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Hövel I, Bader R, Louwers M, Haring M, Peek K, Gent JI, Stam M. RNA-directed DNA methylation mutants reduce histone methylation at the paramutated maize booster1 enhancer. PLANT PHYSIOLOGY 2024; 195:1161-1179. [PMID: 38366582 PMCID: PMC11142347 DOI: 10.1093/plphys/kiae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/19/2023] [Accepted: 12/25/2023] [Indexed: 02/18/2024]
Abstract
Paramutation is the transfer of mitotically and meiotically heritable silencing information between two alleles. With paramutation at the maize (Zea mays) booster1 (b1) locus, the low-expressed B' epiallele heritably changes the high-expressed B-I epiallele into B' with 100% frequency. This requires specific tandem repeats and multiple components of the RNA-directed DNA methylation pathway, including the RNA-dependent RNA polymerase (encoded by mediator of paramutation1, mop1), the second-largest subunit of RNA polymerase IV and V (NRP(D/E)2a, encoded by mop2), and the largest subunit of RNA Polymerase IV (NRPD1, encoded by mop3). Mutations in mop genes prevent paramutation and release silencing at the B' epiallele. In this study, we investigated the effect of mutations in mop1, mop2, and mop3 on chromatin structure and DNA methylation at the B' epiallele, and especially the regulatory hepta-repeat 100 kb upstream of the b1 gene. Mutations in mop1 and mop3 resulted in decreased repressive histone modifications H3K9me2 and H3K27me2 at the hepta-repeat. Associated with this decrease were partial activation of the hepta-repeat enhancer function, formation of a multi-loop structure, and elevated b1 expression. In mop2 mutants, which do not show elevated b1 expression, H3K9me2, H3K27me2 and a single-loop structure like in wild-type B' were retained. Surprisingly, high CG and CHG methylation levels at the B' hepta-repeat remained in all three mutants, and CHH methylation was low in both wild type and mutants. Our results raise the possibility of MOP factors mediating RNA-directed histone methylation rather than RNA-directed DNA methylation at the b1 locus.
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Affiliation(s)
- Iris Hövel
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
| | - Rechien Bader
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
| | - Marieke Louwers
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
- argenx BV, Industriepark Zwijnaarde 7, 9052 Zwijnaarde (Ghent), Belgium
| | - Max Haring
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
- University Library, Universiteit van Amsterdam, P.O. Box 19185, 1000 GD Amsterdam, The Netherlands
| | - Kevin Peek
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, P.O. Box 1210, 1090 GE Amsterdam, The Netherlands
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2
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Ghate NB, Nadkarni KS, Barik GK, Tat SS, Sahay O, Santra MK. Histone ubiquitination: Role in genome integrity and chromatin organization. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195044. [PMID: 38763317 DOI: 10.1016/j.bbagrm.2024.195044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/21/2024]
Abstract
Maintenance of genome integrity is a precise but tedious and complex job for the cell. Several post-translational modifications (PTMs) play vital roles in maintaining the genome integrity. Although ubiquitination is one of the most crucial PTMs, which regulates the localization and stability of the nonhistone proteins in various cellular and developmental processes, ubiquitination of the histones is a pivotal epigenetic event critically regulating chromatin architecture. In addition to genome integrity, importance of ubiquitination of core histones (H2A, H2A, H3, and H4) and linker histone (H1) have been reported in several cellular processes. However, the complex interplay of histone ubiquitination and other PTMs, as well as the intricate chromatin architecture and dynamics, pose a significant challenge to unravel how histone ubiquitination safeguards genome stability. Therefore, further studies are needed to elucidate the interactions between histone ubiquitination and other PTMs, and their role in preserving genome integrity. Here, we review all types of histone ubiquitinations known till date in maintaining genomic integrity during transcription, replication, cell cycle, and DNA damage response processes. In addition, we have also discussed the role of histone ubiquitination in regulating other histone PTMs emphasizing methylation and acetylation as well as their potential implications in chromatin architecture. Further, we have also discussed the involvement of deubiquitination enzymes (DUBs) in controlling histone ubiquitination in modulating cellular processes.
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Affiliation(s)
- Nikhil Baban Ghate
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India.
| | - Kaustubh Sanjay Nadkarni
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Ganesh Kumar Barik
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Sharad Shriram Tat
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Osheen Sahay
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Manas Kumar Santra
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India.
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3
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Francois AK, Rohani A, Loftus M, Dochnal S, Hrit J, McFarlane S, Whitford A, Lewis A, Krakowiak P, Boutell C, Rothbart SB, Kashatus D, Cliffe AR. Single-genome analysis reveals a heterogeneous association of the herpes simplex virus genome with H3K27me2 and the reader PHF20L1 following infection of human fibroblasts. mBio 2024; 15:e0327823. [PMID: 38411116 PMCID: PMC11005365 DOI: 10.1128/mbio.03278-23] [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: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 02/28/2024] Open
Abstract
The fate of herpesvirus genomes following entry into different cell types is thought to regulate the outcome of infection. For the Herpes simplex virus 1 (HSV-1), latent infection of neurons is characterized by association with repressive heterochromatin marked with Polycomb silencing-associated lysine 27 methylation on histone H3 (H3K27me). However, whether H3K27 methylation plays a role in repressing lytic gene expression in non-neuronal cells is unclear. To address this gap in knowledge, and with consideration that the fate of the viral genome and outcome of HSV-1 infection could be heterogeneous, we developed an assay to quantify the abundance of histone modifications within single viral genome foci of infected fibroblasts. Using this approach, combined with bulk epigenetic techniques, we were unable to detect any role for H3K27me3 during HSV-1 lytic infection of fibroblasts. By contrast, we could detect the lesser studied H3K27me2 on a subpopulation of viral genomes, which was consistent with a role for H3K27 demethylases in promoting lytic gene expression. In addition, viral genomes co-localized with the H3K27me2 reader protein PHF20L1, and this association was enhanced by inhibition of the H3K27 demethylases UTX and JMJD3. Notably, targeting of H3K27me2 to viral genomes was enhanced following infection with a transcriptionally defective virus in the absence of Promyelocytic leukemia nuclear bodies. Collectively, these studies implicate a role for H3K27me2 in fibroblast-associated HSV genome silencing in a manner dependent on genome sub-nuclear localization and transcriptional activity. IMPORTANCE Investigating the potential mechanisms of gene silencing for DNA viruses in different cell types is important to understand the differential outcomes of infection, particularly for viruses like herpesviruses that can undergo distinct types of infection in different cell types. In addition, investigating chromatin association with viral genomes informs on the mechanisms of epigenetic regulation of DNA processes. However, there is a growing appreciation for heterogeneity in the outcome of infection at the single cell, and even single viral genome, level. Here we describe a novel assay for quantifying viral genome foci with chromatin proteins and show that a portion of genomes are targeted for silencing by H3K27me2 and associate with the reader protein PHF20L1. This study raises important questions regarding the mechanism of H3K27me2-specific targeting to viral genomes, the contribution of epigenetic heterogeneity to herpesvirus infection, and the role of PHF20L1 in regulating the outcome of DNA virus infection.
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Affiliation(s)
- Alison K. Francois
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Ali Rohani
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Matt Loftus
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Sara Dochnal
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Joel Hrit
- Department of Epigenetics, Van Andel Institute, Grand Rapids, USA
| | - Steven McFarlane
- MRC - University of Glasgow, Centre for Virus Research, Glasgow, United Kingdom
| | - Abigail Whitford
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Anna Lewis
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Patryk Krakowiak
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Chris Boutell
- MRC - University of Glasgow, Centre for Virus Research, Glasgow, United Kingdom
| | | | - David Kashatus
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Anna R. Cliffe
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
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4
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Ryan CW, Peirent ER, Regan SL, Guxholli A, Bielas SL. H2A monoubiquitination: insights from human genetics and animal models. Hum Genet 2024; 143:511-527. [PMID: 37086328 DOI: 10.1007/s00439-023-02557-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/10/2023] [Indexed: 04/23/2023]
Abstract
Metazoan development arises from spatiotemporal control of gene expression, which depends on epigenetic regulators like the polycomb group proteins (PcG) that govern the chromatin landscape. PcG proteins facilitate the addition and removal of histone 2A monoubiquitination at lysine 119 (H2AK119ub1), which regulates gene expression, cell fate decisions, cell cycle progression, and DNA damage repair. Regulation of these processes by PcG proteins is necessary for proper development, as pathogenic variants in these genes are increasingly recognized to underly developmental disorders. Overlapping features of developmental syndromes associated with pathogenic variants in specific PcG genes suggest disruption of central developmental mechanisms; however, unique clinical features observed in each syndrome suggest additional non-redundant functions for each PcG gene. In this review, we describe the clinical manifestations of pathogenic PcG gene variants, review what is known about the molecular functions of these gene products during development, and interpret the clinical data to summarize the current evidence toward an understanding of the genetic and molecular mechanism.
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Affiliation(s)
- Charles W Ryan
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
- Medical Science Training Program, University of Michigan Medical School, 3703 Med Sci II, 1241 E. Catherine St., Ann Arbor, MI, 48109-5618, USA
| | - Emily R Peirent
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Samantha L Regan
- Department of Human Genetics, University of Michigan Medical School, 3703 Med Sci II, 1241 E. Catherine St., Ann Arbor, MI, 48109-5618, USA
| | - Alba Guxholli
- Department of Human Genetics, University of Michigan Medical School, 3703 Med Sci II, 1241 E. Catherine St., Ann Arbor, MI, 48109-5618, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48199-5618, USA
| | - Stephanie L Bielas
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA.
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA.
- Department of Human Genetics, University of Michigan Medical School, 3703 Med Sci II, 1241 E. Catherine St., Ann Arbor, MI, 48109-5618, USA.
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48199-5618, USA.
