1
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Seif E, Francis NJ. A Two-Step Mechanism for Creating Stable, Condensed Chromatin with the Polycomb Complex PRC1. Molecules 2024; 29:323. [PMID: 38257239 PMCID: PMC10821450 DOI: 10.3390/molecules29020323] [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: 12/07/2023] [Revised: 12/26/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
The Drosophila PRC1 complex regulates gene expression by modifying histone proteins and chromatin architecture. Two PRC1 subunits, PSC and Ph, are most implicated in chromatin architecture. In vitro, PRC1 compacts chromatin and inhibits transcription and nucleosome remodeling. The long disordered C-terminal region of PSC (PSC-CTR) is important for these activities, while Ph has little effect. In cells, Ph is important for condensate formation, long-range chromatin interactions, and gene regulation, and its polymerizing sterile alpha motif (SAM) is implicated in these activities. In vitro, truncated Ph containing the SAM and two other conserved domains (mini-Ph) undergoes phase separation with chromatin, suggesting a mechanism for SAM-dependent condensate formation in vivo. How the distinct activities of PSC and Ph on chromatin function together in PRC1 is not known. To address this question, we analyzed structures formed with large chromatin templates and PRC1 in vitro. PRC1 bridges chromatin into extensive fibrillar networks. Ph, its SAM, and SAM polymerization activity have little effect on these structures. Instead, the PSC-CTR controls their growth, and is sufficient for their formation. To understand how phase separation driven by Ph SAM intersects with the chromatin bridging activity of the PSC-CTR, we used mini-Ph to form condensates with chromatin and then challenged them with PRC1 lacking Ph (PRC1ΔPh). PRC1ΔPh converts mini-Ph chromatin condensates into clusters of small non-fusing condensates and bridged fibers. These condensates retain a high level of chromatin compaction and do not intermix. Thus, phase separation of chromatin by mini-Ph, followed by the action of the PSC-CTR, creates a unique chromatin organization with regions of high nucleosome density and extraordinary stability. We discuss how this coordinated sequential activity of two proteins found in the same complex may occur and the possible implications of stable chromatin architectures in maintaining transcription states.
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Affiliation(s)
- Elias Seif
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada;
| | - Nicole J. Francis
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada;
- Division of Experimental Medicine, McGill University, 1001 Decarie Boulevard, Montréal, QC H4A 3J1, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC H3T 1J4, Canada
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2
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Rey-Millet M, Pousse M, Soithong C, Ye J, Mendez-Bermudez A, Gilson E. Senescence-associated transcriptional derepression in subtelomeres is determined in a chromosome-end-specific manner. Aging Cell 2023; 22:e13804. [PMID: 36924026 DOI: 10.1111/acel.13804] [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: 09/28/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 03/18/2023] Open
Abstract
Aging is a continuous process leading to physiological deterioration with age. One of the factors contributing to aging is telomere shortening, causing alterations in the protein protective complex named shelterin and replicative senescence. Here, we address the question of the link between this telomere shortening and the transcriptional changes occurring in senescent cells. We found that in replicative senescent cells, the genes whose expression escaped repression are enriched in subtelomeres. The shelterin protein TRF2 and the nuclear lamina factor Lamin B1, both downregulated in senescent cells, are involved in the regulation of some but not all of these subtelomeric genes, suggesting complex mechanisms of transcriptional regulation. Indeed, the subtelomeres containing these derepressed genes are enriched in factors of polycomb repression (EZH2 and H3K27me3), insulation (CTCF and MAZ), and cohesion (RAD21 and SMC3) while being associated with the open A-type chromatin compartment. These findings unveil that the subtelomere transcriptome associated with senescence is determined in a chromosome-end-specific manner according to the type of higher-order chromatin structure.
