]
Abstract
The compositional complexity of Polycomb Repressive Complex 1 (PRC1) increased dramatically during vertebrate evolution. What is considered the "canonical" PRC1 complex consists of four subunits originally identified as regulators of body segmentation in Drosophila. In mammals, each of these four canonical subunits consists of two to six paralogs that associate in a combinatorial manner to produce over a hundred possible distinct PRC1 complexes with unknown function. Genetic studies have begun to define the phenotypic roles for different PRC1 paralogs; however, relating these phenotypes to unique biochemical and transcriptional function for the different paralogs has been challenging. In this review, we attempt to address how the compositional diversity of canonical PRC1 complexes relates to unique roles for individual PRC1 paralogs in transcriptional regulation. This review focuses primarily on PRC1 complex composition, genome targeting, and biochemical function.
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Affiliation(s)
- Katelyn E Connelly
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 201 S. University St., West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, 201 S. University St., West Lafayette, IN 47907, USA.
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41
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Kahn TG, Dorafshan E, Schultheis D, Zare A, Stenberg P, Reim I, Pirrotta V, Schwartz YB. Interdependence of PRC1 and PRC2 for recruitment to Polycomb Response Elements. Nucleic Acids Res 2016; 44:10132-10149. [PMID: 27557709 PMCID: PMC5137424 DOI: 10.1093/nar/gkw701] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 12/31/2022] Open
Abstract
Polycomb Group (PcG) proteins are epigenetic repressors essential for control of development and cell differentiation. They form multiple complexes of which PRC1 and PRC2 are evolutionary conserved and obligatory for repression. The targeting of PRC1 and PRC2 is poorly understood and was proposed to be hierarchical and involve tri-methylation of histone H3 (H3K27me3) and/or monoubiquitylation of histone H2A (H2AK118ub). Here, we present a strict test of this hypothesis using the Drosophila model. We discover that neither H3K27me3 nor H2AK118ub is required for targeting PRC complexes to Polycomb Response Elements (PREs). We find that PRC1 can bind PREs in the absence of PRC2 but at many PREs PRC2 requires PRC1 to be targeted. We show that one role of H3K27me3 is to allow PcG complexes anchored at PREs to interact with surrounding chromatin. In contrast, the bulk of H2AK118ub is unrelated to PcG repression. These findings radically change our view of how PcG repression is targeted and suggest that PRC1 and PRC2 can communicate independently of histone modifications.
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Affiliation(s)
- Tatyana G Kahn
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Eshagh Dorafshan
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Dorothea Schultheis
- Friedrich-Alexander University of Erlangen-Nürnberg, Department of Biology, Division of Developmental Biology, Erlangen, D-91058, Germany
| | - Aman Zare
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Per Stenberg
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden.,Division of CBRN Defense and Security, Swedish Defense Research Agency, FOI, Umeå, 906 21, Sweden
| | - Ingolf Reim
- Friedrich-Alexander University of Erlangen-Nürnberg, Department of Biology, Division of Developmental Biology, Erlangen, D-91058, Germany
| | - Vincenzo Pirrotta
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Yuri B Schwartz
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
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42
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Dupret B, Völkel P, Le Bourhis X, Angrand PO. The Polycomb Group Protein Pcgf1 Is Dispensable in Zebrafish but Involved in Early Growth and Aging. PLoS One 2016; 11:e0158700. [PMID: 27442247 PMCID: PMC4956247 DOI: 10.1371/journal.pone.0158700] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/19/2016] [Indexed: 12/31/2022] Open
Abstract
Polycomb Repressive Complex (PRC) 1 regulates the control of gene expression programs via chromatin structure reorganization. Through mutual exclusion, different PCGF members generate a variety of PRC1 complexes with potentially distinct cellular functions. In this context, the molecular function of each of the PCGF family members remains elusive. The study of PCGF family member expression in zebrafish development and during caudal fin regeneration reveals that the zebrafish pcgf genes are subjected to different regulations and that all PRC1 complexes in terms of Pcgf subunit composition are not always present in the same tissues. To unveil the function of Pcgf1 in zebrafish, a mutant line was generated using the TALEN technology. Mutant pcgf1-/- fish are viable and fertile, but the growth rate at early developmental stages is reduced in absence of pcgf1 gene function and a significant number of pcgf1-/- fish show signs of premature aging. This first vertebrate model lacking Pcgf1 function shows that this Polycomb Group protein is involved in cell proliferation during early embryogenesis and establishes a link between epigenetics and aging.
