1
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Brown K, Chew PY, Ingersoll S, Espinosa JR, Aguirre A, Espinoza A, Wen J, Astatike K, Kutateladze TG, Collepardo-Guevara R, Ren X. Principles of assembly and regulation of condensates of Polycomb repressive complex 1 through phase separation. Cell Rep 2023; 42:113136. [PMID: 37756159 PMCID: PMC10862386 DOI: 10.1016/j.celrep.2023.113136] [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: 01/19/2023] [Revised: 07/01/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Polycomb repressive complex 1 (PRC1) undergoes phase separation to form Polycomb condensates that are multi-component hubs for silencing Polycomb target genes. In this study, we demonstrate that formation and regulation of PRC1 condensates are consistent with the scaffold-client model, where the Chromobox 2 (CBX2) protein behaves as the scaffold while the other PRC1 proteins are clients. Such clients induce a re-entrant phase transition of CBX2 condensates. The composition of the multi-component PRC1 condensates (1) determines the dynamic properties of the scaffold protein; (2) selectively promotes the formation of CBX4-PRC1 condensates while dissolving condensates of CBX6-, CBX7-, and CBX8-PRC1; and (3) controls the enrichment of CBX4-, CBX7-, and CBX8-PRC1 in CBX2-PRC1 condensates and the exclusion of CBX6-PRC1 from CBX2-PRC1 condensates. Our findings uncover how multi-component PRC1 condensates are assembled via an intricate scaffold-client mechanism whereby the properties of the PRC1 condensates are sensitively regulated by its composition and stoichiometry.
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Affiliation(s)
- Kyle Brown
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Pin Yu Chew
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Steven Ingersoll
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Jorge R Espinosa
- Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
| | - Anne Aguirre
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Axel Espinoza
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Joey Wen
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Kalkidan Astatike
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK; Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA; Department of Integrative Biology, University of Colorado Denver, Denver, CO 80217-3364, USA.
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2
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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: 41] [Impact Index Per Article: 20.5] [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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3
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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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4
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Hart D, Rodríguez Gutiérrez D, Biason-Lauber A. CBX2 in DSD: The Quirky Kid on the Block. Sex Dev 2022; 16:162-170. [PMID: 35263754 DOI: 10.1159/000522164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 01/21/2022] [Indexed: 11/19/2022] Open
Abstract
Sex development is an intricate and crucial process in all vertebrates that ensures the continued propagation of genetic diversity within a species, and ultimately their survival. Perturbations in this process can manifest as disorders/differences of sex development (DSD). Various transcriptional networks have been linked to development of the gonad into either male or female, which is actively driven by a set of genes that function in a juxtaposed manner and is maintained through the developmental stages to preserve the final sexual identity. One such identified gene is Chromobox homolog 2 (CBX2), an important ortholog of the Polycomb group (PcG) proteins, that functions as both chromatin modifier and highly dynamic transactivator. CBX2 was shown to be an essential factor for gonadal development in mammals, as genetic variants or loss-of-function of CBX2 can cause sex reversal in mice and humans. Here we will provide an overview of CBX2, its biological functions at molecular level, and the CBX2-dependent transcriptional landscape in gonadal development and DSD.
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Affiliation(s)
- Dirk Hart
- Endocrinology Division, Department of Endocrinology, Metabolism and Cardiovascular System, Section of Medicine, University of Fribourg, Fribourg, Switzerland,
| | - Daniel Rodríguez Gutiérrez
- Endocrinology Division, Department of Endocrinology, Metabolism and Cardiovascular System, Section of Medicine, University of Fribourg, Fribourg, Switzerland
| | - Anna Biason-Lauber
- Endocrinology Division, Department of Endocrinology, Metabolism and Cardiovascular System, Section of Medicine, University of Fribourg, Fribourg, Switzerland
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5
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Lan HC, Du TH, Yao YL, Yang WM. Ocular disease-associated mutations diminish the mitotic chromosome retention ability of PAX6. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194751. [PMID: 34500082 DOI: 10.1016/j.bbagrm.2021.194751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 10/20/2022]
Abstract
Transcription factors play a key role in maintaining cell identity. One mechanism of such cell memory after multiple rounds of cell division cycles is through persistent mitotic chromosome binding, although how individual transcription factors achieve mitotic chromosome retention is not completely understood. Here we show that PAX6, a lineage-determining transcription factor, coats mitotic chromosomes. Using deletion and point mutants associated with human ocular diseases in live-cell imaging analysis, we identified two regions, MCR-D1 and MCR-D2, that were responsible for mitotic chromosome retention of PAX6. We also identified three nuclear localization signals (NLSs) that contributed to mitotic chromosome retention independent of their nuclear import functions. Full mitotic chromosome retention required the presence of DNA-binding domains as well as NLSs within MCR-Ds. Furthermore, disease-associated mutations and NLS mutations changed the distribution of intrinsically disordered regions (IDRs) in PAX6. Our findings not only identify PAX6 as a novel mitotic chromosome retention factor but also demonstrate that the mechanism of mitotic chromosome retention involves sequence-specific DNA binding, NLSs, and molecular conformation determined by IDRs. These findings link mitotic chromosome retention with PAX6-related pathogenesis and imply similar mechanisms for other lineage-determining factors in the PAX family.
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Affiliation(s)
- Hsin-Chi Lan
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ting-Huei Du
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ya-Li Yao
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 41354, Taiwan.
| | - Wen-Ming Yang
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40227, Taiwan; Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan.
