1
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Crain AT, Butler MB, Hill CA, Huynh M, McGinty RK, Duronio RJ. Drosophila melanogaster Set8 and L(3)mbt function in gene expression independently of histone H4 lysine 20 methylation. Genes Dev 2024; 38:455-472. [PMID: 38866557 PMCID: PMC11216177 DOI: 10.1101/gad.351698.124] [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: 03/12/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024]
Abstract
Monomethylation of lysine 20 of histone H4 (H4K20me1) is catalyzed by Set8 and thought to play important roles in many aspects of genome function that are mediated by H4K20me binding proteins. We interrogated this model in a developing animal by comparing in parallel the transcriptomes of Set8 null , H4 K20R/A , and l(3)mbt mutant Drosophila melanogaster We found that the gene expression profiles of H4 K20A and H4 K20R larvae are markedly different than Set8 null larvae despite similar reductions in H4K20me1. Set8 null mutant cells have a severely disrupted transcriptome and fail to proliferate in vivo, but these phenotypes are not recapitulated by mutation of H4 K20 , indicating that the developmental defects of Set8 null animals are largely due to H4K20me1-independent effects on gene expression. Furthermore, the H4K20me1 binding protein L(3)mbt is recruited to the transcription start sites of most genes independently of H4K20me even though genes bound by L(3)mbt have high levels of H4K20me1. Moreover, both Set8 and L(3)mbt bind to purified H4K20R nucleosomes in vitro. We conclude that gene expression changes in Set8 null and H4 K20 mutants cannot be explained by loss of H4K20me1 or L(3)mbt binding to chromatin and therefore that H4K20me1 does not play a large role in gene expression.
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Affiliation(s)
- Aaron T Crain
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599 USA
| | - Megan B Butler
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599 USA
| | - Christina A Hill
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599 USA
| | - Mai Huynh
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599 USA
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599 USA
| | - Robert K McGinty
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599 USA
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599 USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599 USA
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599 USA;
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599 USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599 USA
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599 USA
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2
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Crain AT, Butler MB, Hill CA, Huynh M, McGinty RK, Duronio RJ. Drosophila melanogaster Set8 and L(3)mbt function in gene expression independently of histone H4 lysine 20 methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584710. [PMID: 38559189 PMCID: PMC10980064 DOI: 10.1101/2024.03.12.584710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Mono-methylation of Lysine 20 of histone H4 (H4K20me1) is catalyzed by Set8 and thought to play important roles in many aspects of genome function that are mediated by H4K20me-binding proteins. We interrogated this model in a developing animal by comparing in parallel the transcriptomes of Set8 null , H4 K20R/A , and l(3)mbt mutant Drosophila melanogaster . We found that the gene expression profiles of H4 K20A and H4 K20R larvae are markedly different than Set8 null larvae despite similar reductions in H4K20me1. Set8 null mutant cells have a severely disrupted transcriptome and fail to proliferate in vivo , but these phenotypes are not recapitulated by mutation of H4 K20 indicating that the developmental defects of Set8 null animals are largely due to H4K20me1-independent effects on gene expression. Further, the H4K20me1 binding protein L(3)mbt is recruited to the transcription start sites of most genes independently of H4K20me even though genes bound by L(3)mbt have high levels of H4K20me1. Moreover, both Set8 and L(3)mbt bind to purified H4K20R nucleosomes in vitro. We conclude that gene expression changes in Set8 null and H4 K20 mutants cannot be explained by loss of H4K20me1 or L(3)mbt binding to chromatin, and therefore that H4K20me1 does not play a large role in gene expression.
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3
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Yamamoto‐Matsuda H, Miyoshi K, Moritoh M, Yoshitane H, Fukada Y, Saito K, Yamanaka S, Siomi MC. Lint‐O
cooperates with L(3)mbt in target gene suppression to maintain homeostasis in fly ovary and brain. EMBO Rep 2022; 23:e53813. [PMID: 35993198 PMCID: PMC9535798 DOI: 10.15252/embr.202153813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/23/2022] Open
Abstract
Loss‐of‐function mutations in Drosophila lethal(3)malignant brain tumor [l(3)mbt] cause ectopic expression of germline genes and brain tumors. Loss of L(3)mbt function in ovarian somatic cells (OSCs) aberrantly activates germ‐specific piRNA amplification and leads to infertility. However, the underlying mechanism remains unclear. Here, ChIP‐seq for L(3)mbt in cultured OSCs and RNA‐seq before and after L(3)mbt depletion shows that L(3)mbt genomic binding is not necessarily linked to gene regulation and that L(3)mbt controls piRNA pathway genes in multiple ways. Lack of known L(3)mbt co‐repressors, such as Lint‐1, has little effect on the levels of piRNA amplifiers. Identification of L(3)mbt interactors in OSCs and subsequent analysis reveals CG2662 as a novel co‐regulator of L(3)mbt, termed “L(3)mbt interactor in OSCs” (Lint‐O). Most of the L(3)mbt‐bound piRNA amplifier genes are also bound by Lint‐O in a similar fashion. Loss of Lint‐O impacts the levels of piRNA amplifiers, similar to the lack of L(3)mbt. The lint‐O‐deficient flies exhibit female sterility and tumorous brains. Thus, L(3)mbt and its novel co‐suppressor Lint‐O cooperate in suppressing target genes to maintain homeostasis in the ovary and brain.