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Affiliation(s)
- Barbara Dupret
- Cell Plasticity & Cancer, Inserm U908 / University of Lille, Lille, France
| | - Pamela Völkel
- Cell Plasticity & Cancer, Inserm U908 / University of Lille, Lille, France
- CNRS, Lille, France
| | - Xuefen Le Bourhis
- Cell Plasticity & Cancer, Inserm U908 / University of Lille, Lille, France
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43
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Piunti A, Shilatifard A. Epigenetic balance of gene expression by Polycomb and COMPASS families. Science 2016; 352:aad9780. [PMID: 27257261 DOI: 10.1126/science.aad9780] [Citation(s) in RCA: 326] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetic regulation of gene expression in metazoans is central for establishing cellular diversity, and its deregulation can result in pathological conditions. Although transcription factors are essential for implementing gene expression programs, they do not function in isolation and require the recruitment of various chromatin-modifying and -remodeling machineries. A classic example of developmental chromatin regulation is the balanced activities of the Polycomb group (PcG) proteins within the PRC1 and PRC2 complexes, and the Trithorax group (TrxG) proteins within the COMPASS family, which are highly mutated in a large number of human diseases. In this review, we will discuss the latest findings regarding the properties of the PcG and COMPASS families and the insight they provide into the epigenetic control of transcription under physiological and pathological settings.
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Affiliation(s)
- Andrea Piunti
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA.
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44
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Josson S, Chung LWK, Gururajan M. microRNAs and Prostate Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 889:105-18. [PMID: 26658999 DOI: 10.1007/978-3-319-23730-5_7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
microRNAs are noncoding RNAs that are important for embryonic stem cell development and epithelial to mesenchymal transition (EMT). Tumor cells hijack EMT and stemness to grow and metastasize to distant organs including bone. In the tumor microenvironment, tumor cells interact with the stromal fibroblasts at the primary and metastatic sites and this interaction leads to tumor growth, EMT, and bone metastasis. Tumor-stromal interactions are a dynamic process that involves both cell-cell communications and extracellular vesicles and soluble factors. Growing body of evidence suggests that microRNAs are part of the payload that comprises the extracellular vesicles. microRNAs induce reactive stroma and thus convert normal stroma into tumor-associated stroma to promote aggressive tumorigenicity in vitro and in vivo. Landmark published studies demonstrate that expression of specific microRNAs of DLK1-DIO3 stem cell cluster correlates with patient survival in metastatic prostate cancer. Thus, microRNAs mediate tumor growth, EMT, and metastasis through cell intrinsic mechanisms and extracellular communications and could be novel biomarkers and therapeutic targets in bone metastatic prostate cancer.
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Affiliation(s)
- Sajni Josson
- Uro-Oncology Research Program, Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA. .,Neostrata Inc., Princeton, NJ, 08540, USA.
| | - Leland W K Chung
- Uro-Oncology Research Program, Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
| | - Murali Gururajan
- Uro-Oncology Research Program, Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA. .,Bristol-Myers Squibb Inc., Princeton, NJ, 08543, USA.
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Sowpati DT, Ramamoorthy S, Mishra RK. Expansion of the polycomb system and evolution of complexity. Mech Dev 2015; 138 Pt 2:97-112. [DOI: 10.1016/j.mod.2015.07.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 07/27/2015] [Accepted: 07/29/2015] [Indexed: 11/28/2022]
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Khan AA, Lee AJ, Roh TY. Polycomb group protein-mediated histone modifications during cell differentiation. Epigenomics 2015; 7:75-84. [PMID: 25687468 DOI: 10.2217/epi.14.61] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Polycomb group (PcG) proteins play an important role in the regulation of gene expression, especially genes encoding lineage-specific factors. Perturbations in PcG protein expression may trigger an unexpected developmental pathway, resulting in birth defects and developmental disabilities. Two Polycomb repressive complexes, PRC1 and PRC2, have been identified and are related with diverse cellular processes through histone modifications. Many developmental genes are trimethylated at histone H3 lysine 27 (H3K27me3) mediated by PRC2, which provides a binding site for PRC1. These processes contribute to chromatin compaction and transcriptional repression. In this review, we discuss about the complex formation of PcG proteins, the mechanism through which they are recruited to target sites and their functional roles in cell differentiation.