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5
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Shen X, Chen C, Wang Y, Zheng W, Zheng J, Jones AE, Zhu B, Zhang H, Lyons C, Rijal A, Moley JA, Cao G, Liu K, Winn R, Dickinson A, Zhang K, Wang H. Role of histone variants H2BC1 and H2AZ.2 in H2AK119ub nucleosome organization and Polycomb gene silencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575234. [PMID: 38293106 PMCID: PMC10827191 DOI: 10.1101/2024.01.16.575234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Ubiquitination of histone H2A at lysine 119 residue (H2AK119ub) plays critical roles in a wide range of physiological processes, including Polycomb gene silencing 1,2 , replication 3-5 , DNA damage repair 6-10 , X inactivation 11,12 , and heterochromatin organization 13,14 . However, the underlying mechanism and structural basis of H2AK119ub remains largely elusive. In this study, we report that H2AK119ub nucleosomes have a unique composition, containing histone variants H2BC1 and H2AZ.2, and importantly, this composition is required for H2AK119ub and Polycomb gene silencing. Using the UAB domain of RSF1, we purified H2AK119ub nucleosomes to a sufficient amount and purity. Mass spectrometry analyses revealed that H2AK119ub nucleosomes contain the histone variants H2BC1 and H2AZ.2. A cryo-EM study resolved the structure of native H2AK119ub nucleosomes to a 2.6A resolution, confirming H2BC1 in one subgroup of H2AK119ub nucleosomes. Tandem GST-UAB pulldown, Flag-H2AZ.2, and HA-H2BC1 immunoprecipitation revealed that H2AK119ub nucleosomes could be separated into distinct subgroups, suggesting their composition heterogeneity and potential dynamic organization. Knockout or knockdown of H2BC1 or H2AZ.2 reduced cellular H2AK119ub levels, establishing H2BC1 and H2AZ.2 as critical determinants of H2AK119ub. Furthermore, genomic binding profiles of H2BC1 and H2AZ.2 overlapped significantly with H2AK119ub binding, with the most significant overlapping in the gene body and intergenic regions. Finally, assays in developing embryos reveal an interaction of H2AZ.2, H2BC1, and RING1A in vivo . Thus, this study revealed, for the first time, that the H2AK119ub nucleosome has a unique composition, and this composition is required for H2AK119ub and Polycomb gene silencing.
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6
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Lundkvist MJ, Lizana L, Schwartz YB. Forecasting histone methylation by Polycomb complexes with minute-scale precision. SCIENCE ADVANCES 2023; 9:eadj8198. [PMID: 38134278 PMCID: PMC10745708 DOI: 10.1126/sciadv.adj8198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Animals use the Polycomb system to epigenetically repress developmental genes. The repression requires trimethylation of lysine 27 of histone H3 (H3K27me3) by Polycomb Repressive Complex 2 (PRC2), but the dynamics of this process is poorly understood. To bridge the gap, we developed a computational model that forecasts H3K27 methylation in Drosophila with high temporal resolution and spatial accuracy of contemporary experimental techniques. Using this model, we show that pools of methylated H3K27 in dividing cells are defined by the effective concentration of PRC2 and the replication frequency. We find that the allosteric stimulation by preexisting H3K27me3 makes PRC2 better in methylating developmental genes as opposed to indiscriminate methylation throughout the genome. Applied to Drosophila development, our model argues that, in this organism, the intergenerationally inherited H3K27me3 does not "survive" rapid cycles of embryonic chromatin replication and is unlikely to transmit the memory of epigenetic repression to the offspring. Our model is adaptable to other organisms, including mice and humans.
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Affiliation(s)
| | - Ludvig Lizana
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
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7
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Francois AK, Rohani A, Loftus M, Dochnal S, Hrit J, McFarlane S, Whitford A, Lewis A, Krakowiak P, Boutell C, Rothbart SB, Kashatus D, Cliffe AR. Single-genome analysis reveals heterogeneous association of the Herpes Simplex Virus genome with H3K27me2 and the reader PHF20L1 following infection of human fibroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.03.569766. [PMID: 38076966 PMCID: PMC10705572 DOI: 10.1101/2023.12.03.569766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The fate of herpesvirus genomes following entry into different cell types is thought to regulate the outcome of infection. For the Herpes simplex virus 1 (HSV-1), latent infection of neurons is characterized by association with repressive heterochromatin marked with Polycomb silencing-associated lysine 27 methylation on histone H3 (H3K27me). However, whether H3K27 methylation plays a role in repressing lytic gene expression in non-neuronal cells is unclear. To address this gap in knowledge, and with consideration that the fate of the viral genome and outcome of HSV-1 infection could be heterogeneous, we developed an assay to quantify the abundance of histone modifications within single viral genome foci of infected fibroblasts. Using this approach, combined with bulk epigenetic techniques, we were unable to detect any role for H3K27me3 during HSV-1 lytic infection of fibroblasts. In contrast, we could detect the lesser studied H3K27me2 on a subpopulation of viral genomes, which was consistent with a role for H3K27 demethylases in promoting lytic gene expression. This was consistent with a role for H3K27 demethylases in promoting lytic gene expression. In addition, viral genomes co-localized with the H3K27me2 reader protein PHF20L1, and this association was enhanced by inhibition of the H3K27 demethylases UTX and JMJD3. Notably, targeting of H3K27me2 to viral genomes was enhanced following infection with a transcriptionally defective virus in the absence of Promyelocytic leukemia nuclear bodies. Collectively, these studies implicate a role for H3K27me2 in fibroblast-associated HSV genome silencing in a manner dependent on genome sub-nuclear localization and transcriptional activity.
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Affiliation(s)
- Alison K Francois
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Ali Rohani
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Matt Loftus
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Sara Dochnal
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Joel Hrit
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503
| | - Steven McFarlane
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland
| | - Abigail Whitford
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Anna Lewis
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Patryk Krakowiak
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Chris Boutell
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, Scotland
| | - Scott B. Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503
| | - David Kashatus
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
| | - Anna R Cliffe
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, 22908
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8
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Barrasa JI, Kahn TG, Lundkvist MJ, Schwartz YB. DNA elements tether canonical Polycomb Repressive Complex 1 to human genes. Nucleic Acids Res 2023; 51:11613-11633. [PMID: 37855680 PMCID: PMC10681801 DOI: 10.1093/nar/gkad889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 09/25/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023] Open
Abstract
Development of multicellular animals requires epigenetic repression by Polycomb group proteins. The latter assemble in multi-subunit complexes, of which two kinds, Polycomb Repressive Complex 1 (PRC1) and Polycomb Repressive Complex 2 (PRC2), act together to repress key developmental genes. How PRC1 and PRC2 recognize specific genes remains an open question. Here we report the identification of several hundreds of DNA elements that tether canonical PRC1 to human developmental genes. We use the term tether to describe a process leading to a prominent presence of canonical PRC1 at certain genomic sites, although the complex is unlikely to interact with DNA directly. Detailed analysis indicates that sequence features associated with PRC1 tethering differ from those that favour PRC2 binding. Throughout the genome, the two kinds of sequence features mix in different proportions to yield a gamut of DNA elements that range from those tethering predominantly PRC1 or PRC2 to ones capable of tethering both complexes. The emerging picture is similar to the paradigmatic targeting of Polycomb complexes by Polycomb Response Elements (PREs) of Drosophila but providing for greater plasticity.
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Affiliation(s)
- Juan I Barrasa
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Tatyana G Kahn
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Moa J Lundkvist
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Yuri B Schwartz
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
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9
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Hamali B, Amine AAA, Al-Sady B. Regulation of the heterochromatin spreading reaction by trans-acting factors. Open Biol 2023; 13:230271. [PMID: 37935357 PMCID: PMC10645111 DOI: 10.1098/rsob.230271] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/03/2023] [Indexed: 11/09/2023] Open
Abstract
Heterochromatin is a gene-repressive protein-nucleic acid ultrastructure that is initially nucleated by DNA sequences. However, following nucleation, heterochromatin can then propagate along the chromatin template in a sequence-independent manner in a reaction termed spreading. At the heart of this process are enzymes that deposit chemical information on chromatin, which attracts the factors that execute chromatin compaction and transcriptional or co/post-transcriptional gene silencing. Given that these enzymes deposit guiding chemical information on chromatin they are commonly termed 'writers'. While the processes of nucleation and central actions of writers have been extensively studied and reviewed, less is understood about how the spreading process is regulated. We discuss how the chromatin substrate is prepared for heterochromatic spreading, and how trans-acting factors beyond writer enzymes regulate it. We examine mechanisms by which trans-acting factors in Suv39, PRC2, SETDB1 and SIR writer systems regulate spreading of the respective heterochromatic marks across chromatin. While these systems are in some cases evolutionarily and mechanistically quite distant, common mechanisms emerge which these trans-acting factors exploit to tune the spreading reaction.
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Affiliation(s)
- Bulut Hamali
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- The G. W. Hooper Foundation, San Francisco, CA 94143, USA
- College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Ahmed A A Amine
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- The G. W. Hooper Foundation, San Francisco, CA 94143, USA
| | - Bassem Al-Sady
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- The G. W. Hooper Foundation, San Francisco, CA 94143, USA
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10
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Wei X, Dhungana P, Sim C. The diapausing mosquito Culex pipiens exhibits reduced levels of H3K27me2 in the fat body. INSECT MOLECULAR BIOLOGY 2023. [PMID: 37702080 DOI: 10.1111/imb.12871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/21/2023] [Indexed: 09/14/2023]
Abstract
Culex pipiens, the northern house mosquito, is a major vector of West Nile virus. To survive the severe winter, adult mosquitoes enter a diapause programme. Extended lifespan and an increase in lipid storage are key indicators of diapause. Post-translational modifications to histone proteins impact the expression of genes and have been linked to the lifespan and energy utilisation of numerous insects. Here, we investigated the potential contribution of epigenetic alterations in initiating diapause in this mosquito species. Multiple sequence alignment of H3 sequences from other insect species demonstrates a high conservation of the H3 histone in Cx. pipiens throughout evolution. We then compared the levels of histone methylation in the ovaries and fat body tissues of diapausing and non-diapausing Cx. pipiens using western blots. Our data indicate that histone methylation levels in the ovaries of Cx. pipiens do not change during diapause. In contrast, H3K27me2 levels decrease more than twofold in the fat body of diapausing mosquitoes relative to non-diapausing counterparts. H3K27 methylation plays a crucial role in chromosome activation and inactivation during development in many insect species. This is predominantly governed by polycomb repressor complex 2. Intriguingly, a previous ChIP-seq study demonstrated that the transcription factor FOXO (Forkhead box O) targets the genes that comprise this complex. In addition, H3K27me2 exhibits dynamic abundance throughout the diapause programme in Cx. pipiens, suggesting its potential role in the initial activation of the diapause programme. This study expands our understanding of the relationship between alterations in epigenetic regulation and diapause.