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6
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Brown K, Andrianakos H, Ingersoll S, Ren X. Single-molecule imaging of epigenetic complexes in living cells: insights from studies on Polycomb group proteins. Nucleic Acids Res 2021; 49:6621-6637. [PMID: 34009336 PMCID: PMC8266577 DOI: 10.1093/nar/gkab304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 12/30/2022] Open
Abstract
Chromatin-associated factors must locate, bind to, and assemble on specific chromatin regions to execute chromatin-templated functions. These dynamic processes are essential for understanding how chromatin achieves regulation, but direct quantification in living mammalian cells remains challenging. Over the last few years, live-cell single-molecule tracking (SMT) has emerged as a new way to observe trajectories of individual chromatin-associated factors in living mammalian cells, providing new perspectives on chromatin-templated activities. Here, we discuss the relative merits of live-cell SMT techniques currently in use. We provide new insights into how Polycomb group (PcG) proteins, master regulators of development and cell differentiation, decipher genetic and epigenetic information to achieve binding stability and highlight that Polycomb condensates facilitate target-search efficiency. We provide perspectives on liquid-liquid phase separation in organizing Polycomb targets. We suggest that epigenetic complexes integrate genetic and epigenetic information for target binding and localization and achieve target-search efficiency through nuclear organization.
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Affiliation(s)
- Kyle Brown
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | | | - Steven Ingersoll
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
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7
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M33 condenses chromatin through nuclear body formation and methylation of both histone H3 lysine 9 and lysine 27. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119100. [PMID: 34274396 DOI: 10.1016/j.bbamcr.2021.119100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 11/23/2022]
Abstract
Heterochromatin, a type of condensed DNA in eukaryotic cells, has two main categories: Constitutive heterochromatin, which contains H3K9 methylation, and facultative heterochromatin, which contains H3K27 methylation. Methylated H3K9 and H3K27 serve as docking sites for chromodomain-containing proteins that compact chromatin. M33 (also known as CBX2) is a chromodomain-containing protein that binds H3K27me3 and compacts chromatin in vitro. However, whether M33 mediates chromatin compaction in cellulo remains unknown. Here we show that M33 compacts chromatin into DAPI-intense heterochromatin domains in cells. The formation of these heterochromatin domains requires H3K27me3, which recruits M33 to form nuclear bodies. G9a and SUV39H1 are sequentially recruited into M33 nuclear bodies to create H3K9 methylated chromatin in a process that is independent of HP1α. Finally, M33 decreases progerin-induced nuclear envelope disruption caused by loss of heterochromatin. Our findings demonstrate that M33 mediates the formation of condensed chromatin by forming nuclear bodies containing both H3K27me3 and H3K9me3. Our model of M33-dependent chromatin condensation suggests H3K27 methylation corroborates with H3K9 methylation during the formation of facultative heterochromatin and provides the theoretical basis for developing novel therapies to treat heterochromatin-related diseases.
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8
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Baumann C, Zhang X, De La Fuente R. Loss of CBX2 induces genome instability and senescence-associated chromosomal rearrangements. J Cell Biol 2021; 219:152063. [PMID: 32870972 PMCID: PMC7594495 DOI: 10.1083/jcb.201910149] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 06/08/2020] [Accepted: 08/02/2020] [Indexed: 01/05/2023] Open
Abstract
The polycomb group protein CBX2 is an important epigenetic reader involved in cell proliferation and differentiation. While CBX2 overexpression occurs in a wide range of human tumors, targeted deletion results in homeotic transformation, proliferative defects, and premature senescence. However, its cellular function(s) and whether it plays a role in maintenance of genome stability remain to be determined. Here, we demonstrate that loss of CBX2 in mouse fibroblasts induces abnormal large-scale chromatin structure and chromosome instability. Integrative transcriptome analysis and ATAC-seq revealed a significant dysregulation of transcripts involved in DNA repair, chromocenter formation, and tumorigenesis in addition to changes in chromatin accessibility of genes involved in lateral sclerosis, basal transcription factors, and folate metabolism. Notably, Cbx2−/− cells exhibit prominent decondensation of satellite DNA sequences at metaphase and increased sister chromatid recombination events leading to rampant chromosome instability. The presence of extensive centromere and telomere defects suggests a prominent role for CBX2 in heterochromatin homeostasis and the regulation of nuclear architecture.