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Affiliation(s)
- Martin Rey-Millet
- CNRS, INSERM, IRCAN, Faculty of Medicine Nice, Université Côte d'Azur, Nice, France
| | - Mélanie Pousse
- CNRS, INSERM, IRCAN, Faculty of Medicine Nice, Université Côte d'Azur, Nice, France
| | - Chan Soithong
- CNRS, INSERM, IRCAN, Faculty of Medicine Nice, Université Côte d'Azur, Nice, France
| | - Jing Ye
- Department of Geriatrics, Medical center on Aging of Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,International Laboratory in Hematology, Cancer and Aging, Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine/CNRS/INSERM/University Côte d'Azur, Shanghai, China
| | - Aaron Mendez-Bermudez
- CNRS, INSERM, IRCAN, Faculty of Medicine Nice, Université Côte d'Azur, Nice, France.,Department of Geriatrics, Medical center on Aging of Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,International Laboratory in Hematology, Cancer and Aging, Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine/CNRS/INSERM/University Côte d'Azur, Shanghai, China
| | - Eric Gilson
- CNRS, INSERM, IRCAN, Faculty of Medicine Nice, Université Côte d'Azur, Nice, France.,Department of Geriatrics, Medical center on Aging of Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.,International Laboratory in Hematology, Cancer and Aging, Pôle Sino-Français de Recherches en Sciences du Vivant et Génomique, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine/CNRS/INSERM/University Côte d'Azur, Shanghai, China.,Department of medical genetics, CHU, Nice, France
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3
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Arya R, Gyonjyan S, Harding K, Sarkissian T, Li Y, Zhou L, White K. A Cut/cohesin axis alters the chromatin landscape to facilitate neuroblast death. Development 2019; 146:dev166603. [PMID: 30952666 PMCID: PMC6526717 DOI: 10.1242/dev.166603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 03/25/2019] [Indexed: 12/24/2022]
Abstract
Precise control of cell death in the nervous system is essential for development. Spatial and temporal factors activate the death of Drosophila neural stem cells (neuroblasts) by controlling the transcription of multiple cell death genes through a shared enhancer. The activity of this enhancer is controlled by abdominal A and Notch, but additional inputs are needed for proper specificity. Here, we show that the Cut DNA binding protein is required for neuroblast death, regulating reaper and grim downstream of the shared enhancer and of abdominal A expression. The loss of cut accelerates the temporal progression of neuroblasts from a state of low overall levels of H3K27me3 to a higher H3K27me3 state. This is reflected in an increase in H3K27me3 modifications in the cell death gene locus in the CNS on Cut knockdown. We also show that cut regulates the expression of the cohesin subunit Stromalin. Stromalin and the cohesin regulatory subunit Nipped-B are required for neuroblast death, and knockdown of Stromalin increases H3K27me3 levels in neuroblasts. Thus, Cut and cohesin regulate apoptosis in the developing nervous system by altering the chromatin landscape.
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Affiliation(s)
- Richa Arya
- Cutaneous Biology Research Center, Massachusetts General Hospital Research Institute/Harvard Medical School, Boston, MA 02129, USA
| | - Seda Gyonjyan
- Cutaneous Biology Research Center, Massachusetts General Hospital Research Institute/Harvard Medical School, Boston, MA 02129, USA
| | - Katherine Harding
- Cutaneous Biology Research Center, Massachusetts General Hospital Research Institute/Harvard Medical School, Boston, MA 02129, USA
| | - Tatevik Sarkissian
- Cutaneous Biology Research Center, Massachusetts General Hospital Research Institute/Harvard Medical School, Boston, MA 02129, USA
| | - Ying Li
- Department of Molecular Genetics and Microbiology, College of Medicine/UF Health Cancer Center/UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Lei Zhou
- Department of Molecular Genetics and Microbiology, College of Medicine/UF Health Cancer Center/UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Kristin White
- Cutaneous Biology Research Center, Massachusetts General Hospital Research Institute/Harvard Medical School, Boston, MA 02129, USA
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4
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Pherson M, Misulovin Z, Gause M, Mihindukulasuriya K, Swain A, Dorsett D. Polycomb repressive complex 1 modifies transcription of active genes. SCIENCE ADVANCES 2017; 3:e1700944. [PMID: 28782042 PMCID: PMC5540264 DOI: 10.1126/sciadv.1700944] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 06/28/2017] [Indexed: 05/21/2023]
Abstract
This study examines the role of Polycomb repressive complex 1 (PRC1) at active genes. The PRC1 and PRC2 complexes are crucial for epigenetic silencing during development of an organism. They are recruited to Polycomb response elements (PREs) and establish silenced domains over several kilobases. Recent studies show that PRC1 is also directly recruited to active genes by the cohesin complex. Cohesin participates broadly in control of gene transcription, but it is unknown whether cohesin-recruited PRC1 also plays a role in transcriptional control of active genes. We address this question using genome-wide RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq). The results show that PRC1 influences transcription of active genes, and a significant fraction of its effects are likely direct. The roles of different PRC1 subunits can also vary depending on the gene. Depletion of PRC1 subunits by RNA interference alters phosphorylation of RNA polymerase II (Pol II) and occupancy by the Spt5 pausing-elongation factor at most active genes. These effects on Pol II phosphorylation and Spt5 are likely linked to changes in elongation and RNA processing detected by nascent RNA-seq, although the mechanisms remain unresolved. The experiments also reveal that PRC1 facilitates association of Spt5 with enhancers and PREs. Reduced Spt5 levels at these regulatory sequences upon PRC1 depletion coincide with changes in Pol II occupancy and phosphorylation. Our findings indicate that, in addition to its repressive roles in epigenetic gene silencing, PRC1 broadly influences transcription of active genes and may suppress transcription of nonpromoter regulatory sequences.