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Affiliation(s)
- Abdul Aziz Khan
- Division of Integrative Biosciences & Biotechnology, Pohang University of Science & Technology (POSTECH), Pohang, Gyeongbuk 790-784, Republic of Korea
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Abstract
The chromatin environment is essential for the correct specification and preservation of cell identity through modulation and maintenance of transcription patterns. Many chromatin regulators are required for development, stem cell maintenance, and differentiation. Here, we review the roles of the polycomb repressive complexes, PRC1 and PRC2, and the HDAC1- and HDAC2-containing complexes, NuRD, Sin3, and CoREST, in stem cells, development, and cancer, as well as the ongoing efforts to develop therapies targeting these complexes in human cancer. Furthermore, we discuss the role of repressive complexes in modulating thresholds for gene activation and their importance for specification and maintenance of cell fate.
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Affiliation(s)
- Anne Laugesen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark; The Danish Stem Cell Center (DanStem), University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark; The Danish Stem Cell Center (DanStem), University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark.
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Kitazawa T, Fujisawa K, Narboux-Nême N, Arima Y, Kawamura Y, Inoue T, Wada Y, Kohro T, Aburatani H, Kodama T, Kim KS, Sato T, Uchijima Y, Maeda K, Miyagawa-Tomita S, Minoux M, Rijli FM, Levi G, Kurihara Y, Kurihara H. Distinct effects of Hoxa2 overexpression in cranial neural crest populations reveal that the mammalian hyomandibular-ceratohyal boundary maps within the styloid process. Dev Biol 2015; 402:162-74. [PMID: 25889273 DOI: 10.1016/j.ydbio.2015.04.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 03/30/2015] [Accepted: 04/08/2015] [Indexed: 10/23/2022]
Abstract
Most gnathostomata craniofacial structures derive from pharyngeal arches (PAs), which are colonized by cranial neural crest cells (CNCCs). The anteroposterior and dorsoventral identities of CNCCs are defined by the combinatorial expression of Hox and Dlx genes. The mechanisms associating characteristic Hox/Dlx expression patterns with the topology and morphology of PAs derivatives are only partially known; a better knowledge of these processes might lead to new concepts on the origin of taxon-specific craniofacial morphologies and of certain craniofacial malformations. Here we show that ectopic expression of Hoxa2 in Hox-negative CNCCs results in distinct phenotypes in different CNCC subpopulations. Namely, while ectopic Hoxa2 expression is sufficient for the morphological and molecular transformation of the first PA (PA1) CNCC derivatives into the second PA (PA2)-like structures, this same genetic alteration does not provoke the transformation of derivatives of other CNCC subpopulations, but severely impairs their development. Ectopic Hoxa2 expression results in the transformation of the proximal Meckel's cartilage and of the malleus, two ventral PA1 CNCCs derivatives, into a supernumerary styloid process (SP), a PA2-derived mammalian-specific skeletal structure. These results, together with experiments to inactivate and ectopically activate the Edn1-Dlx5/6 pathway, indicate a dorsoventral PA2 (hyomandibular/ceratohyal) boundary passing through the middle of the SP. The present findings suggest context-dependent function of Hoxa2 in CNCC regional specification and morphogenesis, and provide novel insights into the evolution of taxa-specific patterning of PA-derived structures.
