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Sin HS, Kartashov AV, Hasegawa K, Barski A, Namekawa SH. Poised chromatin and bivalent domains facilitate the mitosis-to-meiosis transition in the male germline. BMC Biol 2015. [PMID: 26198001 PMCID: PMC4508805 DOI: 10.1186/s12915-015-0159-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Background The male germline transcriptome changes dramatically during the mitosis-to-meiosis transition to activate late spermatogenesis genes and to transiently suppress genes commonly expressed in somatic lineages and spermatogenesis progenitor cells, termed somatic/progenitor genes. Results These changes reflect epigenetic regulation. Induction of late spermatogenesis genes during spermatogenesis is facilitated by poised chromatin established in the stem cell phases of spermatogonia, whereas silencing of somatic/progenitor genes during meiosis and postmeiosis is associated with formation of bivalent domains which also allows the recovery of the somatic/progenitor program after fertilization. Importantly, during spermatogenesis mechanisms of epigenetic regulation on sex chromosomes are different from autosomes: X-linked somatic/progenitor genes are suppressed by meiotic sex chromosome inactivation without deposition of H3K27me3. Conclusions Our results suggest that bivalent H3K27me3 and H3K4me2/3 domains are not limited to developmental promoters (which maintain bivalent domains that are silent throughout the reproductive cycle), but also underlie reversible silencing of somatic/progenitor genes during the mitosis-to-meiosis transition in late spermatogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0159-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ho-Su Sin
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 49229, USA.,Present address: Department of Developmental Biology, Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Andrey V Kartashov
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 49229, USA
| | - Kazuteru Hasegawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 49229, USA.,Present address: Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Artem Barski
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 49229, USA.
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 49229, USA.
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Burg JM, Link JE, Morgan BS, Heller FJ, Hargrove AE, McCafferty DG. KDM1 class flavin-dependent protein lysine demethylases. Biopolymers 2015; 104:213-46. [PMID: 25787087 PMCID: PMC4747437 DOI: 10.1002/bip.22643] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/02/2015] [Accepted: 03/07/2015] [Indexed: 12/11/2022]
Abstract
Flavin-dependent, lysine-specific protein demethylases (KDM1s) are a subfamily of amine oxidases that catalyze the selective posttranslational oxidative demethylation of methyllysine side chains within protein and peptide substrates. KDM1s participate in the widespread epigenetic regulation of both normal and disease state transcriptional programs. Their activities are central to various cellular functions, such as hematopoietic and neuronal differentiation, cancer proliferation and metastasis, and viral lytic replication and establishment of latency. Interestingly, KDM1s function as catalytic subunits within complexes with coregulatory molecules that modulate enzymatic activity of the demethylases and coordinate their access to specific substrates at distinct sites within the cell and chromatin. Although several classes of KDM1-selective small molecule inhibitors have been recently developed, these pan-active site inhibition strategies lack the ability to selectively discriminate between KDM1 activity in specific, and occasionally opposing, functional contexts within these complexes. Here we review the discovery of this class of demethylases, their structures, chemical mechanisms, and specificity. Additionally, we review inhibition of this class of enzymes as well as emerging interactions with coregulatory molecules that regulate demethylase activity in highly specific functional contexts of biological and potential therapeutic importance.
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Hasegawa K, Sin HS, Maezawa S, Broering TJ, Kartashov AV, Alavattam KG, Ichijima Y, Zhang F, Bacon WC, Greis KD, Andreassen PR, Barski A, Namekawa SH. SCML2 establishes the male germline epigenome through regulation of histone H2A ubiquitination. Dev Cell 2015; 32:574-88. [PMID: 25703348 PMCID: PMC4391279 DOI: 10.1016/j.devcel.2015.01.014] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 12/23/2014] [Accepted: 01/16/2015] [Indexed: 01/03/2023]
Abstract
Gametogenesis is dependent on the expression of germline-specific genes. However, it remains unknown how the germline epigenome is distinctly established from that of somatic lineages. Here we show that genes commonly expressed in somatic lineages and spermatogenesis-progenitor cells undergo repression in a genome-wide manner in late stages of the male germline and identify underlying mechanisms. SCML2, a germline-specific subunit of a Polycomb repressive complex 1 (PRC1), establishes the unique epigenome of the male germline through two distinct antithetical mechanisms. SCML2 works with PRC1 and promotes RNF2-dependent ubiquitination of H2A, thereby marking somatic/progenitor genes on autosomes for repression. Paradoxically, SCML2 also prevents RNF2-dependent ubiquitination of H2A on sex chromosomes during meiosis, thereby enabling unique epigenetic programming of sex chromosomes for male reproduction. Our results reveal divergent mechanisms involving a shared regulator by which the male germline epigenome is distinguished from that of the soma and progenitor cells.