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Affiliation(s)
- Claudia Baumann
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, GA.,Regenerative Bioscience Center, University of Georgia, Athens, GA
| | - Xiangyu Zhang
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, GA.,Regenerative Bioscience Center, University of Georgia, Athens, GA
| | - Rabindranath De La Fuente
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, GA.,Regenerative Bioscience Center, University of Georgia, Athens, GA
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9
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Iqbal MA, Siddiqui S, Ur Rehman A, Siddiqui FA, Singh P, Kumar B, Saluja D. Multiomics integrative analysis reveals antagonistic roles of CBX2 and CBX7 in metabolic reprogramming of breast cancer. Mol Oncol 2021; 15:1450-1465. [PMID: 33400401 PMCID: PMC8096797 DOI: 10.1002/1878-0261.12894] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/07/2020] [Accepted: 12/31/2020] [Indexed: 12/24/2022] Open
Abstract
Striking similarity exists between metabolic changes associated with embryogenesis and tumorigenesis. Chromobox proteins‐CBX2/4/6/7/8, core components of canonical polycomb repressor complex 1, play essential roles in embryonic development and aberrantly expressed in breast cancer. Understanding how altered CBX expression relates to metabolic reprogramming in breast cancer may reveal vulnerabilities of therapeutic pertinence. Using transcriptomic and metabolomic data from breast cancer patients (N > 3000 combined), we performed pathway‐based analysis and identified outstanding roles of CBX2 and CBX7 in positive and negative regulation of glucose metabolism, respectively. Genetic ablation experiments validated the contrasting roles of two isoforms in cancer metabolism and cell growth. Furthermore, we provide evidence for the role of mammalian target of rapamycin complex 1 signaling in mediating contrary effects of CBX2 and CBX7 on breast cancer metabolism. Underpinning the biological significance of metabolic roles, CBX2 and CBX7 were found to be the most up‐ and downregulated isoforms, respectively, in breast tumors compared with normal tissues. Moreover, CBX2 and CBX7 expression (not other isoforms) correlated strongly, but oppositely, with breast tumor subtype aggressiveness and the proliferation markers. Consistently, genomic data also showed higher amplification frequency of CBX2, not CBX7, in breast tumors. Highlighting the clinical significance of findings, disease‐specific survival and drug sensitivity analysis revealed that CBX2 and CBX7 predicted patient outcome and sensitivity to FDA‐approved/investigational drugs. In summary, this work identifies novel cross talk between CBX2/7 and breast tumor metabolism, and the results presented may have implications in strategies targeting breast cancer.
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Affiliation(s)
- Mohammad Askandar Iqbal
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Shumaila Siddiqui
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Asad Ur Rehman
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, India
| | - Farid Ahmad Siddiqui
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India.,Turku Centre for Biotechnology, BioCity, University of Turku and Abo Akademi, Finland
| | - Prithvi Singh
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia (A Central University), New Delhi, India.,Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Bhupender Kumar
- Department of Biochemistry, Institute of Home Economics, University of Delhi, India
| | - Daman Saluja
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, India
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10
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Kent S, Brown K, Yang CH, Alsaihati N, Tian C, Wang H, Ren X. Phase-Separated Transcriptional Condensates Accelerate Target-Search Process Revealed by Live-Cell Single-Molecule Imaging. Cell Rep 2020; 33:108248. [PMID: 33053359 PMCID: PMC7593837 DOI: 10.1016/j.celrep.2020.108248] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/07/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
Compartmentalization by liquid-liquid phase separation is implicated in transcription. It remains unclear whether and how transcriptional condensates accelerate the search of transcriptional regulatory factors for their target sites. Furthermore, the molecular mechanisms by which regulatory factors nucleate on chromatin to assemble transcriptional condensates remain incompletely understood. The CBX-PRC1 complexes compartmentalize key developmental regulators for repression through phase-separated condensates driven by the chromobox 2 (CBX2) protein. Here, by using live-cell single-molecule imaging, we show that CBX2 nucleates on chromatin independently of H3K27me3 and CBX-PRC1. The interactions between CBX2 and DNA are essential for nucleating CBX-PRC1 on chromatin to assemble condensates. The assembled condensates shorten 3D diffusion time and reduce trials for finding specific sites through revisiting the same or adjacent sites repetitively, thereby accelerating CBX2 in searching for target sites. Overall, our data suggest a generic mechanism by which transcriptional regulatory factors nucleate to assemble condensates that accelerate their target-search process. Kent et al. demonstrate that CBX2 phase separates to assemble Polycomb condensates on chromatin through CBX2 interactions with DNA rather than H3K27me3. The assembled condensates accelerate the search of CBX2 for its cognate binding sites by revisiting the same or adjacent sites repetitively, thereby enhancing the genomic occupancy of CBX2.
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Affiliation(s)
- Samantha Kent
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Kyle Brown
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Chou-Hsun Yang
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Njood Alsaihati
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Christina Tian
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Haobin Wang
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA.
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11
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Wang W, Li X, Guan C, Hu Z, Zhao Y, Li W, Jiang X. LncRNA PCAT6 promotes the proliferation, migration and invasion of pancreatic ductal adenocarcinoma via regulating miR-185-5p/CBX2 axis. Pathol Res Pract 2020; 216:153074. [PMID: 32825947 DOI: 10.1016/j.prp.2020.153074] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/31/2020] [Accepted: 06/17/2020] [Indexed: 12/18/2022]
Abstract
Emerging evidence has revealed markedly roles for long noncoding RNAs (lncRNAs) in various cancer processes. Prostate cancer associated transcript 6 (PCAT6) is a novel lncRNA which displays vital regulatory functions in multiple cancers. However, the functions of PCAT6 in pancreatic ductal adenocarcinoma (PDAC) remain unclear. Our study confirmed that PCAT6 expression was upregulated in PDAC and the expression of PCAT6 was related to TNM stage, lymph node invasion and overall survival of PDAC patients. PCAT6 might act as an effective tumor biomarker for PDAC patients. Moreover, knockdown of PCAT6 inhibited cell proliferation, migration and invasion of PDAC in vitro. For the mechanism, miR-185-5p expression was decreased and chromobox 2 (CBX2) expression was increased in PDAC, and further PCAT6 could upregulated the expression of oncogene CBX2 by sponging miR-185-5p. The results above suggested that PCAT6/miR-185-5p/CBX2 exerted crucial functions in tumorigenesis and progression of PDAC.
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Affiliation(s)
- Weina Wang
- Department of Anesthesiology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Xiang Li
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Canghai Guan
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Zengtao Hu
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Yuqiao Zhao
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, China
| | - Wenzhi Li
- Department of Anesthesiology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, China.
| | - Xingming Jiang
- Department of General Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin 150086, China.