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5
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Kassis JA, Kennison JA, Tamkun JW. Polycomb and Trithorax Group Genes in Drosophila. Genetics 2017; 206:1699-1725. [PMID: 28778878 PMCID: PMC5560782 DOI: 10.1534/genetics.115.185116] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/15/2017] [Indexed: 01/08/2023] Open
Abstract
Polycomb group (PcG) and Trithorax group (TrxG) genes encode important regulators of development and differentiation in metazoans. These two groups of genes were discovered in Drosophila by their opposing effects on homeotic gene (Hox) expression. PcG genes collectively behave as genetic repressors of Hox genes, while the TrxG genes are necessary for HOX gene expression or function. Biochemical studies showed that many PcG proteins are present in two protein complexes, Polycomb repressive complexes 1 and 2, which repress transcription via chromatin modifications. TrxG proteins activate transcription via a variety of mechanisms. Here we summarize the large body of genetic and biochemical experiments in Drosophila on these two important groups of genes.
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Affiliation(s)
- Judith A Kassis
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - James A Kennison
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - John W Tamkun
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064
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6
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Monribot-Villanueva J, Zurita M, Vázquez M. Developmental transcriptional regulation by SUMOylation, an evolving field. Genesis 2017; 55. [PMID: 27935206 DOI: 10.1002/dvg.23009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/29/2016] [Accepted: 11/29/2016] [Indexed: 02/05/2023]
Abstract
SUMOylation is a reversible post-translational protein modification that affects the intracellular localization, stability, activity, and interactions of its protein targets. The SUMOylation pathway influences several nuclear and cytoplasmic processes. The expression of many genes, in particular those involved in development is finely tuned in space and time by several groups of proteins. There is growing evidence that transcriptional regulation mechanisms involve direct SUMOylation of transcriptional-related proteins such as initiation and elongation factors, and subunits of chromatin modifier and remodeling complexes originally described as members of the trithorax and Polycomb groups in Drosophila. Therefore, it is being unveiled that SUMOylation has a role in both, gene silencing and gene activation mechanisms. The goal of this review is to discuss the information on how SUMO modification in components of these multi-subunit complexes may have an effect in genome architecture and function and, therefore, in the regulation of gene expression in time and space.
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Affiliation(s)
- Juan Monribot-Villanueva
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología-Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Mario Zurita
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología-Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Martha Vázquez
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología-Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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7
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Tang X, Xu S, Li R, Zhang H, Chen Q, Wu W, Liu H. Polycomb repressive complex 1 (PRC1) regulates meiotic initiation of ovarian germ cells in chick embryos. Mol Cell Endocrinol 2016; 437:171-182. [PMID: 27546728 DOI: 10.1016/j.mce.2016.08.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 07/26/2016] [Accepted: 08/15/2016] [Indexed: 10/21/2022]
Abstract
Meiosis is essential for gametogenesis and exhibits sex-specific property during embryonic development. Retinoic acid (RA) signalling initiates germ cell meiosis by activating Stra8 (stimulated by RA gene 8). Although additional factors are involved in regulating the meiotic initiation of germ cells, their regulatory mechanisms are unclear. In this study, we found that Polycomb repressive complex 1 (PRC1) is largely expressed in chicken ovarian germ and somatic cells during early stages of meiosis. We demonstrated that PRC1 regulates Stra8, pluripotent factors and paracrine factors (Notch ligands) leading to a synergistic effect on the suppression of germ cell meiotic initiation. Finally, we observed that repression of PRC1 resulted in precocious meiotic initiation and apoptosis of ovarian cells in vivo. These results aid in understanding the regulation of meiotic initiation in germ cells by PRC1 and provide evidence to support the hypothesis that regulation of meiotic initiation is conserved in higher vertebrates.