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Affiliation(s)
- Kazuteru Hasegawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Ho-Su Sin
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - So Maezawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Tyler J Broering
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Andrey V Kartashov
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Kris G Alavattam
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Yosuke Ichijima
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Fan Zhang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - W Clark Bacon
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Kenneth D Greis
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Paul R Andreassen
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Artem Barski
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.
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Hulur I, Gamazon ER, Skol AD, Xicola RM, Llor X, Onel K, Ellis NA, Kupfer SS. Enrichment of inflammatory bowel disease and colorectal cancer risk variants in colon expression quantitative trait loci. BMC Genomics 2015; 16:138. [PMID: 25766683 PMCID: PMC4351699 DOI: 10.1186/s12864-015-1292-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/29/2015] [Indexed: 12/20/2022] Open
Abstract
Background Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with diseases of the colon including inflammatory bowel diseases (IBD) and colorectal cancer (CRC). However, the functional role of many of these SNPs is largely unknown and tissue-specific resources are lacking. Expression quantitative trait loci (eQTL) mapping identifies target genes of disease-associated SNPs. This study provides a comprehensive eQTL map of distal colonic samples obtained from 40 healthy African Americans and demonstrates their relevance for GWAS of colonic diseases. Results 8.4 million imputed SNPs were tested for their associations with 16,252 expression probes representing 12,363 unique genes. 1,941 significant cis-eQTL, corresponding to 122 independent signals, were identified at a false discovery rate (FDR) of 0.01. Overall, among colon cis-eQTL, there was significant enrichment for GWAS variants for IBD (Crohn’s disease [CD] and ulcerative colitis [UC]) and CRC as well as type 2 diabetes and body mass index. ERAP2, ADCY3, INPP5E, UBA7, SFMBT1, NXPE1 and REXO2 were identified as target genes for IBD-associated variants. The CRC-associated eQTL rs3802842 was associated with the expression of C11orf93 (COLCA2). Enrichment of colon eQTL near transcription start sites and for active histone marks was demonstrated, and eQTL with high population differentiation were identified. Conclusions Through the comprehensive study of eQTL in the human colon, this study identified novel target genes for IBD- and CRC-associated genetic variants. Moreover, bioinformatic characterization of colon eQTL provides a tissue-specific tool to improve understanding of biological differences in diseases between different ethnic groups. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1292-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Imge Hulur
- Committee on Genetics, Genomics and Systems Biology, Chicago, IL, 60637, USA.
| | - Eric R Gamazon
- Department of Medicine, 900 East 57th Street, MB#9, Chicago, IL, 60637, USA. .,Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, 37232, USA.
| | - Andrew D Skol
- Department of Medicine, 900 East 57th Street, MB#9, Chicago, IL, 60637, USA.
| | - Rosa M Xicola
- Department of Medicine, Yale University, New Haven, CT, 06510, USA.
| | - Xavier Llor
- Department of Medicine, Yale University, New Haven, CT, 06510, USA.
| | - Kenan Onel
- Department of Pediatrics, University of Chicago, Chicago, IL, 60637, USA.
| | - Nathan A Ellis
- University of Arizona Cancer Center, Tucson, AZ, 85724, USA.
| | - Sonia S Kupfer
- Department of Medicine, 900 East 57th Street, MB#9, Chicago, IL, 60637, USA.