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Affiliation(s)
- Xueyan Wei
- Department of Biology, Baylor University, Waco, Texas, USA
| | | | - Cheolho Sim
- Department of Biology, Baylor University, Waco, Texas, USA
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11
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Park J, Kim JY, Park JW, Kang JY, Oh H, Hahm J, Chae YC, Chakravarti D, Seo S. INHAT subunit SET/TAF-Iβ regulates PRC1-independent H2AK119 mono-ubiquitination via E3 ligase MIB1 in colon cancer. NAR Cancer 2023; 5:zcad050. [PMID: 37746636 PMCID: PMC10516711 DOI: 10.1093/narcan/zcad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/21/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023] Open
Abstract
SET/TAF-Iβ, a subunit of the inhibitor of acetyltransferases (INHAT) complex, exhibits transcriptional repression activity by inhibiting histone acetylation. We find that SET/TAF-Iβ regulates mono-ubiquitination of histone H2A at lysine 119 (H2AK119ub), which is involved in polycomb-mediated transcriptional repression, in HCT116 cells. In this report, we demonstrate that SET/TAF-Iβ acts as an E2 ubiquitin-conjugating enzyme for PRC1-independent H2AK119ub. Furthermore, we identify that MIB1 is the E3 ligase partner for SET/TAF-Iβ using LC-MS/MS and in vitro ubiquitination assays. Transcriptome analysis reveals that SET/TAF-Iβ and MIB1 regulate the expression of genes related to DNA replication and cell cycle progression in HCT116 cells, and knockdown of either protein reduces proliferation of HCT116 cells by impeding cell cycle progression. Together, our study reveals a novel PRC1-independent epigenetic regulatory mechanism for H2AK119ub by SET/TAF-Iβ and MIB1 in colon cancer.
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Affiliation(s)
- Junyoung Park
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ji-Young Kim
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jin Woo Park
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Joo Young Kang
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyein Oh
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ja Young Hahm
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Yun-Cheol Chae
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Debabrata Chakravarti
- Division of Reproductive Sciences in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sang Beom Seo
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
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12
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Kim JJ, Kingston RE. Context-specific Polycomb mechanisms in development. Nat Rev Genet 2022; 23:680-695. [PMID: 35681061 PMCID: PMC9933872 DOI: 10.1038/s41576-022-00499-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2022] [Indexed: 12/11/2022]
Abstract
Polycomb group (PcG) proteins are crucial chromatin regulators that maintain repression of lineage-inappropriate genes and are therefore required for stable cell fate. Recent advances show that PcG proteins form distinct multi-protein complexes in various cellular environments, such as in early development, adult tissue maintenance and cancer. This surprising compositional diversity provides the basis for mechanistic diversity. Understanding this complexity deepens and refines the principles of PcG complex recruitment, target-gene repression and inheritance of memory. We review how the core molecular mechanism of Polycomb complexes operates in diverse developmental settings and propose that context-dependent changes in composition and mechanism are essential for proper epigenetic regulation in development.
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Affiliation(s)
- Jongmin J. Kim
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Robert E. Kingston
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,
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13
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Kang H, Cabrera JR, Zee BM, Kang HA, Jobe JM, Hegarty MB, Barry AE, Glotov A, Schwartz YB, Kuroda MI. Variant Polycomb complexes in Drosophila consistent with ancient functional diversity. SCIENCE ADVANCES 2022; 8:eadd0103. [PMID: 36070387 PMCID: PMC9451159 DOI: 10.1126/sciadv.add0103] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Polycomb group (PcG) mutants were first identified in Drosophila on the basis of their failure to maintain proper Hox gene repression during development. The proteins encoded by the corresponding fly genes mainly assemble into one of two discrete Polycomb repressive complexes: PRC1 or PRC2. However, biochemical analyses in mammals have revealed alternative forms of PRC2 and multiple distinct types of noncanonical or variant PRC1. Through a series of proteomic analyses, we identify analogous PRC2 and variant PRC1 complexes in Drosophila, as well as a broader repertoire of interactions implicated in early development. Our data provide strong support for the ancient diversity of PcG complexes and a framework for future analysis in a longstanding and versatile genetic system.
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Affiliation(s)
- Hyuckjoon Kang
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Janel R. Cabrera
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Biology Department, Emmanuel College, Boston, MA 02115, USA
| | - Barry M. Zee
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Heather A. Kang
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Alexander Glotov
- Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
| | - Yuri B. Schwartz
- Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
| | - Mitzi I. Kuroda
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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14
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German B, Ellis L. Polycomb Directed Cell Fate Decisions in Development and Cancer. EPIGENOMES 2022; 6:28. [PMID: 36135315 PMCID: PMC9497807 DOI: 10.3390/epigenomes6030028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
The polycomb group (PcG) proteins are a subset of transcription regulators highly conserved throughout evolution. Their principal role is to epigenetically modify chromatin landscapes and control the expression of master transcriptional programs to determine cellular identity. The two mayor PcG protein complexes that have been identified in mammals to date are Polycomb Repressive Complex 1 (PRC1) and 2 (PRC2). These protein complexes selectively repress gene expression via the induction of covalent post-translational histone modifications, promoting chromatin structure stabilization. PRC2 catalyzes the histone H3 methylation at lysine 27 (H3K27me1/2/3), inducing heterochromatin structures. This activity is controlled by the formation of a multi-subunit complex, which includes enhancer of zeste (EZH2), embryonic ectoderm development protein (EED), and suppressor of zeste 12 (SUZ12). This review will summarize the latest insights into how PRC2 in mammalian cells regulates transcription to orchestrate the temporal and tissue-specific expression of genes to determine cell identity and cell-fate decisions. We will specifically describe how PRC2 dysregulation in different cell types can promote phenotypic plasticity and/or non-mutational epigenetic reprogramming, inducing the development of highly aggressive epithelial neuroendocrine carcinomas, including prostate, small cell lung, and Merkel cell cancer. With this, EZH2 has emerged as an important actionable therapeutic target in such cancers.
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Affiliation(s)
- Beatriz German
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Leigh Ellis
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Cedars-Sinai Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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15
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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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16
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De Novo Polycomb Recruitment and Repressive Domain Formation. EPIGENOMES 2022; 6:epigenomes6030025. [PMID: 35997371 PMCID: PMC9397058 DOI: 10.3390/epigenomes6030025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022] Open
Abstract
Every cell of an organism shares the same genome; even so, each cellular lineage owns a different transcriptome and proteome. The Polycomb group proteins (PcG) are essential regulators of gene repression patterning during development and homeostasis. However, it is unknown how the repressive complexes, PRC1 and PRC2, identify their targets and elicit new Polycomb domains during cell differentiation. Classical recruitment models consider the pre-existence of repressive histone marks; still, de novo target binding overcomes the absence of both H3K27me3 and H2AK119ub. The CpG islands (CGIs), non-core proteins, and RNA molecules are involved in Polycomb recruitment. Nonetheless, it is unclear how de novo targets are identified depending on the physiological context and developmental stage and which are the leading players stabilizing Polycomb complexes at domain nucleation sites. Here, we examine the features of de novo sites and the accessory elements bridging its recruitment and discuss the first steps of Polycomb domain formation and transcriptional regulation, comprehended by the experimental reconstruction of the repressive domains through time-resolved genomic analyses in mammals.
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17
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DNA Damage Response Regulation by Histone Ubiquitination. Int J Mol Sci 2022; 23:ijms23158187. [PMID: 35897775 PMCID: PMC9332593 DOI: 10.3390/ijms23158187] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 11/30/2022] Open
Abstract
Cells are constantly exposed to numerous genotoxic stresses that induce DNA damage. DNA double-strand breaks (DSBs) are among the most serious damages and should be systematically repaired to preserve genomic integrity. The efficiency of repair is closely associated with chromatin structure, which is regulated by posttranslational modifications of histones, including ubiquitination. Recent evidence shows crosstalk between histone ubiquitination and DNA damage responses, suggesting an integrated model for the systematic regulation of DNA repair. There are two major pathways for DSB repair, viz., nonhomologous end joining and homologous recombination, and the choice of the pathway is partially controlled by posttranslational modifications of histones, including ubiquitination. Histone ubiquitination changes chromatin structure in the vicinity of DSBs and serves as a platform to select and recruit repair proteins; the removal of these modifications by deubiquitinating enzymes suppresses the recruitment of repair proteins and promotes the convergence of repair reactions. This article provides a comprehensive overview of the DNA damage response regulated by histone ubiquitination in response to DSBs.