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Affiliation(s)
- Hitomi Yamamoto‐Matsuda
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
| | - Keita Miyoshi
- Department of Chromosome Science National Institute of Genetics, Research Organization of Information and Systems Shizuoka Japan
- Department of Genetics School of Life Science, SOKENDAI Shizuoka Japan
| | - Mai Moritoh
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
| | - Hikari Yoshitane
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
| | - Yoshitaka Fukada
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
| | - Kuniaki Saito
- Department of Chromosome Science National Institute of Genetics, Research Organization of Information and Systems Shizuoka Japan
- Department of Genetics School of Life Science, SOKENDAI Shizuoka Japan
| | - Soichiro Yamanaka
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
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4
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Oxidative Stress Is Associated with Overgrowth in Drosophila l(3)mbt Mutant Imaginal Discs. Cells 2022; 11:cells11162542. [PMID: 36010619 PMCID: PMC9406541 DOI: 10.3390/cells11162542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/04/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022] Open
Abstract
The loss-of-function conditions for an l(3)malignant brain tumour (l(3)mbt) in larvae reared at 29 °C results in malignant brain tumours and hyperplastic imaginal discs. Unlike the former that have been extensively characterised, little is known about the latter. Here we report the results of a study of the hyperplastic l(3)mbt mutant wing imaginal discs. We identify the l(3)mbt wing disc tumour transcriptome and find it to include genes involved in reactive oxygen species (ROS) metabolism. Furthermore, we show the presence of oxidative stress in l(3)mbt hyperplastic discs, even in apoptosis-blocked conditions, but not in l(3)mbt brain tumours. We also find that chemically blocking oxidative stress in l(3)mbt wing discs reduces the incidence of wing disc overgrowths. Our results reveal the involvement of oxidative stress in l(3)mbt wing discs hyperplastic growth.
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5
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Ullah I, Thölken C, Zhong Y, John M, Rossbach O, Lenz J, Gößringer M, Nist A, Albert L, Stiewe T, Hartmann R, Vázquez O, Chung HR, Mackay JP, Brehm A. RNA inhibits dMi-2/CHD4 chromatin binding and nucleosome remodeling. Cell Rep 2022; 39:110895. [PMID: 35649367 DOI: 10.1016/j.celrep.2022.110895] [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: 08/13/2021] [Revised: 03/30/2022] [Accepted: 05/09/2022] [Indexed: 11/03/2022] Open
Abstract
The ATP-dependent nucleosome remodeler Mi-2/CHD4 broadly modulates chromatin landscapes to repress transcription and to maintain genome integrity. Here we use individual nucleotide resolution crosslinking and immunoprecipitation (iCLIP) to show that Drosophila Mi-2 associates with thousands of mRNA molecules in vivo. Biochemical data reveal that recombinant dMi-2 preferentially binds to G-rich RNA molecules using two intrinsically disordered regions of unclear function. Pharmacological inhibition of transcription and RNase digestion approaches establish that RNA inhibits the association of dMi-2 with chromatin. We also show that RNA inhibits dMi-2-mediated nucleosome mobilization by competing with the nucleosome substrate. Importantly, this activity is shared by CHD4, the human homolog of dMi-2, strongly suggesting that RNA-mediated regulation of remodeler activity is an evolutionary conserved mechanism. Our data support a model in which RNA serves to protect actively transcribed regions of the genome from dMi-2/CHD4-mediated establishment of repressive chromatin structures.
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Affiliation(s)
- Ikram Ullah
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Marburg, Germany
| | - Clemens Thölken
- Institute for Medical Bioinformatics and Biostatistic, Philipps-University, Marburg, Germany
| | - Yichen Zhong
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Mara John
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Marburg, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, Department of Biology and Chemistry, Justus Liebig University Giessen, Giessen, Germany
| | - Jonathan Lenz
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Marburg, Germany
| | - Markus Gößringer
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University, Marburg, Germany
| | - Lea Albert
- Faculty of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35043 Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University, Marburg, Germany
| | - Roland Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | - Olalla Vázquez
- Faculty of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35043 Marburg, Germany
| | - Ho-Ryung Chung
- Institute for Medical Bioinformatics and Biostatistic, Philipps-University, Marburg, Germany
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Alexander Brehm
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Marburg, Germany.