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Lee MC, Spradling AC. The progenitor state is maintained by lysine-specific demethylase 1-mediated epigenetic plasticity during Drosophila follicle cell development. Genes Dev 2015; 28:2739-49. [PMID: 25512561 PMCID: PMC4265677 DOI: 10.1101/gad.252692.114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Progenitors are early lineage cells that proliferate before the onset of terminal differentiation. Although widespread, the epigenetic mechanisms that control the progenitor state and the onset of differentiation remain elusive. By studying Drosophila ovarian follicle cell progenitors, we identified lysine-specific demethylase 1 (lsd1) and CoRest as differentiation regulators using a GAL4∷GFP variegation assay. The follicle cell progenitors in lsd1 or CoRest heterozygotes prematurely lose epigenetic plasticity, undergo the Notch-dependent mitotic-endocycle transition, and stop dividing before a normal number of follicle cells can be produced. Simultaneously reducing the dosage of the histone H3K4 methyltransferase Trithorax reverses these effects, suggesting that an Lsd1/CoRest complex times progenitor differentiation by controlling the stability of H3K4 methylation levels. Individual cells or small clones initially respond to Notch; hence, a critical level of epigenetic stabilization is acquired cell-autonomously and initiates differentiation by making progenitors responsive to pre-existing external signals.
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Affiliation(s)
- Ming-Chia Lee
- Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution, Baltimore, Maryland 21218, USA
| | - Allan C Spradling
- Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution, Baltimore, Maryland 21218, USA
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Epigenetic regulation of Atrophin1 by lysine-specific demethylase 1 is required for cortical progenitor maintenance. Nat Commun 2014; 5:5815. [PMID: 25519973 PMCID: PMC4284801 DOI: 10.1038/ncomms6815] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 11/10/2014] [Indexed: 12/16/2022] Open
Abstract
Lysine-specific demethylase 1 (LSD1) is involved in gene regulation and development; however, its precise function, molecular targets and underlying mechanisms during development are poorly understood. Here we show that LSD1 is required for neuronal progenitor cell (NPC) maintenance during cortical development. A ChIP-seq analysis identified a LSD1-binding site (LBAL) downstream of Atrophin1 (ATN1). Surprisingly, tranylcypromine (LSD1 inhibitor) treatment increased H3K4 methylation at LBAL, leading to ATN1 repression and NPC differentiation. Knockdown of LSD1 and ATN1 phenocopied each other in inducing NPC premature differentiation and depletion, which could be rescued by ATN1 overexpression, suggesting that LSD1 controls NPC differentiation via regulation of ATN1 methylation status and expression. The involvement of LSD1 in ATN1 expression and NPC maintenance were confirmed in knockout mice. These findings hint at the potential application for the clinical drug, tranylcypromine, in the prevention and/or treatment of ATN1-associated degenerative disease, dentatorubral-pallidoluysian atrophy. Histone modification is critical for gene expression regulation during development. Here, the authors show that the demethylase LSD1 and its target gene ATN1 are responsible for maintenance of neural progenitor cells during mouse cortical development.
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Meier K, Brehm A. Chromatin regulation: how complex does it get? Epigenetics 2014; 9:1485-95. [PMID: 25482055 PMCID: PMC4622878 DOI: 10.4161/15592294.2014.971580] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 08/18/2014] [Accepted: 09/29/2014] [Indexed: 12/16/2022] Open
Abstract
Gene transcription is tightly regulated at different levels to ensure that the transcriptome of the cell is appropriate for developmental stage and cell type. The chromatin state in which a gene is embedded determines its expression level to a large extent. Activation or repression of transcription is typically accomplished by the recruitment of chromatin-associated multisubunit protein complexes that combine several molecular tools, such as histone-binding and chromatin-modifying activities. Recent biochemical purifications of such complexes have revealed a substantial diversity. On the one hand, complexes that were thought to be unique have been revealed to be part of large complex families. On the other hand, protein subunits that were thought to only exist in separate complexes have been shown to coexist in novel assemblies. In this review we discuss our current knowledge of repressor complexes that contain MBT domain proteins and/or the CoREST co-repressor and use them as a paradigm to illustrate the unexpected heterogeneity and tool sharing of chromatin regulating protein complexes. These recent insights also challenge the ways we define and think about protein complexes in general.