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18
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Melo GA, Calôba C, Brum G, Passos TO, Martinez GJ, Pereira RM. Epigenetic regulation of T cells by Polycomb group proteins. J Leukoc Biol 2022; 111:1253-1267. [DOI: 10.1002/jlb.2ri0122-039r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Guilherme A. Melo
- Instituto de Microbiologia Paulo de Góes, Departamento de Imunologia Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Carolina Calôba
- Instituto de Microbiologia Paulo de Góes, Departamento de Imunologia Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Gabrielle Brum
- Instituto de Microbiologia Paulo de Góes, Departamento de Imunologia Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Thaís O. Passos
- Instituto de Microbiologia Paulo de Góes, Departamento de Imunologia Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Gustavo J. Martinez
- Center for Cancer Cell Biology, Immunology and Infection, Discipline of Microbiology and Immunology Rosalind Franklin University of Medicine and Science Chicago Illinois USA
| | - Renata M. Pereira
- Instituto de Microbiologia Paulo de Góes, Departamento de Imunologia Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
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19
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Zhang P, Guergues J, Alleyne AR, Cirino TJ, Nadeau O, Figueroa AM, Stacy HM, Suzuki T, McLaughlin JP, Stevens SM, Liu B. Novel Histone Modifications in Microglia Derived from a Mouse Model of Chronic Pain. Proteomics 2022; 22:e2100137. [PMID: 35081661 DOI: 10.1002/pmic.202100137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 11/06/2022]
Abstract
As the resident immune cells in the central nervous system, microglia play an important role in the maintenance of its homeostasis. Dysregulation of microglia has been associated with the development and maintenance of chronic pain. However, the relevant molecular pathways remain poorly defined. In this study, we used a mass spectrometry-based proteomic approach to screen potential changes of histone protein modifications in microglia isolated from the brain of control and cisplatin-induced neuropathic pain adult C57BL/6J male mice. We identified several novel microglial histone modifications associated with pain including statistically significantly decreased histone H3.1 lysine 27 mono-methylation (H3.1K27me1, 54.8% of control) and lysine 56 tri-methylation (7.5% of control), as well as a trend suggesting increased histone 3 tyrosine 41 nitration. We further investigated the functional role of H3.1K27me1 and found that treatment of cultured microglial cells for 4 consecutive days with 1-10 μM of NCDM-64, a potent and selective inhibitor of lysine demethylase 7A, an enzyme responsible for the demethylation of H3K27me1, dose-dependently elevated its levels with a greater than a 2-fold increase observed at 10 μM compared to vehicle-treated control cells. Moreover, pre-treatment of mice with NCDM-64 (10 or 25 mg/kg/day, i.p.) prior to cisplatin treatment prevented the development of neuropathic pain in mice. The identification of specific chromatin marks in microglia associated with chronic pain may yield critical insight into the contribution of microglia to the development and maintenance of pain, and opens new avenues for the development of novel non-opioid therapeutics for the effective management of chronic pain. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ping Zhang
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Jennifer Guergues
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, USA
| | - Amy R Alleyne
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Thomas J Cirino
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Owen Nadeau
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT, USA
| | - Ariana M Figueroa
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Heather M Stacy
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Takayoshi Suzuki
- The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Jay P McLaughlin
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Stanley M Stevens
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, USA
| | - Bin Liu
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
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20
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Vijayanathan M, Trejo-Arellano MG, Mozgová I. Polycomb Repressive Complex 2 in Eukaryotes-An Evolutionary Perspective. EPIGENOMES 2022; 6:3. [PMID: 35076495 PMCID: PMC8788455 DOI: 10.3390/epigenomes6010003] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 12/23/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) represents a group of evolutionarily conserved multi-subunit complexes that repress gene transcription by introducing trimethylation of lysine 27 on histone 3 (H3K27me3). PRC2 activity is of key importance for cell identity specification and developmental phase transitions in animals and plants. The composition, biochemistry, and developmental function of PRC2 in animal and flowering plant model species are relatively well described. Recent evidence demonstrates the presence of PRC2 complexes in various eukaryotic supergroups, suggesting conservation of the complex and its function. Here, we provide an overview of the current understanding of PRC2-mediated repression in different representatives of eukaryotic supergroups with a focus on the green lineage. By comparison of PRC2 in different eukaryotes, we highlight the possible common and diverged features suggesting evolutionary implications and outline emerging questions and directions for future research of polycomb repression and its evolution.
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Affiliation(s)
- Mallika Vijayanathan
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
| | - María Guadalupe Trejo-Arellano
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
| | - Iva Mozgová
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (M.V.); (M.G.T.-A.)
- Faculty of Science, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic
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21
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Baile F, Gómez-Zambrano Á, Calonje M. Roles of Polycomb complexes in regulating gene expression and chromatin structure in plants. PLANT COMMUNICATIONS 2022; 3:100267. [PMID: 35059633 PMCID: PMC8760139 DOI: 10.1016/j.xplc.2021.100267] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/09/2021] [Accepted: 11/23/2021] [Indexed: 05/16/2023]
Abstract
The evolutionary conserved Polycomb Group (PcG) repressive system comprises two central protein complexes, PcG repressive complex 1 (PRC1) and PRC2. These complexes, through the incorporation of histone modifications on chromatin, have an essential role in the normal development of eukaryotes. In recent years, a significant effort has been made to characterize these complexes in the different kingdoms, and despite there being remarkable functional and mechanistic conservation, some key molecular principles have diverged. In this review, we discuss current views on the function of plant PcG complexes. We compare the composition of PcG complexes between animals and plants, highlight the role of recently identified plant PcG accessory proteins, and discuss newly revealed roles of known PcG partners. We also examine the mechanisms by which the repression is achieved and how these complexes are recruited to target genes. Finally, we consider the possible role of some plant PcG proteins in mediating local and long-range chromatin interactions and, thus, shaping chromatin 3D architecture.
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Affiliation(s)
- Fernando Baile
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092 Seville, Spain
| | - Ángeles Gómez-Zambrano
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092 Seville, Spain
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092 Seville, Spain
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22
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Wang YZ, Liu C, Zhao J, Yu J, Luo A, Xiao X, Dou SX, Ma L, Wang PY, Li M, Li G, Yan J, Chen P, Li W. H2A mono-ubiquitination differentiates FACT's functions in nucleosome assembly and disassembly. Nucleic Acids Res 2021; 50:833-846. [PMID: 34951461 PMCID: PMC8789066 DOI: 10.1093/nar/gkab1271] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/06/2021] [Accepted: 12/14/2021] [Indexed: 11/26/2022] Open
Abstract
The histone chaperone FACT (FAcilitates Chromatin Transcription) plays an essential role in transcription and DNA replication by its dual functions on nucleosome assembly to maintain chromatin integrity and nucleosome disassembly to destabilize nucleosome and facilitate its accessibility simultaneously. Mono-ubiquitination at Lysine 119 of H2A (ubH2A) has been suggested to repress transcription by preventing the recruitment of FACT at early elongation process. However, up to date, how ubH2A directly affects FACT on nucleosome assembly and disassembly remains elusive. In this study, we demonstrated that the dual functions of FACT are differently regulated by ubH2A. The H2A ubiquitination does not affect FACT’s chaperone function in nucleosome assembly and FACT can deposit ubH2A–H2B dimer on tetrasome to form intact nucleosome. However, ubH2A greatly restricts FACT binding on nucleosome and inhibits its activity of nucleosome disassembly. Interestingly, deubiquitination of ubH2A rescues the nucleosome disassembly function of FACT to activate gene transcription. Our findings provide mechanistic insights of how H2A ubiquitination affects FACT in breaking nucleosome and maintaining its integrity, which sheds light on the biological function of ubH2A and various FACT’s activity under different chromatin states.
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Affiliation(s)
- Yi-Zhou Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Cuifang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jicheng Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Juan Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Anfeng Luo
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Xue Xiao
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Shuo-Xing Dou
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Ma
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Peng-Ye Wang
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Ming Li
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianbin Yan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Li
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.,Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
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23
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Blackledge NP, Klose RJ. The molecular principles of gene regulation by Polycomb repressive complexes. Nat Rev Mol Cell Biol 2021; 22:815-833. [PMID: 34400841 PMCID: PMC7612013 DOI: 10.1038/s41580-021-00398-y] [Citation(s) in RCA: 170] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 12/12/2022]
Abstract
Precise control of gene expression is fundamental to cell function and development. Although ultimately gene expression relies on DNA-binding transcription factors to guide the activity of the transcription machinery to genes, it has also become clear that chromatin and histone post-translational modification have fundamental roles in gene regulation. Polycomb repressive complexes represent a paradigm of chromatin-based gene regulation in animals. The Polycomb repressive system comprises two central protein complexes, Polycomb repressive complex 1 (PRC1) and PRC2, which are essential for normal gene regulation and development. Our early understanding of Polycomb function relied on studies in simple model organisms, but more recently it has become apparent that this system has expanded and diverged in mammals. Detailed studies are now uncovering the molecular mechanisms that enable mammalian PRC1 and PRC2 to identify their target sites in the genome, communicate through feedback mechanisms to create Polycomb chromatin domains and control transcription to regulate gene expression. In this Review, we discuss and contextualize the emerging principles that define how this fascinating chromatin-based system regulates gene expression in mammals.
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Affiliation(s)
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK.
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24
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Lindehell H, Glotov A, Dorafshan E, Schwartz YB, Larsson J. The role of H3K36 methylation and associated methyltransferases in chromosome-specific gene regulation. SCIENCE ADVANCES 2021; 7:eabh4390. [PMID: 34597135 PMCID: PMC10938550 DOI: 10.1126/sciadv.abh4390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
In Drosophila, two chromosomes require special mechanisms to balance their transcriptional output to the rest of the genome. These are the male-specific lethal complex targeting the male X chromosome and Painting of fourth targeting chromosome 4. Here, we explore the role of histone H3 methylated at lysine-36 (H3K36) and the associated methyltransferases—Set2, NSD, and Ash1—in these two chromosome-specific systems. We show that the loss of Set2 impairs the MSL complex–mediated dosage compensation; however, the effect is not recapitulated by H3K36 replacement and indicates an alternative target of Set2. Unexpectedly, balanced transcriptional output from the fourth chromosome requires intact H3K36 and depends on the additive functions of NSD and Ash1. We conclude that H3K36 methylation and the associated methyltransferases are important factors to balance transcriptional output of the male X chromosome and the fourth chromosome. Furthermore, our study highlights the pleiotropic effects of these enzymes.