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Affiliation(s)
- Taro Kitazawa
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo 102-0076, Japan
| | - Kou Fujisawa
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Nicolas Narboux-Nême
- Evolution des Régulations Endocriniennes, CNRS, UMR7221, Muséum National d'Histoire Naturelle, 7 rue Cuvier, 75231 Paris Cedex 05, France
| | - Yuichiro Arima
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yumiko Kawamura
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo 102-0076, Japan
| | - Tsuyoshi Inoue
- Laboratory for Systems Biology and Medicine, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan; Department of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Youichiro Wada
- Laboratory for Systems Biology and Medicine, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Takahide Kohro
- Laboratory for Systems Biology and Medicine, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan; Department of Translational Research for Healthcare and Clinical Science, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyuki Aburatani
- Division of Genome Science, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Tatsuhiko Kodama
- Laboratory for Systems Biology and Medicine, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Ki-Sung Kim
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takahiro Sato
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasunobu Uchijima
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo 102-0076, Japan
| | - Kazuhiro Maeda
- Division of Cardiovascular Development and Differentiation, Medical Research Institute, Department of Pediatric Cardiology, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Sachiko Miyagawa-Tomita
- Division of Cardiovascular Development and Differentiation, Medical Research Institute, Department of Pediatric Cardiology, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Maryline Minoux
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculté de chirurgie dentaire, 1, place de l'hôpital, 67 000 Strasbourg, France
| | - Filippo M Rijli
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; University of Basel, CH-4056 Basel, Switzerland
| | - Giovanni Levi
- Evolution des Régulations Endocriniennes, CNRS, UMR7221, Muséum National d'Histoire Naturelle, 7 rue Cuvier, 75231 Paris Cedex 05, France
| | - Yukiko Kurihara
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo 102-0076, Japan
| | - Hiroki Kurihara
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo 102-0076, Japan; Institute for Biology and Mathematics of Dynamical Cell Processes (iBMath), The University of Tokyo, 3-8-1 Komaba, Tokyo 153-8914, Japan.
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MK3 modulation affects BMI1-dependent and independent cell cycle check-points. PLoS One 2015; 10:e0118840. [PMID: 25853770 PMCID: PMC4390245 DOI: 10.1371/journal.pone.0118840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 01/14/2015] [Indexed: 01/04/2023] Open
Abstract
Although the MK3 gene was originally found deleted in some cancers, it is highly expressed in others. The relevance of MK3 for oncogenesis is currently not clear. We recently reported that MK3 controls ERK activity via a negative feedback mechanism. This prompted us to investigate a potential role for MK3 in cell proliferation. We here show that overexpression of MK3 induces a proliferative arrest in normal diploid human fibroblasts, characterized by enhanced expression of replication stress- and senescence-associated markers. Surprisingly, MK3 depletion evokes similar senescence characteristics in the fibroblast model. We previously identified MK3 as a binding partner of Polycomb Repressive Complex 1 (PRC1) proteins. In the current study we show that MK3 overexpression results in reduced cellular EZH2 levels and concomitant loss of epigenetic H3K27me3-marking and PRC1/chromatin-occupation at the CDKN2A/INK4A locus. In agreement with this, the PRC1 oncoprotein BMI1, but not the PCR2 protein EZH2, bypasses MK3-induced senescence in fibroblasts and suppresses P16INK4A expression. In contrast, BMI1 does not rescue the MK3 loss-of-function phenotype, suggesting the involvement of multiple different checkpoints in gain and loss of MK3 function. Notably, MK3 ablation enhances proliferation in two different cancer cells. Finally, the fibroblast model was used to evaluate the effect of potential tumorigenic MK3 driver-mutations on cell proliferation and M/SAPK signaling imbalance. Taken together, our findings support a role for MK3 in control of proliferation and replicative life-span, in part through concerted action with BMI1, and suggest that the effect of MK3 modulation or mutation on M/SAPK signaling and, ultimately, proliferation, is cell context-dependent.
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Abstract
USP7 is a protein deubiquitinase with an essential role in development. Here, we provide evidence that USP7 regulates the activity of Polycomb repressive complex 1 (PRC1) in coordination with SCML2. There are six versions of PRC1 defined by the association of one of the PCGF homologues (PCGF1 to PCGF6) with the common catalytic subunit RING1B. First, we show that SCML2, a Polycomb group protein that associates with PRC1.2 (containing PCGF2/MEL18) and PRC1.4 (containing PCGF4/BMI1), modulates the localization of USP7 and bridges USP7 with PRC1.4, allowing for the stabilization of BMI1. Chromatin immunoprecipitation (ChIP) experiments demonstrate that USP7 is found at SCML2 and BMI1 target genes. Second, inhibition of USP7 leads to a reduction in the level of ubiquitinated histone H2A (H2Aub), the catalytic product of PRC1 and key for its repressive activity. USP7 regulates the posttranslational status of RING1B and BMI1, a specific component of PRC1.4. Thus, not only does USP7 stabilize PRC1 components, its catalytic activity is also necessary to maintain a functional PRC1, thereby ensuring appropriate levels of repressive H2Aub.
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