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Key Words
- ATP, adenosine triphosphate
- BAP, brahma associated protein
- BHC80, BRAF-histone deacetylase complex 80
- BRG1, brahma Related Gene 1
- CHD, chromo domain helicase DNA binding
- CoREST
- CoREST REST, corepressor
- DNA, deoxyribonucleic acid
- DNMT, DNA methyltransferase
- DP-1, dimerization partner 1
- E2F, E2 transcription Factor
- ELM2, EGL-27 and MTA1 homology 2
- ES cell, embryonic stem cells
- H, histone
- HDAC, histone deacetylas
- HMTase, histone methylase
- HP1, heterochromatin protein 1
- K, lysine
- L3MBTL, lethal 3 malignant brain tumor-like
- LINT, l(3)mbt interacting
- LSD1, lysine-specific demethylase 1
- Lint-1, l(3)mbt interacting 1
- MBT protein
- MBT, malignant brain tumor
- MBTS, malignant brain tumor signature
- NPA1, nucleosome assembly protein
- NRSF, neural-restrictive silencing factor
- NuRD, nucleosome remodeling and deacetylase
- PBAP, polybromo-associated BAP
- PHD, plant homeo domain
- PRC1, polycomb repressive complex 1
- PRE, polycomb responsive element
- Pc, polycomb
- PcG, polycomb group
- Ph, polyhomeotic
- Pho, pleiohomeotic
- PhoRC, Pho repressive complex
- Psc, posterior sex combs
- RB, retinoblastoma
- REST, repressor element 1 silencing transcription factor
- RNA, ribonucleic acid
- Rpd3, reduced potassium dependency 3
- SANT, SWI/ADA2/N-CoR/TFIIIB
- SCML, sex combs on midleg-like
- SLC, SFMBT1, LSD1, CoREST
- SWH, Salvador-Warts-Hippo
- SWI/SNF, switching defective/sucrose non-fermenting
- Sce, sex combs extra
- Scm, sex combs on midleg
- Sfmbt, Scm-related gene containing 4 mbt domains
- TSS, transcription start site
- YY1, ying-yang 1
- ZNF, zinc finger
- complex family
- dL(3)mbt, Drosophila Lethal 3 malignant brain tumor
- hBRM, human Brahma
- l(3)mbt, lethal 3 malignant brain tumor
- protein complex
- transcriptional regulation
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Affiliation(s)
- Karin Meier
- Institut für Molekularbiologie und Tumorforschung; Philipps-Universität Marburg; Marburg, Germany
- Instituto de Fisiología Celular; Departamento de Genética Molecular; Universidad Nacional Autónoma de México; México City, México
| | - Alexander Brehm
- Institut für Molekularbiologie und Tumorforschung; Philipps-Universität Marburg; Marburg, Germany
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Human-Chromatin-Related Protein Interactions Identify a Demethylase Complex Required for Chromosome Segregation. Cell Rep 2014; 8:297-310. [DOI: 10.1016/j.celrep.2014.05.050] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 04/24/2014] [Accepted: 05/27/2014] [Indexed: 01/14/2023] Open
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Wagner T, Robaa D, Sippl W, Jung M. Mind the Methyl: Methyllysine Binding Proteins in Epigenetic Regulation. ChemMedChem 2014; 9:466-83. [DOI: 10.1002/cmdc.201300422] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Indexed: 11/07/2022]
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Alfieri C, Gambetta MC, Matos R, Glatt S, Sehr P, Fraterman S, Wilm M, Müller J, Müller CW. Structural basis for targeting the chromatin repressor Sfmbt to Polycomb response elements. Genes Dev 2013; 27:2367-79. [PMID: 24186981 PMCID: PMC3828522 DOI: 10.1101/gad.226621.113] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Polycomb group (PcG) complexes repress developmental regulator genes by modifying their chromatin. However, how PcG proteins assemble into complexes and are