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Affiliation(s)
- Henrik Lindehell
- Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
| | - Alexander Glotov
- Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
| | - Eshagh Dorafshan
- Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
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25
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Conway E, Rossi F, Fernandez-Perez D, Ponzo E, Ferrari KJ, Zanotti M, Manganaro D, Rodighiero S, Tamburri S, Pasini D. BAP1 enhances Polycomb repression by counteracting widespread H2AK119ub1 deposition and chromatin condensation. Mol Cell 2021; 81:3526-3541.e8. [PMID: 34186021 PMCID: PMC8428331 DOI: 10.1016/j.molcel.2021.06.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 12/15/2022]
Abstract
BAP1 is mutated or deleted in many cancer types, including mesothelioma, uveal melanoma, and cholangiocarcinoma. It is the catalytic subunit of the PR-DUB complex, which removes PRC1-mediated H2AK119ub1, essential for maintaining transcriptional repression. However, the precise relationship between BAP1 and Polycombs remains elusive. Using embryonic stem cells, we show that BAP1 restricts H2AK119ub1 deposition to Polycomb target sites. This increases the stability of Polycomb with their targets and prevents diffuse accumulation of H2AK119ub1 and H3K27me3. Loss of BAP1 results in a broad increase in H2AK119ub1 levels that is primarily dependent on PCGF3/5-PRC1 complexes. This titrates PRC2 away from its targets and stimulates H3K27me3 accumulation across the genome, leading to a general chromatin compaction. This provides evidence for a unifying model that resolves the apparent contradiction between BAP1 catalytic activity and its role in vivo, uncovering molecular vulnerabilities that could be useful for BAP1-related pathologies.
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Affiliation(s)
- Eric Conway
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Federico Rossi
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Daniel Fernandez-Perez
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Eleonora Ponzo
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Karin Johanna Ferrari
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Marika Zanotti
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Daria Manganaro
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Simona Rodighiero
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Simone Tamburri
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Via A. di Rudini 8, Department of Health Sciences, 20142 Milan, Italy.
| | - Diego Pasini
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Via A. di Rudini 8, Department of Health Sciences, 20142 Milan, Italy.
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26
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Moretti C, Stévant I, Ghavi-Helm Y. 3D genome organisation in Drosophila. Brief Funct Genomics 2021; 19:92-100. [PMID: 31796947 DOI: 10.1093/bfgp/elz029] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/02/2019] [Accepted: 09/20/2019] [Indexed: 12/17/2022] Open
Abstract
Ever since Thomas Hunt Morgan's discovery of the chromosomal basis of inheritance by using Drosophila melanogaster as a model organism, the fruit fly has remained an essential model system in studies of genome biology, including chromatin organisation. Very much as in vertebrates, in Drosophila, the genome is organised in territories, compartments and topologically associating domains (TADs). However, these domains might be formed through a slightly different mechanism than in vertebrates due to the presence of a large and potentially redundant set of insulator proteins and the minor role of dCTCF in TAD boundary formation. Here, we review the different levels of chromatin organisation in Drosophila and discuss mechanisms and factors that might be involved in TAD formation. The dynamics of TADs and enhancer-promoter interactions in the context of transcription are covered in the light of currently conflicting results. Finally, we illustrate the value of polymer modelling approaches to infer the principles governing the three-dimensional organisation of the Drosophila genome.
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Affiliation(s)
- Charlotte Moretti
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie F-69364 Lyon, France
| | - Isabelle Stévant
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie F-69364 Lyon, France
| | - Yad Ghavi-Helm
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie F-69364 Lyon, France
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27
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Fursova NA, Turberfield AH, Blackledge NP, Findlater EL, Lastuvkova A, Huseyin MK, Dobrinić P, Klose RJ. BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome. Genes Dev 2021; 35:749-770. [PMID: 33888563 PMCID: PMC8091973 DOI: 10.1101/gad.347005.120] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/02/2021] [Indexed: 12/21/2022]
Abstract
Histone-modifying systems play fundamental roles in gene regulation and the development of multicellular organisms. Histone modifications that are enriched at gene regulatory elements have been heavily studied, but the function of modifications found more broadly throughout the genome remains poorly understood. This is exemplified by histone H2A monoubiquitylation (H2AK119ub1), which is enriched at Polycomb-repressed gene promoters but also covers the genome at lower levels. Here, using inducible genetic perturbations and quantitative genomics, we found that the BAP1 deubiquitylase plays an essential role in constraining H2AK119ub1 throughout the genome. Removal of BAP1 leads to pervasive genome-wide accumulation of H2AK119ub1, which causes widespread reductions in gene expression. We show that elevated H2AK119ub1 preferentially counteracts Ser5 phosphorylation on the C-terminal domain of RNA polymerase II at gene regulatory elements and causes reductions in transcription and transcription-associated histone modifications. Furthermore, failure to constrain pervasive H2AK119ub1 compromises Polycomb complex occupancy at a subset of Polycomb target genes, which leads to their derepression, providing a potential molecular rationale for why the BAP1 ortholog in Drosophila has been characterized as a Polycomb group gene. Together, these observations reveal that the transcriptional potential of the genome can be modulated by regulating the levels of a pervasive histone modification.
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Affiliation(s)
- Nadezda A Fursova
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Anne H Turberfield
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Neil P Blackledge
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Emma L Findlater
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Anna Lastuvkova
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Miles K Huseyin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Paula Dobrinić
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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28
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Macrae TA, Ramalho-Santos M. The deubiquitinase Usp9x regulates PRC2-mediated chromatin reprogramming during mouse development. Nat Commun 2021; 12:1865. [PMID: 33767158 PMCID: PMC7994559 DOI: 10.1038/s41467-021-21910-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 02/19/2021] [Indexed: 01/31/2023] Open
Abstract
Pluripotent cells of the mammalian embryo undergo extensive chromatin rewiring to prepare for lineage commitment after implantation. Repressive H3K27me3, deposited by Polycomb Repressive Complex 2 (PRC2), is reallocated from large blankets in pre-implantation embryos to mark promoters of developmental genes. The regulation of this global redistribution of H3K27me3 is poorly understood. Here we report a post-translational mechanism that destabilizes PRC2 to constrict H3K27me3 during lineage commitment. Using an auxin-inducible degron system, we show that the deubiquitinase Usp9x is required for mouse embryonic stem (ES) cell self-renewal. Usp9x-high ES cells have high PRC2 levels and bear a chromatin and transcriptional signature of the pre-implantation embryo, whereas Usp9x-low ES cells resemble the post-implantation, gastrulating epiblast. We show that Usp9x interacts with, deubiquitinates and stabilizes PRC2. Deletion of Usp9x in post-implantation embryos results in the derepression of genes that normally gain H3K27me3 after gastrulation, followed by the appearance of morphological abnormalities at E9.5, pointing to a recurrent link between Usp9x and PRC2 during development. Usp9x is a marker of "stemness" and is mutated in various neurological disorders and cancers. Our results unveil a Usp9x-PRC2 regulatory axis that is critical at peri-implantation and may be redeployed in other stem cell fate transitions and disease states.
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Affiliation(s)
- Trisha A Macrae
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Miguel Ramalho-Santos
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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29
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Tauc HM, Rodriguez-Fernandez IA, Hackney JA, Pawlak M, Ronnen Oron T, Korzelius J, Moussa HF, Chaudhuri S, Modrusan Z, Edgar BA, Jasper H. Age-related changes in polycomb gene regulation disrupt lineage fidelity in intestinal stem cells. eLife 2021; 10:62250. [PMID: 33724181 PMCID: PMC7984841 DOI: 10.7554/elife.62250] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 03/15/2021] [Indexed: 01/01/2023] Open
Abstract
Tissue homeostasis requires long-term lineage fidelity of somatic stem cells. Whether and how age-related changes in somatic stem cells impact the faithful execution of lineage decisions remains largely unknown. Here, we address this question using genome-wide chromatin accessibility and transcriptome analysis as well as single-cell RNA-seq to explore stem-cell-intrinsic changes in the aging Drosophila intestine. These studies indicate that in stem cells of old flies, promoters of Polycomb (Pc) target genes become differentially accessible, resulting in the increased expression of enteroendocrine (EE) cell specification genes. Consistently, we find age-related changes in the composition of the EE progenitor cell population in aging intestines, as well as a significant increase in the proportion of EE-specified intestinal stem cells (ISCs) and progenitors in aging flies. We further confirm that Pc-mediated chromatin regulation is a critical determinant of EE cell specification in the Drosophila intestine. Pc is required to maintain expression of stem cell genes while ensuring repression of differentiation and specification genes. Our results identify Pc group proteins as central regulators of lineage identity in the intestinal epithelium and highlight the impact of age-related decline in chromatin regulation on tissue homeostasis.
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Affiliation(s)
- Helen M Tauc
- Immunology Discovery, Genentech, South San Francisco, United States
| | | | - Jason A Hackney
- OMNI Bioinformatics, Genentech, South San Francisco, United States
| | - Michal Pawlak
- Institute of Hematology and Blood Transfusion, Warsaw, Poland
| | | | - Jerome Korzelius
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Hagar F Moussa
- Department of Biomedical Engineering and Biological Design Center,Boston University, Boston, United States
| | - Subhra Chaudhuri
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, United States
| | - Zora Modrusan
- Immunology Discovery, Genentech, South San Francisco, United States.,Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, United States
| | - Bruce A Edgar
- Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Heinrich Jasper
- Immunology Discovery, Genentech, South San Francisco, United States
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30
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Huseyin MK, Klose RJ. Live-cell single particle tracking of PRC1 reveals a highly dynamic system with low target site occupancy. Nat Commun 2021; 12:887. [PMID: 33563969 PMCID: PMC7873255 DOI: 10.1038/s41467-021-21130-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 01/13/2021] [Indexed: 01/04/2023] Open
Abstract
Polycomb repressive complex 1 (PRC1) is an essential chromatin-based repressor of gene transcription. How PRC1 engages with chromatin to identify its target genes and achieve gene repression remains poorly defined, representing a major hurdle to our understanding of Polycomb system function. Here, we use genome engineering and single particle tracking to dissect how PRC1 binds to chromatin in live mouse embryonic stem cells. We observe that PRC1 is highly dynamic, with only a small fraction stably interacting with chromatin. By integrating subunit-specific dynamics, chromatin binding, and abundance measurements, we discover that PRC1 exhibits low occupancy at target sites. Furthermore, we employ perturbation approaches to uncover how specific components of PRC1 define its kinetics and chromatin binding. Together, these discoveries provide a quantitative understanding of chromatin binding by PRC1 in live cells, suggesting that chromatin modification, as opposed to PRC1 complex occupancy, is central to gene repression.