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12
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Liu Z, Tardat M, Gill ME, Royo H, Thierry R, Ozonov EA, Peters AH. SUMOylated PRC1 controls histone H3.3 deposition and genome integrity of embryonic heterochromatin. EMBO J 2020; 39:e103697. [PMID: 32395866 PMCID: PMC7327501 DOI: 10.15252/embj.2019103697] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 12/14/2022] Open
Abstract
Chromatin integrity is essential for cellular homeostasis. Polycomb group proteins modulate chromatin states and transcriptionally repress developmental genes to maintain cell identity. They also repress repetitive sequences such as major satellites and constitute an alternative state of pericentromeric constitutive heterochromatin at paternal chromosomes (pat‐PCH) in mouse pre‐implantation embryos. Remarkably, pat‐PCH contains the histone H3.3 variant, which is absent from canonical PCH at maternal chromosomes, which is marked by histone H3 lysine 9 trimethylation (H3K9me3), HP1, and ATRX proteins. Here, we show that SUMO2‐modified CBX2‐containing Polycomb Repressive Complex 1 (PRC1) recruits the H3.3‐specific chaperone DAXX to pat‐PCH, enabling H3.3 incorporation at these loci. Deficiency of Daxx or PRC1 components Ring1 and Rnf2 abrogates H3.3 incorporation, induces chromatin decompaction and breakage at PCH of exclusively paternal chromosomes, and causes their mis‐segregation. Complementation assays show that DAXX‐mediated H3.3 deposition is required for chromosome stability in early embryos. DAXX also regulates repression of PRC1 target genes during oogenesis and early embryogenesis. The study identifies a novel critical role for Polycomb in ensuring heterochromatin integrity and chromosome stability in mouse early development.
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Affiliation(s)
- Zichuan Liu
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Mathieu Tardat
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Mark E Gill
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Helene Royo
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Raphael Thierry
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Evgeniy A Ozonov
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Antoine Hfm Peters
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Sciences, University of Basel, Basel, Switzerland
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13
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Flyamer IM, Illingworth RS, Bickmore WA. Coolpup.py: versatile pile-up analysis of Hi-C data. Bioinformatics 2020; 36:2980-2985. [PMID: 32003791 PMCID: PMC7214034 DOI: 10.1093/bioinformatics/btaa073] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/16/2020] [Accepted: 01/27/2020] [Indexed: 01/08/2023] Open
Abstract
MOTIVATION Hi-C is currently the method of choice to investigate the global 3D organization of the genome. A major limitation of Hi-C is the sequencing depth required to robustly detect loops in the data. A popular approach used to mitigate this issue, even in single-cell Hi-C data, is genome-wide averaging (piling-up) of peaks, or other features, annotated in high-resolution datasets, to measure their prominence in less deeply sequenced data. However, current tools do not provide a computationally efficient and versatile implementation of this approach. RESULTS Here, we describe coolpup.py-a versatile tool to perform pile-up analysis on Hi-C data. We demonstrate its utility by replicating previously published findings regarding the role of cohesin and CTCF in 3D genome organization, as well as discovering novel details of Polycomb-driven interactions. We also present a novel variation of the pile-up approach that can aid the statistical analysis of looping interactions. We anticipate that coolpup.py will aid in Hi-C data analysis by allowing easy to use, versatile and efficient generation of pile-ups. AVAILABILITY AND IMPLEMENTATION Coolpup.py is cross-platform, open-source and free (MIT licensed) software. Source code is available from https://github.com/Phlya/coolpuppy and it can be installed from the Python Packaging Index.
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Affiliation(s)
- Ilya M Flyamer
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Robert S Illingworth
- MRC Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, EH4 2XU, UK
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14
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Cbx2, a PcG Family Gene, Plays a Regulatory Role in Medaka Gonadal Development. Int J Mol Sci 2020; 21:ijms21041288. [PMID: 32075028 PMCID: PMC7072964 DOI: 10.3390/ijms21041288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 02/07/2023] Open
Abstract
Chromobox homolog 2 (CBX2), a key member of the polycomb group (PcG) family, is essential for gonadal development in mammals. A functional deficiency or genetic mutation in cbx2 can lead to sex reversal in mice and humans. However, little is known about the function of cbx2 in gonadal development in fish. In this study, the cbx2 gene was identified in medaka, which is a model species for the study of gonadal development in fish. Transcription of cbx2 was abundant in the gonads, with testicular levels relatively higher than ovarian levels. In situ hybridization (ISH) revealed that cbx2 mRNA was predominately localized in spermatogonia and spermatocytes, and was also observed in oocytes at stages I, II, and III. Furthermore, cbx2 and vasa (a marker gene) were co-localized in germ cells by fluorescent in situ hybridization (FISH). After cbx2 knockdown in the gonads by RNA interference (RNAi), the sex-related genes, including sox9 and foxl2, were influenced. These results suggest that cbx2 not only plays a positive role in spermatogenesis and oogenesis but is also involved in gonadal differentiation through regulating the expression levels of sex-related genes in fish.