recruited to their target genes is poorly understood. Here, Alfieri et al. report the crystal structure of the core of the PcG complex PhoRC, which contains the DNA-binding protein Pho and corepressor Sfmbt. The authors show that tethering of Sfmbt by Pho to Polycomb response elements is essential for Polycomb repression of developmental regulator genes in Drosophila. This study thus reveals the molecular basis for PcG protein complex assembly at specific genomic sites. Polycomb group (PcG) protein complexes repress developmental regulator genes by modifying their chromatin. How different PcG proteins assemble into complexes and are recruited to their target genes is poorly understood. Here, we report the crystal structure of the core of the Drosophila PcG protein complex Pleiohomeotic (Pho)-repressive complex (PhoRC), which contains the Polycomb response element (PRE)-binding protein Pho and Sfmbt. The spacer region of Pho, separated from the DNA-binding domain by a long flexible linker, forms a tight complex with the four malignant brain tumor (4MBT) domain of Sfmbt. The highly conserved spacer region of the human Pho ortholog YY1 binds three of the four human 4MBT domain proteins in an analogous manner but with lower affinity. Comparison of the Drosophila Pho:Sfmbt and human YY1:MBTD1 complex structures provides a molecular explanation for the lower affinity of YY1 for human 4MBT domain proteins. Structure-guided mutations that disrupt the interaction between Pho and Sfmbt abolish formation of a ternary Sfmbt:Pho:DNA complex in vitro and repression of developmental regulator genes in Drosophila. PRE tethering of Sfmbt by Pho is therefore essential for Polycomb repression in Drosophila. Our results support a model where DNA tethering of Sfmbt by Pho and multivalent interactions of Sfmbt with histone modifications and other PcG proteins create a hub for PcG protein complex assembly at PREs.
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Affiliation(s)
- Claudio Alfieri
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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Miri K, Latham K, Panning B, Zhong Z, Andersen A, Varmuza S. The imprinted polycomb group gene Sfmbt2 is required for trophoblast maintenance and placenta development. Development 2013; 140:4480-9. [PMID: 24154523 PMCID: PMC3817938 DOI: 10.1242/dev.096511] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 08/19/2013] [Indexed: 12/27/2022]
Abstract
Imprinted genes play important roles in placenta development and function. Parthenogenetic embryos, deficient in paternally expressed imprinted genes, lack extra-embryonic tissues of the trophoblast lineage. Parthenogenetic trophoblast stem cells (TSCs) are extremely difficult to derive, suggesting that an imprinted gene(s) is necessary for TSC establishment or maintenance. In a candidate study, we were able to narrow the list to one known paternally expressed gene, Sfmbt2. We show that mouse embryos inheriting a paternal Sfmbt2 gene trap null allele have severely reduced placentae and die before E12.5 due to reduction of all trophoblast cell types. We infected early embryos with lentivirus vectors expressing anti-Sfmbt2 shRNAs and found that TSC derivation was significantly reduced. Together, these observations support the hypothesis that loss of SFMBT2 results in defects in maintenance of trophoblast cell types necessary for development of the extra-embryonic tissues, the placenta in particular.