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Affiliation(s)
- Miles K Huseyin
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
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31
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Polycomb group-mediated histone H2A monoubiquitination in epigenome regulation and nuclear processes. Nat Commun 2020; 11:5947. [PMID: 33230107 PMCID: PMC7683540 DOI: 10.1038/s41467-020-19722-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 10/12/2020] [Indexed: 12/19/2022] Open
Abstract
Histone posttranslational modifications are key regulators of chromatin-associated processes including gene expression, DNA replication and DNA repair. Monoubiquitinated histone H2A, H2Aub (K118 in Drosophila or K119 in vertebrates) is catalyzed by the Polycomb group (PcG) repressive complex 1 (PRC1) and reversed by the PcG-repressive deubiquitinase (PR-DUB)/BAP1 complex. Here we critically assess the current knowledge regarding H2Aub deposition and removal, its crosstalk with PcG repressive complex 2 (PRC2)-mediated histone H3K27 methylation, and the recent attempts toward discovering its readers and solving its enigmatic functions. We also discuss mounting evidence of the involvement of H2A ubiquitination in human pathologies including cancer, while highlighting some knowledge gaps that remain to be addressed. Histone H2A monoubiquitination on lysine 119 in vertebrate and lysine 118 in Drosophila (H2Aub) is an epigenomic mark usually associated with gene repression by Polycomb group factors. Here the authors review the current knowledge on the deposition and removal of H2Aub, its function in transcription and other DNA-associated processes as well as its relevance to human disease.
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32
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Seif E, Kang JJ, Sasseville C, Senkovich O, Kaltashov A, Boulier EL, Kapur I, Kim CA, Francis NJ. Phase separation by the polyhomeotic sterile alpha motif compartmentalizes Polycomb Group proteins and enhances their activity. Nat Commun 2020; 11:5609. [PMID: 33154383 PMCID: PMC7644731 DOI: 10.1038/s41467-020-19435-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023] Open
Abstract
Polycomb Group (PcG) proteins organize chromatin at multiple scales to regulate gene expression. A conserved Sterile Alpha Motif (SAM) in the Polycomb Repressive Complex 1 (PRC1) subunit Polyhomeotic (Ph) has been shown to play an important role in chromatin compaction and large-scale chromatin organization. Ph SAM forms helical head to tail polymers, and SAM-SAM interactions between chromatin-bound Ph/PRC1 are believed to compact chromatin and mediate long-range interactions. To understand the underlying mechanism, here we analyze the effects of Ph SAM on chromatin in vitro. We find that incubation of chromatin or DNA with a truncated Ph protein containing the SAM results in formation of concentrated, phase-separated condensates. Ph SAM-dependent condensates can recruit PRC1 from extracts and enhance PRC1 ubiquitin ligase activity towards histone H2A. We show that overexpression of Ph with an intact SAM increases ubiquitylated H2A in cells. Thus, SAM-induced phase separation, in the context of Ph, can mediate large-scale compaction of chromatin into biochemical compartments that facilitate histone modification.
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Affiliation(s)
- Elias Seif
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Jin Joo Kang
- 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, Montreal, QC, H4A 3J1, Canada
| | - Charles Sasseville
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Olga Senkovich
- Department of Biochemistry and Molecular Genetics, Midwestern University, 19555N. 59th St., Glendale, AZ, 85308, USA
| | - Alexander Kaltashov
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Elodie L Boulier
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Ibani Kapur
- 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, Montreal, QC, H4A 3J1, Canada
| | - Chongwoo A Kim
- Department of Biochemistry and Molecular Genetics, Midwestern University, 19555N. 59th St., Glendale, AZ, 85308, USA
| | - 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, Montreal, 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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33
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The genetic basis for PRC1 complex diversity emerged early in animal evolution. Proc Natl Acad Sci U S A 2020; 117:22880-22889. [PMID: 32868440 DOI: 10.1073/pnas.2005136117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Polycomb group proteins are essential regulators of developmental processes across animals. Despite their importance, studies on Polycomb are often restricted to classical model systems and, as such, little is known about the evolution of these important chromatin regulators. Here we focus on Polycomb Repressive Complex 1 (PRC1) and trace the evolution of core components of canonical and non-canonical PRC1 complexes in animals. Previous work suggested that a major expansion in the number of PRC1 complexes occurred in the vertebrate lineage. We show that the expansion of the Polycomb Group RING Finger (PCGF) protein family, an essential step for the establishment of the large diversity of PRC1 complexes found in vertebrates, predates the bilaterian-cnidarian ancestor. This means that the genetic repertoire necessary to form all major vertebrate PRC1 complexes emerged early in animal evolution, over 550 million years ago. We further show that PCGF5, a gene conserved in cnidarians and vertebrates but lost in all other studied groups, is expressed in the nervous system in the sea anemone Nematostella vectensis, similar to its mammalian counterpart. Together this work provides a framework for understanding the evolution of PRC1 complex diversity and it establishes Nematostella as a promising model system in which the functional ramifications of this diversification can be further explored.
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34
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Giner-Laguarda N, Vidal M. Functions of Polycomb Proteins on Active Targets. EPIGENOMES 2020; 4:17. [PMID: 34968290 PMCID: PMC8594714 DOI: 10.3390/epigenomes4030017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022] Open
Abstract
Chromatin regulators of the Polycomb group of genes are well-known by their activities as transcriptional repressors. Characteristically, their presence at genomic sites occurs with specific histone modifications and sometimes high-order chromatin structures correlated with silencing of genes involved in cell differentiation. However, evidence gathered in recent years, on flies and mammals, shows that in addition to these sites, Polycomb products bind to a large number of active regulatory regions. Occupied sites include promoters and also intergenic regions, containing enhancers and super-enhancers. Contrasting with occupancies at repressed targets, characteristic histone modifications are low or undetectable. Functions on active targets are dual, restraining gene expression at some targets while promoting activity at others. Our aim here is to summarize the evidence available and discuss the convenience of broadening the scope of research to include Polycomb functions on active targets.
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Affiliation(s)
| | - Miguel Vidal
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, Ramiro de Maeztu 9, 28040 Madrid, Spain;
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35
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DeLuca SZ, Ghildiyal M, Pang LY, Spradling AC. Differentiating Drosophila female germ cells initiate Polycomb silencing by regulating PRC2-interacting proteins. eLife 2020; 9:56922. [PMID: 32773039 PMCID: PMC7438113 DOI: 10.7554/elife.56922] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/06/2020] [Indexed: 01/18/2023] Open
Abstract
Polycomb silencing represses gene expression and provides a molecular memory of chromatin state that is essential for animal development. We show that Drosophila female germline stem cells (GSCs) provide a powerful system for studying Polycomb silencing. GSCs have a non-canonical distribution of PRC2 activity and lack silenced chromatin like embryonic progenitors. As GSC daughters differentiate into nurse cells and oocytes, nurse cells, like embryonic somatic cells, silence genes in traditional Polycomb domains and in generally inactive chromatin. Developmentally controlled expression of two Polycomb repressive complex 2 (PRC2)-interacting proteins, Pcl and Scm, initiate silencing during differentiation. In GSCs, abundant Pcl inhibits PRC2-dependent silencing globally, while in nurse cells Pcl declines and newly induced Scm concentrates PRC2 activity on traditional Polycomb domains. Our results suggest that PRC2-dependent silencing is developmentally regulated by accessory proteins that either increase the concentration of PRC2 at target sites or inhibit the rate that PRC2 samples chromatin.
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Affiliation(s)
- Steven Z DeLuca
- Howard Hughes Medical Institute Research Laboratories Department of Embryology, Carnegie Institution for Science, Baltimore, United States
| | - Megha Ghildiyal
- Howard Hughes Medical Institute Research Laboratories Department of Embryology, Carnegie Institution for Science, Baltimore, United States
| | - Liang-Yu Pang
- Howard Hughes Medical Institute Research Laboratories Department of Embryology, Carnegie Institution for Science, Baltimore, United States
| | - Allan C Spradling
- Howard Hughes Medical Institute Research Laboratories Department of Embryology, Carnegie Institution for Science, Baltimore, United States
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36
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Abstract
Predicting regulatory potential from primary DNA sequences or transcription factor binding patterns is not possible. However, the annotation of the genome by chromatin proteins, histone modifications, and differential compaction is largely sufficient to reveal the locations of genes and their differential activity states. The Polycomb Group (PcG) and Trithorax Group (TrxG) proteins are the central players in this cell type-specific chromatin organization. PcG function was originally viewed as being solely repressive and irreversible, as observed at the homeotic loci in flies and mammals. However, it is now clear that modular and reversible PcG function is essential at most developmental genes. Focusing mainly on recent advances, we review evidence for how PcG and TrxG patterns change dynamically during cell type transitions. The ability to implement cell type-specific transcriptional programming with exquisite fidelity is essential for normal development.
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Affiliation(s)
- Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA; ,
| | - Hyuckjoon Kang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA; ,
| | - Sandip De
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
| | - Judith A Kassis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
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Béguelin W, Teater M, Meydan C, Hoehn KB, Phillip JM, Soshnev AA, Venturutti L, Rivas MA, Calvo-Fernández MT, Gutierrez J, Camarillo JM, Takata K, Tarte K, Kelleher NL, Steidl C, Mason CE, Elemento O, Allis CD, Kleinstein SH, Melnick AM. Mutant EZH2 Induces a Pre-malignant Lymphoma Niche by Reprogramming the Immune Response. Cancer Cell 2020; 37:655-673.e11. [PMID: 32396861 PMCID: PMC7298875 DOI: 10.1016/j.ccell.2020.04.004] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 02/04/2020] [Accepted: 04/08/2020] [Indexed: 10/24/2022]
Abstract
Follicular lymphomas (FLs) are slow-growing, indolent tumors containing extensive follicular dendritic cell (FDC) networks and recurrent EZH2 gain-of-function mutations. Paradoxically, FLs originate from highly proliferative germinal center (GC) B cells with proliferation strictly dependent on interactions with T follicular helper cells. Herein, we show that EZH2 mutations initiate FL by attenuating GC B cell requirement for T cell help and driving slow expansion of GC centrocytes that become enmeshed with and dependent on FDCs. By impairing T cell help, mutant EZH2 prevents induction of proliferative MYC programs. Thus, EZH2 mutation fosters malignant transformation by epigenetically reprograming B cells to form an aberrant immunological niche that reflects characteristic features of human FLs, explaining how indolent tumors arise from GC B cells.