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Affiliation(s)
- Xiaochuan Tang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Shiyong Xu
- College of Animal Science and Technology, Jingling Institute of Technology, Nanjing 210095, People's Republic of China
| | - Rongyang Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Hongpeng Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Qing Chen
- College of Animal Science and Technology, Jingling Institute of Technology, Nanjing 210095, People's Republic of China
| | - Wangjun Wu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Honglin Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.
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8
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Papadopoulou T, Richly H. On-site remodeling at chromatin: How multiprotein complexes are rebuilt during DNA repair and transcriptional activation. Bioessays 2016; 38:1130-1140. [PMID: 27599465 DOI: 10.1002/bies.201600094] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this review, we discuss a novel on-site remodeling function that is mediated by the H2A-ubiquitin binding protein ZRF1. ZRF1 facilitates the remodeling of multiprotein complexes at chromatin and lies at the heart of signaling processes that occur at DNA damage sites and during transcriptional activation. In nucleotide excision repair ZRF1 remodels E3 ubiquitin ligase complexes at the damage site. During embryonic stem cell differentiation, it contributes to retinoic acid-mediated gene activation by altering the subunit composition of the Mediator complex. We postulate that ZRF1 operates in conjunction with cellular remodeling machines and suggest that on-site remodeling might be a hallmark of many chromatin-associated signaling pathways. We discuss yet unexplored functions of ZRF1-mediated remodeling in replication and double strand break repair. In conclusion, we postulate that on-site remodeling of multiprotein complexes is essential for the timing of chromatin signaling processes.
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Affiliation(s)
- Thaleia Papadopoulou
- Laboratory of Molecular Epigenetics, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Holger Richly
- Laboratory of Molecular Epigenetics, Institute of Molecular Biology (IMB), Mainz, Germany.
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9
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Swain A, Misulovin Z, Pherson M, Gause M, Mihindukulasuriya K, Rickels RA, Shilatifard A, Dorsett D. Drosophila TDP-43 RNA-Binding Protein Facilitates Association of Sister Chromatid Cohesion Proteins with Genes, Enhancers and Polycomb Response Elements. PLoS Genet 2016; 12:e1006331. [PMID: 27662615 PMCID: PMC5035082 DOI: 10.1371/journal.pgen.1006331] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/30/2016] [Indexed: 12/22/2022] Open
Abstract
The cohesin protein complex mediates sister chromatid cohesion and participates in transcriptional control of genes that regulate growth and development. Substantial reduction of cohesin activity alters transcription of many genes without disrupting chromosome segregation. Drosophila Nipped-B protein loads cohesin onto chromosomes, and together Nipped-B and cohesin occupy essentially all active transcriptional enhancers and a large fraction of active genes. It is unknown why some active genes bind high levels of cohesin and some do not. Here we show that the TBPH and Lark RNA-binding proteins influence association of Nipped-B and cohesin with genes and gene regulatory sequences. In vitro, TBPH and Lark proteins specifically bind RNAs produced by genes occupied by Nipped-B and cohesin. By genomic chromatin immunoprecipitation these RNA-binding proteins also bind to chromosomes at cohesin-binding genes, enhancers, and Polycomb response elements (PREs). RNAi depletion reveals that TBPH facilitates association of Nipped-B and cohesin with genes and regulatory sequences. Lark reduces binding of Nipped-B and cohesin at many promoters and aids their association with several large enhancers. Conversely, Nipped-B facilitates TBPH and Lark association with genes and regulatory sequences, and interacts with TBPH and Lark in affinity chromatography and immunoprecipitation experiments. Blocking transcription does not ablate binding of Nipped-B and the RNA-binding proteins to chromosomes, indicating transcription is not required to maintain binding once established. These findings demonstrate that RNA-binding proteins help govern association of sister chromatid cohesion proteins with genes and enhancers.
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Affiliation(s)
- Amanda Swain
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Ziva Misulovin
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Michelle Pherson
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Maria Gause
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Kathie Mihindukulasuriya
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Ryan A Rickels
- Department of Biochemistry and Molecular Genetics, Northwestern Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
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10
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Dorsett D. The Drosophila melanogaster model for Cornelia de Lange syndrome: Implications for etiology and therapeutics. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2016; 172:129-37. [PMID: 27097273 DOI: 10.1002/ajmg.c.31490] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Discovery of genetic alterations that cause human birth defects provide key opportunities to improve the diagnosis, treatment, and family counseling. Frequently, however, these opportunities are limited by the lack of knowledge about the normal functions of the affected genes. In many cases, there is more information about the gene's orthologs in model organisms, including Drosophila melanogaster. Despite almost a billion years of evolutionary divergence, over three-quarters of genes linked to human diseases have Drosophila homologs. With a short generation time, a twenty-fold smaller genome, and unique genetic tools, the conserved functions of genes are often more easily elucidated in Drosophila than in other organisms. Here we present how this applies to Cornelia de Lange syndrome, as a model for how Drosophila can be used to increase understanding of genetic syndromes caused by mutations with broad effects on gene transcription and exploited to develop novel therapies. © 2016 Wiley Periodicals, Inc.