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Affiliation(s)
- Kamelia Miri
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Sreet, Toronto, Ontario M5S 3G5, Canada
| | - Keith Latham
- The Fels Institute of Cancer Research and Molecular Biology and Department of Biochemistry, Temple University School of Medicine, 3307 North Broad Street, Philadelphia, PA 19140, USA
| | - Barbara Panning
- Biochemistry and Biophysics Department, University of California at San Francisco, Genentech Hall, 600 16th Street, San Francisco, CA 94158-2517, USA
| | - Zhisheng Zhong
- The Fels Institute of Cancer Research and Molecular Biology and Department of Biochemistry, Temple University School of Medicine, 3307 North Broad Street, Philadelphia, PA 19140, USA
| | - Angela Andersen
- Biochemistry and Biophysics Department, University of California at San Francisco, Genentech Hall, 600 16th Street, San Francisco, CA 94158-2517, USA
| | - Susannah Varmuza
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Sreet, Toronto, Ontario M5S 3G5, Canada
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Tang M, Shen H, Jin Y, Lin T, Cai Q, Pinard MA, Biswas S, Tran Q, Li G, Shenoy AK, Tongdee E, Lin S, Gu Y, Law BK, Zhou L, Mckenna R, Wu L, Lu J. The malignant brain tumor (MBT) domain protein SFMBT1 is an integral histone reader subunit of the LSD1 demethylase complex for chromatin association and epithelial-to-mesenchymal transition. J Biol Chem 2013; 288:27680-27691. [PMID: 23928305 DOI: 10.1074/jbc.m113.482349] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chromatin readers decipher the functional readouts of histone modifications by recruiting specific effector complexes for subsequent epigenetic reprogramming. The LSD1 (also known as KDM1A) histone demethylase complex modifies chromatin and represses transcription in part by catalyzing demethylation of dimethylated histone H3 lysine 4 (H3K4me2), a mark for active transcription. However, none of its currently known subunits recognizes methylated histones. The Snai1 family transcription factors are central drivers of epithelial-to-mesenchymal transition (EMT) by which epithelial cells acquire enhanced invasiveness. Snai1-mediated transcriptional repression of epithelial genes depends on its recruitment of the LSD1 complex and ensuing demethylation of H3K4me2 at its target genes. Through biochemical purification, we identified the MBT domain-containing protein SFMBT1 as a novel component of the LSD1 complex associated with Snai1. Unlike other mammalian MBT domain proteins characterized to date that selectively recognize mono- and dimethylated lysines, SFMBT1 binds di- and trimethyl H3K4, both of which are enriched at active promoters. We show that SFMBT1 is essential for Snai1-dependent recruitment of LSD1 to chromatin, demethylation of H3K4me2, transcriptional repression of epithelial markers, and induction of EMT by TGFβ. Carcinogenic metal nickel is a widespread environmental and occupational pollutant. Nickel alters gene expression and induces EMT. We demonstrate the nickel-initiated effects are dependent on LSD1-SFMBT1-mediated chromatin modification. Furthermore, in human cancer, expression of SFMBT1 is associated with mesenchymal markers and unfavorable prognosis. These results highlight a critical role of SFMBT1 in epigenetic regulation, EMT, and cancer.
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Affiliation(s)
- Ming Tang
- Department of Biochemistry and Molecular Biology; Genetics and Genomics Graduate Program, Genetics Institute, University of Florida, Gainesville, Florida 32610
| | - Huangxuan Shen
- Department of Molecular Genetics and Microbiology; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060 China
| | - Yue Jin
- Department of Biochemistry and Molecular Biology
| | - Tong Lin
- Department of Biochemistry and Molecular Biology; Genetics and Genomics Graduate Program, Genetics Institute, University of Florida, Gainesville, Florida 32610
| | - Qingsong Cai
- Department of Biochemistry and Molecular Biology
| | | | | | - Quyen Tran
- Agnes Scott College, Decatur, Georgia 30030
| | - Guangyao Li
- Genetics and Genomics Graduate Program, Genetics Institute, University of Florida, Gainesville, Florida 32610; Department of Molecular Genetics and Microbiology
| | | | | | - Shuibin Lin
- Department of Molecular Genetics and Microbiology
| | - Yumei Gu
- Department of Molecular Genetics and Microbiology
| | - Brian K Law
- Department of Pharmacology and Therapeutics, Health Cancer Center, University of Florida College of Medicine, Gainesville, Florida 32610
| | - Lei Zhou
- Genetics and Genomics Graduate Program, Genetics Institute, University of Florida, Gainesville, Florida 32610; Department of Molecular Genetics and Microbiology
| | | | - Lizi Wu
- Genetics and Genomics Graduate Program, Genetics Institute, University of Florida, Gainesville, Florida 32610; Department of Molecular Genetics and Microbiology.
| | - Jianrong Lu
- Department of Biochemistry and Molecular Biology; Genetics and Genomics Graduate Program, Genetics Institute, University of Florida, Gainesville, Florida 32610.
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