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MESH Headings
- Animals
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/pathology
- Cellular Reprogramming
- Dendritic Cells/immunology
- Dendritic Cells/metabolism
- Dendritic Cells/pathology
- Enhancer of Zeste Homolog 2 Protein/genetics
- Female
- Germinal Center/immunology
- Germinal Center/metabolism
- Germinal Center/pathology
- Humans
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/immunology
- Lymphoma, B-Cell/pathology
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/immunology
- Lymphoma, Follicular/pathology
- Mice
- Mice, Inbred C57BL
- Mutation
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Affiliation(s)
- Wendy Béguelin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
| | - Matt Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Cem Meydan
- Institute for Computational Biomedicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Kenneth B Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jude M Phillip
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Alexey A Soshnev
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Leandro Venturutti
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Martín A Rivas
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - María T Calvo-Fernández
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Johana Gutierrez
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Jeannie M Camarillo
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL 60208, USA
| | - Katsuyoshi Takata
- Center for Lymphoid Cancer, British Columbia Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Karin Tarte
- UMR 1236, Université Rennes 1, INSERM, Etablissement Français du Sang, 35043 Rennes, France
| | - Neil L Kelleher
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL 60208, USA
| | - Christian Steidl
- Center for Lymphoid Cancer, British Columbia Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Christopher E Mason
- Institute for Computational Biomedicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10021, USA; The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Steven H Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
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39
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Kim J, Kingston RE. The CBX family of proteins in transcriptional repression and memory. J Biosci 2020; 45:16. [PMID: 31965994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
For mammals to develop properly, master regulatory genes must be repressed appropriately in a heritable manner. This review concerns the Polycomb Repressive Complex 1 (PRC1) family and the relationship between the establishment of repression and memory of the repressed state. The primary focus is on the CBX family of proteins in PRC1 complexes and their role in both chromatin compaction and phase separation. These two activities are linked and might contribute to both repression and memory.
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Affiliation(s)
- Jongmin Kim
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA
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40
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Loubiere V, Papadopoulos GL, Szabo Q, Martinez AM, Cavalli G. Widespread activation of developmental gene expression characterized by PRC1-dependent chromatin looping. SCIENCE ADVANCES 2020; 6:eaax4001. [PMID: 31950077 PMCID: PMC6954061 DOI: 10.1126/sciadv.aax4001] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 11/06/2019] [Indexed: 05/21/2023]
Abstract
Polycomb repressive complexes 1 and 2 have been historically described as transcriptional repressors, but recent reports suggest that PRC1 might also support activation, although the underlying mechanisms remain elusive. Here, we show that stage-specific PRC1 binding at a subset of active promoters and enhancers during Drosophila development coincides with the formation of three-dimensional (3D) loops, an increase in expression during development and repression in PRC1 mutants. Dissection of the dachshund locus indicates that PRC1-anchored loops are versatile architectural platforms that persist when surrounding genes are transcriptionally active and fine-tune their expression. The analysis of RING1B binding profiles and 3D contacts during neural differentiation in mice suggests that this role is conserved in mammals.
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Affiliation(s)
- V. Loubiere
- Institute of Human Genetics, UMR 9002, CNRS–University of Montpellier, 34396 Montpellier, France
| | - G. L. Papadopoulos
- Institute of Human Genetics, UMR 9002, CNRS–University of Montpellier, 34396 Montpellier, France
| | - Q. Szabo
- Institute of Human Genetics, UMR 9002, CNRS–University of Montpellier, 34396 Montpellier, France
| | - A-M. Martinez
- Institute of Human Genetics, UMR 9002, CNRS–University of Montpellier, 34396 Montpellier, France
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41
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Cheutin T, Cavalli G. The multiscale effects of polycomb mechanisms on 3D chromatin folding. Crit Rev Biochem Mol Biol 2019; 54:399-417. [PMID: 31698957 DOI: 10.1080/10409238.2019.1679082] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/08/2019] [Accepted: 10/08/2019] [Indexed: 12/30/2022]
Abstract
Polycomb group (PcG) proteins silence master regulatory genes required to properly confer cell identity during the development of both Drosophila and mammals. They may act through chromatin compaction and higher-order folding of chromatin inside the cell nucleus. During the last decade, analysis on interphase chromosome architecture discovered self-interacting regions named topologically associated domains (TADs). TADs result from the 3D chromatin folding of a succession of transcribed and repressed epigenomic domains and from loop extrusion mediated by cohesin/CTCF in mammals. Polycomb silenced chromatin constitutes one type of repressed epigenomic domains which form compacted nano-compartments inside cell nuclei. Recruitment of canonical PcG proteins on chromatin relies on initial binding to discrete elements and further spreading into large chromatin domains covered with H3K27me3. Some of these discrete elements have a bivalent nature both in mammals and Drosophila and are dynamically regulated during development. Loops can occur between them, suggesting that their interaction plays both functional and structural roles. Formation of large chromatin domains covered by H3K27me3 seems crucial for PcG silencing and PcG proteins might exert their function through compaction of these domains in both mammals and flies, rather than by directly controlling the nucleosomal accessibility of discrete regulatory elements. In addition, PcG chromatin domains interact over long genomic distances, shaping a higher-order chromatin network. Therefore, PcG silencing might rely on multiscale chromatin folding to maintain cell identity during differentiation.
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Affiliation(s)
- Thierry Cheutin
- Institute of Human Genetics, CNRS and the University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS and the University of Montpellier, Montpellier, France
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42
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Abstract
Polycomb repressive complex 2 (PRC2) is a conserved chromatin regulator that is responsible for the methylation of histone H3 lysine 27 (H3K27). PRC2 is essential for normal development and its loss of function thus results in a range of developmental phenotypes. Here, we review the latest advances in our understanding of mammalian PRC2 activity and present an updated summary of the phenotypes associated with its loss of function in mice. We then discuss recent studies that have highlighted regulatory interplay between the modifications laid down by PRC2 and other chromatin modifiers, including NSD1 and DNMT3A. Finally, we propose a model in which the dysregulation of these modifications at intergenic regions is a shared molecular feature of genetically distinct but highly phenotypically similar overgrowth syndromes in humans.
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Affiliation(s)
- Orla Deevy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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43
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Healy E, Mucha M, Glancy E, Fitzpatrick DJ, Conway E, Neikes HK, Monger C, Van Mierlo G, Baltissen MP, Koseki Y, Vermeulen M, Koseki H, Bracken AP. PRC2.1 and PRC2.2 Synergize to Coordinate H3K27 Trimethylation. Mol Cell 2019; 76:437-452.e6. [PMID: 31521505 DOI: 10.1016/j.molcel.2019.08.012] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/28/2019] [Accepted: 08/12/2019] [Indexed: 12/12/2022]
Abstract
Polycomb repressive complex 2 (PRC2) is composed of EED, SUZ12, and EZH1/2 and mediates mono-, di-, and trimethylation of histone H3 at lysine 27. At least two independent subcomplexes exist, defined by their specific accessory proteins: PRC2.1 (PCL1-3, EPOP, and PALI1/2) and PRC2.2 (AEBP2 and JARID2). We show that PRC2.1 and PRC2.2 share the majority of target genes in mouse embryonic stem cells. The loss of PCL1-3 is sufficient to evict PRC2.1 from Polycomb target genes but only leads to a partial reduction of PRC2.2 and H3K27me3. Conversely, disruption of PRC2.2 function through the loss of either JARID2 or RING1A/B is insufficient to completely disrupt targeting of SUZ12 by PCLs. Instead, the combined loss of both PRC2.1 and PRC2.2 is required, leading to the global mislocalization of SUZ12. This supports a model in which the specific accessory proteins within PRC2.1 and PRC2.2 cooperate to direct H3K27me3 via both synergistic and independent mechanisms.
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Affiliation(s)
- Evan Healy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Marlena Mucha
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eleanor Glancy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Eric Conway
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Hannah K Neikes
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Craig Monger
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Guido Van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Marijke P Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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44
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Navarro FCP, Hoops J, Bellfy L, Cerveira E, Zhu Q, Zhang C, Lee C, Gerstein MB. TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements. PLoS Comput Biol 2019; 15:e1007293. [PMID: 31425522 PMCID: PMC6715295 DOI: 10.1371/journal.pcbi.1007293] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 08/29/2019] [Accepted: 07/26/2019] [Indexed: 11/19/2022] Open
Abstract
The Long interspersed nuclear element 1 (LINE-1) is a primary source of genetic variation in humans and other mammals. Despite its importance, LINE-1 activity remains difficult to study because of its highly repetitive nature. Here, we developed and validated a method called TeXP to gauge LINE-1 activity accurately. TeXP builds mappability signatures from LINE-1 subfamilies to deconvolve the effect of pervasive transcription from autonomous LINE-1 activity. In particular, it apportions the multiple reads aligned to the many LINE-1 instances in the genome into these two categories. Using our method, we evaluated well-established cell lines, cell-line compartments and healthy tissues and found that the vast majority (91.7%) of transcriptome reads overlapping LINE-1 derive from pervasive transcription. We validated TeXP by independently estimating the levels of LINE-1 autonomous transcription using ddPCR, finding high concordance. Next, we applied our method to comprehensively measure LINE-1 activity across healthy somatic cells, while backing out the effect of pervasive transcription. Unexpectedly, we found that LINE-1 activity is present in many normal somatic cells. This finding contrasts with earlier studies showing that LINE-1 has limited activity in healthy somatic tissues, except for neuroprogenitor cells. Interestingly, we found that the amount of LINE-1 activity was associated with the with the amount of cell turnover, with tissues with low cell turnover rates (e.g. the adult central nervous system) showing lower LINE-1 activity. Altogether, our results show how accounting for pervasive transcription is critical to accurately quantify the activity of highly repetitive regions of the human genome. Repetitive sequences, such as LINEs, comprise more than half of the human genome. Due to their repetitive nature, LINEs are hard to grasp. In particular, we find that pervasive transcription is a major confounding factor in transcriptome data. We observe that, on average, more than 90% of LINE signal derives from pervasive transcription. To investigate this issue, we developed and validated a new method called TeXP. TeXP accounts and removes the effects of pervasive transcription when quantifying LINE activity. Our method uses the broad distribution of LINEs to estimate the effects of pervasive transcription. Using TeXP, we processed thousands of transcriptome datasets to uniformly, and unbiasedly measure LINE-1 activity across healthy somatic cells. By removing the pervasive transcription component, we find that (1) LINE-1 is broadly expressed in healthy somatic tissues; (2) Adult brain show small levels of LINE transcription and; (3) LINE-1 transcription level is correlated with tissue cell turnover. Our method thus offers insights into how repetitive sequences and influenced by pervasive transcription. Moreover, we uncover the activity of LINE-1 in somatic tissues at an unmatched scale.