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15
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Advances in epigenetics link genetics to the environment and disease. Nature 2019; 571:489-499. [DOI: 10.1038/s41586-019-1411-0] [Citation(s) in RCA: 566] [Impact Index Per Article: 113.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 06/14/2019] [Indexed: 12/16/2022]
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16
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Jangal M, Lebeau B, Witcher M. Beyond EZH2: is the polycomb protein CBX2 an emerging target for anti-cancer therapy? Expert Opin Ther Targets 2019; 23:565-578. [PMID: 31177918 DOI: 10.1080/14728222.2019.1627329] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Epigenetic modifications are important regulators of transcription and appropriate gene expression answering an environmental stimulus. In cancer, these epigenetic modifications are altered, which impact the transcriptome, promoting initiation and cancer progression. Thus, targeting epigenetic machinery has proven to be an efficient cancer therapy. Areas covered: We review CBX2 as a therapeutic target. CBX2 is a polycomb protein, responsible for polycomb-repressive complex 1 (PRC1) targeting to chromatin via recognition of the repressive mark H3K27me3. Mechanistically, CBX2 overexpression may be implicated in poor survival by maintaining cancer stem cells in an undifferentiated state and via repression of tumor suppressors. We discuss strategies used to target CBX proteins and provide insights into biomarker considerations that may be important when targeting CBX family members for anti-cancer therapy. Expert opinion: CBX2 inhibition is a promising approach for the targeting of polycomb complexes in the cancer stem cell niche. However, extensive optimization of the current field of small molecules targeting CBX family proteins will be critical to reach in vivo, or clinical, utility.
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Affiliation(s)
- Maïka Jangal
- a The Lady Davis Institute of the Jewish General Hospital, Department of Oncology , McGill University , Montreal , Canada
| | - Benjamin Lebeau
- a The Lady Davis Institute of the Jewish General Hospital, Department of Oncology , McGill University , Montreal , Canada
| | - Michael Witcher
- a The Lady Davis Institute of the Jewish General Hospital, Department of Oncology , McGill University , Montreal , Canada
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17
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Plys AJ, Davis CP, Kim J, Rizki G, Keenen MM, Marr SK, Kingston RE. Phase separation of Polycomb-repressive complex 1 is governed by a charged disordered region of CBX2. Genes Dev 2019; 33:799-813. [PMID: 31171700 PMCID: PMC6601514 DOI: 10.1101/gad.326488.119] [Citation(s) in RCA: 223] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/08/2019] [Indexed: 12/15/2022]
Abstract
Here, Plys et al. demonstrate that reconstituted PRC1 readily phase-separates into droplets in vitro at low concentrations and physiological salt conditions, and this behavior is driven by the CBX2 subunit. Mammalian development requires effective mechanisms to repress genes whose expression would generate inappropriately specified cells. The Polycomb-repressive complex 1 (PRC1) family complexes are central to maintaining this repression. These include a set of canonical PRC1 complexes, each of which contains four core proteins, including one from the CBX family. These complexes have been shown previously to reside in membraneless organelles called Polycomb bodies, leading to speculation that canonical PRC1 might be found in a separate phase from the rest of the nucleus. We show here that reconstituted PRC1 readily phase-separates into droplets in vitro at low concentrations and physiological salt conditions. This behavior is driven by the CBX2 subunit. Point mutations in an internal domain of Cbx2 eliminate phase separation. These same point mutations eliminate the formation of puncta in cells and have been shown previously to eliminate nucleosome compaction in vitro and generate axial patterning defects in mice. Thus, the domain of CBX2 that is important for phase separation is the same domain shown previously to be important for chromatin compaction and proper development, raising the possibility of a mechanistic or evolutionary link between these activities.
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Affiliation(s)
- Aaron J Plys
- Department of Molecular Biology, Massachusetts General Hospital Research Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Christopher P Davis
- Department of Molecular Biology, Massachusetts General Hospital Research Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jongmin Kim
- Department of Molecular Biology, Massachusetts General Hospital Research Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Gizem Rizki
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Madeline M Keenen
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Sharon K Marr
- Department of Molecular Biology, Massachusetts General Hospital Research Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital Research Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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18
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Han Q, Li C, Cao Y, Bao J, Li K, Song R, Chen X, Li J, Wu X. CBX2 is a functional target of miRNA let-7a and acts as a tumor promoter in osteosarcoma. Cancer Med 2019; 8:3981-3991. [PMID: 31150156 PMCID: PMC6639449 DOI: 10.1002/cam4.2320] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 04/27/2019] [Accepted: 05/17/2019] [Indexed: 12/25/2022] Open
Abstract
Osteosarcoma is the most common type of primary malignant tumor of skeletal with poor prognosis in children and adolescents. Accumulating evidence indicates that CBX2 is overexpressed in multiple human neoplasm and play a critical role in tumorigenesis and progression. However, its functional role and upstream regulation mechanism in osteosarcoma remain unknown. In the present study, tissue microarray (TMA) analysis was performed to determine the association between CBX2 expression and clinical prognosis of osteosarcoma patients by immunohistochemistry. We also investigated the functional role of CBX2 using small interfering RNA (siRNA) in vitro and in vivo. Additionally, we confirmed the direct binding between CBX2 and let‐7a via qPCR, western blot and luciferase reporter assay. We found that CBX2 is dramatically upregulated in osteosarcoma tissues and high CBX2 expression was correlated with metastasis, recurrence, and chemotherapy response, as well as unfavorable prognosis in patients with osteosarcoma. Similar results were observed in a sarcoma cohort from The Cancer Genome Atlas (TCGA) dataset. Further experiments revealed that CBX2 knockdown significantly impeded osteosarcoma cell proliferation and invasion ability in vitro, and suppressed the tumor growth in tumor xenografts model. Mechanistically, we confirmed that CBX2 is a functional target of miRNA let‐7a. Overexpression of let‐7a inhibits osteosarcoma cell proliferation, which was reversed by CBX2 overexpression. Taken together, our study demonstrates that let‐7a/CBX2 plays a crucial role in osteosarcoma progression. CBX2 could serve as a promising prognostic biomarker and potential therapeutic target for osteosarcoma patients.