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6
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In situ dissection of domain boundaries affect genome topology and gene transcription in Drosophila. Nat Commun 2020; 11:894. [PMID: 32060283 PMCID: PMC7021724 DOI: 10.1038/s41467-020-14651-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/23/2020] [Indexed: 02/06/2023] Open
Abstract
Chromosomes are organized into high-frequency chromatin interaction domains called topologically associating domains (TADs), which are separated from each other by domain boundaries. The molecular mechanisms responsible for TAD formation are not yet fully understood. In Drosophila, it has been proposed that transcription is fundamental for TAD organization while the participation of genetic sequences bound by architectural proteins (APs) remains controversial. Here, we investigate the contribution of domain boundaries to TAD organization and the regulation of gene expression at the Notch gene locus in Drosophila. We find that deletion of domain boundaries results in TAD fusion and long-range topological defects that are accompanied by loss of APs and RNA Pol II chromatin binding as well as defects in transcription. Together, our results provide compelling evidence of the contribution of discrete genetic sequences bound by APs and RNA Pol II in the partition of the genome into TADs and in the regulation of gene expression in Drosophila. In Drosophila, transcription is thought to be required for TAD formation, while the role of architectural proteins remains controversial. Here, the authors find that deletion of domain boundaries at the fly Notch locus results in TAD fusion and long-range topological defects, loss of architectural protein and RNA Pol II chromatin binding, and transcription defects.
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7
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Pray-Grant MG, Grant PA. Ant-icipating Change: An Epigenetic Switch in Reprogramming the Social Lives of Ants. Mol Cell 2020; 77:205-206. [PMID: 31951544 DOI: 10.1016/j.molcel.2019.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glastad et al. (2019) describe a role for the neuronal CoREST corepressor and changes in juvenile hormone (JH) and ecdysone signaling during the reprogramming of social behavioral phenotypes in ants that are reflective of a natural mechanism differentiating "Major" and "Minor" worker ants.
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Affiliation(s)
- Marilyn G Pray-Grant
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Patrick A Grant
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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8
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Mačinković I, Theofel I, Hundertmark T, Kovač K, Awe S, Lenz J, Forné I, Lamp B, Nist A, Imhof A, Stiewe T, Renkawitz-Pohl R, Rathke C, Brehm A. Distinct CoREST complexes act in a cell-type-specific manner. Nucleic Acids Res 2019; 47:11649-11666. [PMID: 31701127 PMCID: PMC7145674 DOI: 10.1093/nar/gkz1050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 10/16/2019] [Accepted: 10/23/2019] [Indexed: 01/10/2023] Open
Abstract
CoREST has been identified as a subunit of several protein complexes that generate transcriptionally repressive chromatin structures during development. However, a comprehensive analysis of the CoREST interactome has not been carried out. We use proteomic approaches to define the interactomes of two dCoREST isoforms, dCoREST-L and dCoREST-M, in Drosophila. We identify three distinct histone deacetylase complexes built around a common dCoREST/dRPD3 core: A dLSD1/dCoREST complex, the LINT complex and a dG9a/dCoREST complex. The latter two complexes can incorporate both dCoREST isoforms. By contrast, the dLSD1/dCoREST complex exclusively assembles with the dCoREST-L isoform. Genome-wide studies show that the three dCoREST complexes associate with chromatin predominantly at promoters. Transcriptome analyses in S2 cells and testes reveal that different cell lineages utilize distinct dCoREST complexes to maintain cell-type-specific gene expression programmes: In macrophage-like S2 cells, LINT represses germ line-related genes whereas other dCoREST complexes are largely dispensable. By contrast, in testes, the dLSD1/dCoREST complex prevents transcription of germ line-inappropriate genes and is essential for spermatogenesis and fertility, whereas depletion of other dCoREST complexes has no effect. Our study uncovers three distinct dCoREST complexes that function in a lineage-restricted fashion to repress specific sets of genes thereby maintaining cell-type-specific gene expression programmes.