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Affiliation(s)
- Fabio CP Navarro
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Jacob Hoops
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Lauren Bellfy
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Eliza Cerveira
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Chengsheng Zhang
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
- Department of Life Sciences, Ewha Womans University, Seoul, Korea
| | - Mark B. Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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45
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Abstract
As the process that silences gene expression ensues during development, the stage is set for the activity of Polycomb-repressive complex 2 (PRC2) to maintain these repressed gene profiles. PRC2 catalyzes a specific histone posttranslational modification (hPTM) that fosters chromatin compaction. PRC2 also facilitates the inheritance of this hPTM through its self-contained "write and read" activities, key to preserving cellular identity during cell division. As these changes in gene expression occur without changes in DNA sequence and are inherited, the process is epigenetic in scope. Mutants of mammalian PRC2 or of its histone substrate contribute to the cancer process and other diseases, and research into these aberrant pathways is yielding viable candidates for therapeutic targeting. The effectiveness of PRC2 hinges on its being recruited to the proper chromatin sites; however, resolving the determinants to this process in the mammalian case was not straightforward and thus piqued the interest of many in the field. Here, we chronicle the latest advances toward exposing mammalian PRC2 and its high maintenance.
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Affiliation(s)
- Jia-Ray Yu
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Chul-Hwan Lee
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Ozgur Oksuz
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - James M Stafford
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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46
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Ahmad K, Spens AE. Separate Polycomb Response Elements control chromatin state and activation of the vestigial gene. PLoS Genet 2019; 15:e1007877. [PMID: 31425502 PMCID: PMC6730940 DOI: 10.1371/journal.pgen.1007877] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 09/06/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023] Open
Abstract
Patterned expression of many developmental genes is specified by transcription factor gene expression, but is thought to be refined by chromatin-mediated repression. Regulatory DNA sequences called Polycomb Response Elements (PREs) are required to repress some developmental target genes, and are widespread in genomes, suggesting that they broadly affect developmental programs. While PREs in transgenes can nucleate trimethylation on lysine 27 of the histone H3 tail (H3K27me3), none have been demonstrated to be necessary at endogenous chromatin domains. This failure is thought to be due to the fact that most endogenous H3K27me3 domains contain many PREs, and individual PREs may be redundant. In contrast to these ideas, we show here that PREs near the wing selector gene vestigial have distinctive roles at their endogenous locus, even though both PREs are repressors in transgenes. First, a PRE near the promoter is required for vestigial activation and not for repression. Second, only the distal PRE contributes to H3K27me3, but even removal of both PREs does not eliminate H3K27me3 across the vestigial domain. Thus, endogenous chromatin domains appear to be intrinsically marked by H3K27me3, and PREs appear required to enhance this chromatin modification to high levels at inactive genes.
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Affiliation(s)
- Kami Ahmad
- Division of Basic Sciences, FHCRC, Seattle, WA, United States of America
| | - Amy E. Spens
- Division of Basic Sciences, FHCRC, Seattle, WA, United States of America
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47
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Fursova NA, Blackledge NP, Nakayama M, Ito S, Koseki Y, Farcas AM, King HW, Koseki H, Klose RJ. Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene Repression. Mol Cell 2019; 74:1020-1036.e8. [PMID: 31029541 PMCID: PMC6561741 DOI: 10.1016/j.molcel.2019.03.024] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/04/2019] [Accepted: 03/21/2019] [Indexed: 01/30/2023]
Abstract
The Polycomb system modifies chromatin and plays an essential role in repressing gene expression to control normal mammalian development. However, the components and mechanisms that define how Polycomb protein complexes achieve this remain enigmatic. Here, we use combinatorial genetic perturbation coupled with quantitative genomics to discover the central determinants of Polycomb-mediated gene repression in mouse embryonic stem cells. We demonstrate that canonical Polycomb repressive complex 1 (PRC1), which mediates higher-order chromatin structures, contributes little to gene repression. Instead, we uncover an unexpectedly high degree of synergy between variant PRC1 complexes, which is fundamental to gene repression. We further demonstrate that variant PRC1 complexes are responsible for distinct pools of H2A monoubiquitylation that are associated with repression of Polycomb target genes and silencing during X chromosome inactivation. Together, these discoveries reveal a new variant PRC1-dependent logic for Polycomb-mediated gene repression.
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Affiliation(s)
- Nadezda A Fursova
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Neil P Blackledge
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Manabu Nakayama
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Anca M Farcas
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Hamish W King
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; AMED-CREST, Japanese Agency for Medical Research and Development, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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48
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Bracken AP, Brien GL, Verrijzer CP. Dangerous liaisons: interplay between SWI/SNF, NuRD, and Polycomb in chromatin regulation and cancer. Genes Dev 2019; 33:936-959. [PMID: 31123059 PMCID: PMC6672049 DOI: 10.1101/gad.326066.119] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this review, Bracken et al. discuss the functional organization and biochemical activities of remodelers and Polycomb and explore how they work together to control cell differentiation and the maintenance of cell identity. They also discuss how mutations in the genes encoding these various chromatin regulators contribute to oncogenesis by disrupting the chromatin equilibrium. Changes in chromatin structure mediated by ATP-dependent nucleosome remodelers and histone modifying enzymes are integral to the process of gene regulation. Here, we review the roles of the SWI/SNF (switch/sucrose nonfermenting) and NuRD (nucleosome remodeling and deacetylase) and the Polycomb system in chromatin regulation and cancer. First, we discuss the basic molecular mechanism of nucleosome remodeling, and how this controls gene transcription. Next, we provide an overview of the functional organization and biochemical activities of SWI/SNF, NuRD, and Polycomb complexes. We describe how, in metazoans, the balance of these activities is central to the proper regulation of gene expression and cellular identity during development. Whereas SWI/SNF counteracts Polycomb, NuRD facilitates Polycomb repression on chromatin. Finally, we discuss how disruptions of this regulatory equilibrium contribute to oncogenesis, and how new insights into the biological functions of remodelers and Polycombs are opening avenues for therapeutic interventions on a broad range of cancer types.
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Affiliation(s)
- Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Gerard L Brien
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - C Peter Verrijzer
- Department of Biochemistry, Erasmus University Medical Center, 3000 DR Rotterdam, the Netherlands
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United colours of chromatin? Developmental genome organisation in flies. Biochem Soc Trans 2019; 47:691-700. [PMID: 30902925 DOI: 10.1042/bst20180605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 11/17/2022]
Abstract
The organisation of DNA into differing forms of packaging, or chromatin, controls many of the cell fate decisions during development. Although early studies focused on individual forms of chromatin, in the last decade more holistic studies have attempted to determine a complete picture of the different forms of chromatin present within a cell. In the fruit fly, Drosophila melanogaster, the study of chromatin states has been aided by the use of complementary and cell-type-specific techniques that profile the marks that recruit chromatin protein binding or the proteins themselves. Although many questions remain unanswered, a clearer picture of how different chromatin states affect development is now emerging, with more unusual chromatin states such as Black chromatin playing key roles. Here, we discuss recent findings regarding chromatin biology in flies.
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Oksuz O, Narendra V, Lee CH, Descostes N, LeRoy G, Raviram R, Blumenberg L, Karch K, Rocha PP, Garcia BA, Skok JA, Reinberg D. Capturing the Onset of PRC2-Mediated Repressive Domain Formation. Mol Cell 2019; 70:1149-1162.e5. [PMID: 29932905 DOI: 10.1016/j.molcel.2018.05.023] [Citation(s) in RCA: 167] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/10/2018] [Accepted: 05/18/2018] [Indexed: 11/16/2022]
Abstract
Polycomb repressive complex 2 (PRC2) maintains gene silencing by catalyzing methylation of histone H3 at lysine 27 (H3K27me2/3) within chromatin. By designing a system whereby PRC2-mediated repressive domains were collapsed and then reconstructed in an inducible fashion in vivo, a two-step mechanism of H3K27me2/3 domain formation became evident. First, PRC2 is stably recruited by the actions of JARID2 and MTF2 to a limited number of spatially interacting "nucleation sites," creating H3K27me3-forming Polycomb foci within the nucleus. Second, PRC2 is allosterically activated via its binding to H3K27me3 and rapidly spreads H3K27me2/3 both in cis and in far-cis via long-range contacts. As PRC2 proceeds further from the nucleation sites, its stability on chromatin decreases such that domains of H3K27me3 remain proximal, and those of H3K27me2 distal, to the nucleation sites. This study demonstrates the principles of de novo establishment of PRC2-mediated repressive domains across the genome.
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Affiliation(s)
- Ozgur Oksuz
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Varun Narendra
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Chul-Hwan Lee
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Nicolas Descostes
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Gary LeRoy
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Ramya Raviram
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lili Blumenberg
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Kelly Karch
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pedro P Rocha
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Danny Reinberg
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
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