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Affiliation(s)
- Qicai Han
- Department of Bone and Soft Tissue, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chao Li
- Department of Bone and Soft Tissue, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Yuan Cao
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Bao
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kongfei Li
- Department of Hematology, Yinzhou People's Hospital affiliated to Medical College of Ningbo University, Ningbo, China
| | - Ruipeng Song
- Department of Bone and Soft Tissue, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaolong Chen
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Juan Li
- Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xuejian Wu
- Department of Bone and Soft Tissue, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Department of Bone and Soft Tissue, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China.,Key Laboratory of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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19
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Tatavosian R, Kent S, Brown K, Yao T, Duc HN, Huynh TN, Zhen CY, Ma B, Wang H, Ren X. Nuclear condensates of the Polycomb protein chromobox 2 (CBX2) assemble through phase separation. J Biol Chem 2018; 294:1451-1463. [PMID: 30514760 DOI: 10.1074/jbc.ra118.006620] [Citation(s) in RCA: 227] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 11/28/2018] [Indexed: 01/01/2023] Open
Abstract
Polycomb group (PcG) proteins repress master regulators of development and differentiation through organization of chromatin structure. Mutation and dysregulation of PcG genes cause developmental defects and cancer. PcG proteins form condensates in the cell nucleus, and these condensates are the physical sites of PcG-targeted gene silencing via formation of facultative heterochromatin. However, the physiochemical principles underlying the formation of PcG condensates remain unknown, and their determination could shed light on how these condensates compact chromatin. Using fluorescence live-cell imaging, we observed that the Polycomb repressive complex 1 (PRC1) protein chromobox 2 (CBX2), a member of the CBX protein family, undergoes phase separation to form condensates and that the CBX2 condensates exhibit liquid-like properties. Using site-directed mutagenesis, we demonstrated that the conserved residues of CBX2 within the intrinsically disordered region (IDR), which is the region for compaction of chromatin in vitro, promote the condensate formation both in vitro and in vivo We showed that the CBX2 condensates concentrate DNA and nucleosomes. Using genetic engineering, we report that trimethylation of Lys-27 at histone H3 (H3K27me3), a marker of heterochromatin formation produced by PRC2, had minimal effects on the CBX2 condensate formation. We further demonstrated that the CBX2 condensate formation does not require CBX2-PRC1 subunits; however, the condensate formation of CBX2-PRC1 subunits depends on CBX2, suggesting a mechanism underlying the assembly of CBX2-PRC1 condensates. In summary, our results reveal that PcG condensates assemble through liquid-liquid phase separation (LLPS) and suggest that phase-separated condensates can organize PcG-bound chromatin.
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Affiliation(s)
- Roubina Tatavosian
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364
| | - Samantha Kent
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364
| | - Kyle Brown
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Huy Nguyen Duc
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364
| | - Thao Ngoc Huynh
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364
| | - Chao Yu Zhen
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364
| | - Brian Ma
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364
| | - Haobin Wang
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364.
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20
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Abstract
Epigenetic complexes regulate chromatin dynamics via binding to and assembling on chromatin. However, the mechanisms of chromatin binding and assembly of epigenetic complexes within cells remain incompletely understood, partly due to technical challenges. Here, we present a new approach termed single-molecule chromatin immunoprecipitation imaging (Sm-ChIPi) that enables to assess the cellular assembly stoichiometry of epigenetic complexes on chromatin. Sm-ChIPi was developed based on chromatin immunoprecipitation followed by single-molecule fluorescence microscopy imaging. In this method, an epigenetic complex subunit fused with a gene coding for a fluorescent protein is stably expressed in its corresponding knockout cells. Nucleosomes associated with epigenetic complexes are isolated from cells at native conditions and incubated with biotinylated antibodies. The resulting complexes are immobilized on a quartz slide that had been passivated and functionalized with NeutrAvidin. Image stacks are then acquired by using single-molecule TIRF microscopy. The individual spots imaged by TIRF microscopy represent single protein-nucleosome complexes. The number of copies of the protein complexes on a nucleosome is inferred from the fluorescence photobleaching measurements. Sm-ChIPi is a sensitive and direct method that can quantify the cellular assembly stoichiometry of epigenetic complexes on chromatin.
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Affiliation(s)
- Roubina Tatavosian
- Department of Chemistry, University of Colorado Denver, Denver, CO, 80217-3364, USA
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado Denver, Renovated Science Building, Rm 3071, 1151 Arapahoe Street, Denver, CO, 80204, USA.
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21
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Live-cell single-molecule dynamics of PcG proteins imposed by the DIPG H3.3K27M mutation. Nat Commun 2018; 9:2080. [PMID: 29802243 PMCID: PMC5970213 DOI: 10.1038/s41467-018-04455-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 04/26/2018] [Indexed: 01/06/2023] Open
Abstract
Over 80% of diffuse intrinsic pontine gliomas (DIPGs) harbor a point mutation in histone H3.3 where lysine 27 is substituted with methionine (H3.3K27M); however, how the mutation affects kinetics and function of PcG proteins remains elusive. We demonstrate that H3.3K27M prolongs the residence time and search time of Ezh2, but has no effect on its fraction bound to chromatin. In contrast, H3.3K27M has no effect on the residence time of Cbx7, but prolongs its search time and decreases its fraction bound to chromatin. We show that increasing expression of Cbx7 inhibits the proliferation of DIPG cells and prolongs its residence time. Our results highlight that the residence time of PcG proteins directly correlates with their functions and the search time of PcG proteins is critical for regulating their genomic occupancy. Together, our data provide mechanisms in which the cancer-causing histone mutation alters the binding and search dynamics of epigenetic complexes. Diffuse intrinsic pontine gliomas exhibit a characteristic mutation of lysine 27 to methionine (K27M) in genes encoding histone H3.3. Here the authors show that the H3.3K27M mutation imposes a specific pattern of H3.3K27 methylation by altering the target search dynamics of PcG proteins.