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11
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Stelloh C, Reimer MH, Pulakanti K, Blinka S, Peterson J, Pinello L, Jia S, Roumiantsev S, Hessner MJ, Milanovich S, Yuan GC, Rao S. The cohesin-associated protein Wapal is required for proper Polycomb-mediated gene silencing. Epigenetics Chromatin 2016; 9:14. [PMID: 27087855 PMCID: PMC4832553 DOI: 10.1186/s13072-016-0063-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 03/23/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The cohesin complex consists of multiple core subunits that play critical roles in mitosis and transcriptional regulation. The cohesin-associated protein Wapal plays a central role in off-loading cohesin to facilitate sister chromatid separation, but its role in regulating mammalian gene expression is not understood. We used embryonic stem cells as a model, given that the well-defined transcriptional regulatory circuits were established through master transcription factors and epigenetic pathways that regulate their ability to maintain a pluripotent state. RESULTS RNAi-mediated depletion of Wapal causes a loss of pluripotency, phenocopying loss of core cohesin subunits. Using chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq), we determine that Wapal occupies genomic sites distal to genes in combination with CTCF and core cohesin subunits such as Rad21. Interestingly, genomic sites occupied by Wapal appear enriched for cohesin, implying that Wapal does not off-load cohesin at regions it occupies. Wapal depletion induces derepression of Polycomb group (PcG) target genes without altering total levels of Polycomb-mediated histone modifications, implying that PcG enzymatic activity is preserved. By integrating ChIP-seq and gene expression changes data, we identify that Wapal binding is enriched at the promoters of PcG-silenced genes and is required for proper Polycomb repressive complex 2 (PRC2) recruitment. Lastly, we demonstrate that Wapal is required for the interaction of a distal cis-regulatory element (CRE) with the c-Fos promoter. CONCLUSIONS Collectively, this work indicates that Wapal plays a critical role in silencing of PcG target genes through the interaction of distal CREs with promoters.
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Affiliation(s)
- Cary Stelloh
- Blood Research Institute, BloodCenter of Wisconsin, 8727 West Watertown Plank Road, Milwaukee, WI 53226 USA
| | - Michael H Reimer
- Blood Research Institute, BloodCenter of Wisconsin, 8727 West Watertown Plank Road, Milwaukee, WI 53226 USA.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI USA
| | - Kirthi Pulakanti
- Blood Research Institute, BloodCenter of Wisconsin, 8727 West Watertown Plank Road, Milwaukee, WI 53226 USA
| | - Steven Blinka
- Blood Research Institute, BloodCenter of Wisconsin, 8727 West Watertown Plank Road, Milwaukee, WI 53226 USA.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI USA
| | - Jonathan Peterson
- Blood Research Institute, BloodCenter of Wisconsin, 8727 West Watertown Plank Road, Milwaukee, WI 53226 USA
| | - Luca Pinello
- Dana Farber Cancer Institute, Harvard School of Public Health, Boston, MA USA
| | - Shuang Jia
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI USA
| | - Sergei Roumiantsev
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA USA
| | - Martin J Hessner
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI USA
| | - Samuel Milanovich
- Sanford Research Center, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD USA
| | - Guo-Cheng Yuan
- Dana Farber Cancer Institute, Harvard School of Public Health, Boston, MA USA
| | - Sridhar Rao
- Blood Research Institute, BloodCenter of Wisconsin, 8727 West Watertown Plank Road, Milwaukee, WI 53226 USA.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI USA.,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI USA
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12
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Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin. Nat Genet 2016; 48:488-96. [PMID: 27064255 DOI: 10.1038/ng.3539] [Citation(s) in RCA: 263] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/07/2016] [Indexed: 12/15/2022]
Abstract
Discriminating the gene target of a distal regulatory element from other nearby transcribed genes is a challenging problem with the potential to illuminate the causal underpinnings of complex diseases. We present TargetFinder, a computational method that reconstructs regulatory landscapes from diverse features along the genome. The resulting models accurately predict individual enhancer-promoter interactions across multiple cell lines with a false discovery rate up to 15 times smaller than that obtained using the closest gene. By evaluating the genomic features driving this accuracy, we uncover interactions between structural proteins, transcription factors, epigenetic modifications, and transcription that together distinguish interacting from non-interacting enhancer-promoter pairs. Most of this signature is not proximal to the enhancers and promoters but instead decorates the looping DNA. We conclude that complex but consistent combinations of marks on the one-dimensional genome encode the three-dimensional structure of fine-scale regulatory interactions.