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22
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Kawaguchi T, Machida S, Kurumizaka H, Tagami H, Nakayama JI. Phosphorylation of CBX2 controls its nucleosome-binding specificity. J Biochem 2017; 162:343-355. [PMID: 28992316 DOI: 10.1093/jb/mvx040] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 05/22/2017] [Indexed: 01/08/2023] Open
Abstract
Chromobox 2 (CBX2), a component of polycomb repressive complex 1 (PRC1), binds lysine 27-methylated histone H3 (H3K27me3) via its chromodomain (CD) and plays a critical role in repressing developmentally regulated genes. The phosphorylation of CBX2 has been described in several studies, but the biological implications of this modification remain largely elusive. Here, we show that CBX2's phosphorylation plays an important role in its nucleosome binding. CBX2 is stably phosphorylated in vivo, and domain analysis showed that residues in CBX2's serine-rich (SR) region are the predominant phosphorylation sites. The serine residues in an SR region followed by an acidic-residue (AR) cluster coincide with the consensus target of casein kinase II (CK2), and CK2 efficiently phosphorylated the SR region in vitro. A nucleosome pull-down assay revealed that CK2-phosphorylated CBX2 had a high specificity for H3K27me3-modified nucleosomes. An electrophoretic mobility-shift assay showed that CK2-mediated phosphorylation diminished CBX2's AT-hook-associated DNA-binding activity. Mutant CBX2 lacking the SR region or its neighboring AR cluster failed to repress the transcription of p21, a gene targeted by PRC1. These results suggest that CBX2's phosphorylation is critical for its transcriptional repression of target genes.
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Affiliation(s)
- Takayuki Kawaguchi
- Division of Chromatin Regulation, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.,Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan
| | - Shinichi Machida
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hideaki Tagami
- Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan
| | - Jun-Ichi Nakayama
- Division of Chromatin Regulation, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.,Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8501, Japan
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23
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Chen WY, Zhang XY, Liu T, Liu Y, Zhao YS, Pang D. Chromobox homolog 2 protein: A novel biomarker for predicting prognosis and Taxol sensitivity in patients with breast cancer. Oncol Lett 2016; 13:1149-1156. [PMID: 28454227 PMCID: PMC5403172 DOI: 10.3892/ol.2016.5529] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 11/10/2016] [Indexed: 02/06/2023] Open
Abstract
Polycomb group (PcG) complexes modify histones to silence tumor suppressor genes, which exhibit an important function in tumorigenesis and progression. The chromobox (Cbx) protein family is a critical component of PcG-mediated repression. Cbx2, a member of the Cbx protein family, is hypothesized to exhibit a vital role in breast cancer. In the present study, immunohistochemical analysis using tissue microarrays was performed to determine the levels of Cbx2 protein expression in breast cancer. The association between Cbx2 expression and the clinical features and prognosis of 455 breast cancer patients was analyzed. In addition, the efficacy of Taxol was evaluated by comparing the survival of patients with high or low Cbx2 expression. The results revealed that Cbx2 expression was higher in cancer tissues compared with adjacent normal tissues. Furthermore, high Cbx2 expression was significantly associated with large tumor size, lymph node metastasis, high TNM stage and positive human epidermal growth factor receptor-2 (HER-2) status. Patients with high Cbx2 expression also exhibited a shorter mean overall survival (OS) time (74.37 months) compared with patients with low Cbx2 expression (77.37 months). Univariate analysis indicated that high Cbx2 expression increased the risk of mortality by 1.826-fold compared with low Cbx2 expression [hazard ratio (HR), 1.826; 95% confidence interval (CI), 1.069–3.116; P=0.027]. Among patients with high Cbx2 expression, the mean OS time of individuals treated with Taxol (71.01 months) was lower compared with patients that had not received Taxol treatment (78.43 months; log-rank test statistic, 13.03; P<0.001). However, no significant difference in OS time was identified in the low expression group. The results of the current study revealed that Cbx2 may present a novel biomarker for predicting the prognosis of breast cancer patients. Cbx2 may also represent a potential target for treatment due to its important function in Taxol treatment responses.