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13
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Wu Y, Gause M, Xu D, Misulovin Z, Schaaf CA, Mosarla RC, Mannino E, Shannon M, Jones E, Shi M, Chen WF, Katz OL, Sehgal A, Jongens TA, Krantz ID, Dorsett D. Drosophila Nipped-B Mutants Model Cornelia de Lange Syndrome in Growth and Behavior. PLoS Genet 2015; 11:e1005655. [PMID: 26544867 PMCID: PMC4636142 DOI: 10.1371/journal.pgen.1005655] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 10/16/2015] [Indexed: 11/18/2022] Open
Abstract
Individuals with Cornelia de Lange Syndrome (CdLS) display diverse developmental deficits, including slow growth, multiple limb and organ abnormalities, and intellectual disabilities. Severely-affected individuals most often have dominant loss-of-function mutations in the Nipped-B-Like (NIPBL) gene, and milder cases often have missense or in-frame deletion mutations in genes encoding subunits of the cohesin complex. Cohesin mediates sister chromatid cohesion to facilitate accurate chromosome segregation, and NIPBL is required for cohesin to bind to chromosomes. Individuals with CdLS, however, do not display overt cohesion or segregation defects. Rather, studies in human cells and model organisms indicate that modest decreases in NIPBL and cohesin activity alter the transcription of many genes that regulate growth and development. Sister chromatid cohesion factors, including the Nipped-B ortholog of NIPBL, are also critical for gene expression and development in Drosophila melanogaster. Here we describe how a modest reduction in Nipped-B activity alters growth and neurological function in Drosophila. These studies reveal that Nipped-B heterozygous mutant Drosophila show reduced growth, learning, and memory, and altered circadian rhythms. Importantly, the growth deficits are not caused by changes in systemic growth controls, but reductions in cell number and size attributable in part to reduced expression of myc (diminutive) and other growth control genes. The learning, memory and circadian deficits are accompanied by morphological abnormalities in brain structure. These studies confirm that Drosophila Nipped-B mutants provide a useful model for understanding CdLS, and provide new insights into the origins of birth defects. Cornelia de Lange Syndrome (CdLS) alters many aspects of growth and development. CdLS is caused by mutations in genes encoding proteins that ensure that chromosomes are distributed equally when a cell divides. These include genes that encode components of the cohesin complex, and Nipped-B-Like (NIPBL) that puts cohesin onto chromosomes. Individuals with CdLS have only modest reductions in the activities of these genes and do not show changes in chromosome distribution. Instead, they show differences in the expression many genes that control development. Animal models of CdLS will be useful for studies aimed at understanding how development is altered, and testing methods for treating CdLS. We find that Drosophila with one mutant copy of the Nipped-B gene, which is equivalent to the NIPBL gene, show characteristics similar to individuals with CdLS. These include reduced growth, learning, memory, and altered circadian rhythms. These studies thus indicate that Drosophila Nipped-B mutants are a valuable system for investigating the causes of the CdLS birth defects, and developing potential treatments. They also reveal that the slow growth in Drosophila Nipped-B mutants is not caused by disruption of systemic hormonal growth controls, and that the learning and memory deficits may reflect changes in brain structure.
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Affiliation(s)
- Yaning Wu
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Maria Gause
- Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Dongbin Xu
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Ziva Misulovin
- Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Cheri A. Schaaf
- Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Ramya C. Mosarla
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Elizabeth Mannino
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Megan Shannon
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Emily Jones
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Mi Shi
- Howard Hughes Medical Institute and Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Wen-Feng Chen
- Howard Hughes Medical Institute and Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Olivia L. Katz
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Amita Sehgal
- Howard Hughes Medical Institute and Department of Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Thomas A. Jongens
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ian D. Krantz
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (IDK); (DD)
| | - Dale Dorsett
- Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
- * E-mail: (IDK); (DD)
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