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Affiliation(s)
- Wang Yang Chen
- Heilongjiang Academy of Medical Sciences, Harbin, Heilongjiang 150044, P.R. China.,Department of Cancer Epidemiology, Institute of Cancer Prevention and Treatment, Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Xian Yu Zhang
- Department of Breast Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Tong Liu
- Department of Breast Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Yang Liu
- Department of Breast Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Ya Shuang Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang 150040, P.R. China
| | - Da Pang
- Department of Breast Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
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24
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Zhen CY, Tatavosian R, Huynh TN, Duc HN, Das R, Kokotovic M, Grimm JB, Lavis LD, Lee J, Mejia FJ, Li Y, Yao T, Ren X. Live-cell single-molecule tracking reveals co-recognition of H3K27me3 and DNA targets polycomb Cbx7-PRC1 to chromatin. eLife 2016; 5. [PMID: 27723458 PMCID: PMC5056789 DOI: 10.7554/elife.17667] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/29/2016] [Indexed: 12/11/2022] Open
Abstract
The Polycomb PRC1 plays essential roles in development and disease pathogenesis. Targeting of PRC1 to chromatin is thought to be mediated by the Cbx family proteins (Cbx2/4/6/7/8) binding to histone H3 with a K27me3 modification (H3K27me3). Despite this prevailing view, the molecular mechanisms of targeting remain poorly understood. Here, by combining live-cell single-molecule tracking (SMT) and genetic engineering, we reveal that H3K27me3 contributes significantly to the targeting of Cbx7 and Cbx8 to chromatin, but less to Cbx2, Cbx4, and Cbx6. Genetic disruption of the complex formation of PRC1 facilitates the targeting of Cbx7 to chromatin. Biochemical analyses uncover that the CD and AT-hook-like (ATL) motif of Cbx7 constitute a functional DNA-binding unit. Live-cell SMT of Cbx7 mutants demonstrates that Cbx7 is targeted to chromatin by co-recognizing of H3K27me3 and DNA. Our data suggest a novel hierarchical cooperation mechanism by which histone modifications and DNA coordinate to target chromatin regulatory complexes. DOI:http://dx.doi.org/10.7554/eLife.17667.001
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Affiliation(s)
- Chao Yu Zhen
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Roubina Tatavosian
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Thao Ngoc Huynh
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Huy Nguyen Duc
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Raibatak Das
- Department of Integrative Biology, University of Colorado Denver, Denver, United States
| | - Marko Kokotovic
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jun Lee
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Frances J Mejia
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Yang Li
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado Denver, Denver, United States
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25
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Identification of the epigenetic reader CBX2 as a potential drug target in advanced prostate cancer. Clin Epigenetics 2016; 8:16. [PMID: 26877821 PMCID: PMC4751702 DOI: 10.1186/s13148-016-0182-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 02/04/2016] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND While localized prostate cancer (PCa) can be effectively cured, metastatic disease inevitably progresses to a lethal state called castration-resistant prostate cancer (CRPC). Emerging evidence suggests that aberrant epigenetic repression by the polycomb group (PcG) complexes fuels PCa progression, providing novel therapeutic opportunities. RESULTS In the search for potential epigenetic drivers of CRPC, we analyzed the molecular profile of PcG members in patient-derived xenografts and clinical samples. Overall, our results identify the PcG protein and methyl-lysine reader CBX2 as a potential therapeutic target in advanced PCa. We report that CBX2 was recurrently up-regulated in metastatic CRPC and that elevated CBX2 expression was correlated with poor clinical outcome in PCa cohorts. Furthermore, CBX2 depletion abrogated cell viability and induced caspase 3-mediated apoptosis in metastatic PCa cell lines. Mechanistically explaining this phenotype, microarray analysis in CBX2-depleted cells revealed that CBX2 controls the expression of many key regulators of cell proliferation and metastasis. CONCLUSIONS Taken together, this study provides the first evidence that CBX2 inhibition induces cancer cell death, positioning CBX2 as an attractive drug target in lethal CRPC.
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Tatavosian R, Zhen CY, Duc HN, Balas MM, Johnson AM, Ren X. Distinct Cellular Assembly Stoichiometry of Polycomb Complexes on Chromatin Revealed by Single-molecule Chromatin Immunoprecipitation Imaging. J Biol Chem 2015; 290:28038-28054. [PMID: 26381410 DOI: 10.1074/jbc.m115.671115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Indexed: 12/11/2022] Open
Abstract
Epigenetic complexes play an essential role in regulating chromatin structure, but information about their assembly stoichiometry on chromatin within cells is poorly understood. The cellular assembly stoichiometry is critical for appreciating the initiation, propagation, and maintenance of epigenetic inheritance during normal development and in cancer. By combining genetic engineering, chromatin biochemistry, and single-molecule fluorescence imaging, we developed a novel and sensitive approach termed single-molecule chromatin immunoprecipitation imaging (Sm-ChIPi) to enable investigation of the cellular assembly stoichiometry of epigenetic complexes on chromatin. Sm-ChIPi was validated by using chromatin complexes with known stoichiometry. The stoichiometry of subunits within a polycomb complex and the assembly stoichiometry of polycomb complexes on chromatin have been extensively studied but reached divergent views. Moreover, the cellular assembly stoichiometry of polycomb complexes on chromatin remains unexplored. Using Sm-ChIPi, we demonstrated that within mouse embryonic stem cells, one polycomb repressive complex (PRC) 1 associates with multiple nucleosomes, whereas two PRC2s can bind to a single nucleosome. Furthermore, we obtained direct physical evidence that the nucleoplasmic PRC1 is monomeric, whereas PRC2 can dimerize in the nucleoplasm. We showed that ES cell differentiation induces selective alteration of the assembly stoichiometry of Cbx2 on chromatin but not other PRC1 components. We additionally showed that the PRC2-mediated trimethylation of H3K27 is not required for the assembly stoichiometry of PRC1 on chromatin. Thus, these findings uncover that PRC1 and PRC2 employ distinct mechanisms to assemble on chromatin, and the novel Sm-ChIPi technique could provide single-molecule insight into other epigenetic complexes.
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Affiliation(s)
- Roubina Tatavosian
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217-3364
| | - Chao Yu Zhen
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217-3364
| | - Huy Nguyen Duc
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217-3364
| | - Maggie M Balas
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Aaron M Johnson
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217-3364.
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