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Affiliation(s)
- Igor Mačinković
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Ina Theofel
- Department of Biology, Philipps-University, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Tim Hundertmark
- Department of Biology, Philipps-University, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Kristina Kovač
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Stephan Awe
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Jonathan Lenz
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Ignasi Forné
- Protein Analysis Unit, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Großhadernerstrasse 9, 82152 Martinsried, Germany
| | - Boris Lamp
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Axel Imhof
- Protein Analysis Unit, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Großhadernerstrasse 9, 82152 Martinsried, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Renate Renkawitz-Pohl
- Department of Biology, Philipps-University, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Christina Rathke
- Department of Biology, Philipps-University, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Alexander Brehm
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
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9
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Glastad KM, Graham RJ, Ju L, Roessler J, Brady CM, Berger SL. Epigenetic Regulator CoREST Controls Social Behavior in Ants. Mol Cell 2019; 77:338-351.e6. [PMID: 31732456 DOI: 10.1016/j.molcel.2019.10.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/13/2019] [Accepted: 10/11/2019] [Indexed: 11/25/2022]
Abstract
Ants acquire distinct morphological and behavioral phenotypes arising from a common genome, underscoring the importance of epigenetic regulation. In Camponotus floridanus, "Major" workers defend the colony, but can be epigenetically reprogrammed to forage for food analogously to "Minor" workers. Here, we utilize reprogramming to investigate natural behavioral specification. Reprogramming of Majors upregulates Minor-biased genes and downregulates Major-biased genes, engaging molecular pathways fundamental to foraging behavior. We discover the neuronal corepressor for element-1-silencing transcription factor (CoREST) is upregulated upon reprogramming and required for the epigenetic switch to foraging. Genome-wide profiling during reprogramming reveals CoREST represses expression of enzymes that degrade juvenile hormone (JH), a hormone elevated upon reprogramming. High CoREST, low JH-degrader expression, and high JH levels are mirrored in natural Minors, revealing parallel mechanisms of natural and reprogrammed foraging. These results unveil chromatin regulation via CoREST as central to programming of ant social behavior, with potential far-reaching implications for behavioral epigenetics.
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Affiliation(s)
- Karl M Glastad
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Riley J Graham
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Linyang Ju
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Julian Roessler
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cristina M Brady
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shelley L Berger
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA.
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10
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Molnar C, Heinen JP, Reina J, Llamazares S, Palumbo E, Breschi A, Gay M, Villarreal L, Vilaseca M, Pollarolo G, Gonzalez C. The histone code reader PHD finger protein 7 controls sex-linked disparities in gene expression and malignancy in Drosophila. SCIENCE ADVANCES 2019; 5:eaaw7965. [PMID: 31453329 PMCID: PMC6693905 DOI: 10.1126/sciadv.aaw7965] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/11/2019] [Indexed: 05/03/2023]
Abstract
The notable male predominance across many human cancer types remains unexplained. Here, we show that Drosophila l(3)mbt brain tumors are more invasive and develop as malignant neoplasms more often in males than in females. By quantitative proteomics, we have identified a signature of proteins that are differentially expressed between male and female tumor samples. Prominent among them is the conserved chromatin reader PHD finger protein 7 (Phf7). We show that Phf7 depletion reduces sex-dependent differences in gene expression and suppresses the enhanced malignant traits of male tumors. Our results identify potential regulators of sex-linked tumor dimorphism and show that these genes may serve as targets to suppress sex-linked malignant traits.
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Affiliation(s)
- Cristina Molnar
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Jan Peter Heinen
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Jose Reina
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Salud Llamazares
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Emilio Palumbo
- CRG, BIST, Carrer del Dr. Aiguader, 88, 08003 Barcelona, Spain
- UPF, Plaça de la Mercè, 10, 08002 Barcelona, Spain
- IMIM, Carrer del Dr. Aiguader, 88, 08003 Barcelona, Spain
| | | | - Marina Gay
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Laura Villarreal
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Marta Vilaseca
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Giulia Pollarolo
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Cayetano Gonzalez
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
- ICREA, Passeig Lluís Companys, 08010 Barcelona, Spain
- Corresponding author.
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11
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The same domain of Su(Hw) is required for enhancer blocking and direct promoter repression. Sci Rep 2019; 9:5314. [PMID: 30926937 PMCID: PMC6441048 DOI: 10.1038/s41598-019-41761-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/14/2019] [Indexed: 12/22/2022] Open
Abstract
Suppressor of Hairy-wing [Su(Hw)] is a DNA-binding architectural protein that participates in the organization of insulators and repression of promoters in Drosophila. This protein contains acidic regions at both ends and a central cluster of 12 zinc finger domains, some of which are involved in the specific recognition of the binding site. One of the well-described in vivo function of Su(Hw) is the repression of transcription of neuronal genes in oocytes. Here, we have found that the same Su(Hw) C-terminal region (aa 720–892) is required for insulation as well as for promoter repression. The best characterized partners of Su(Hw), CP190 and Mod(mdg4)-67.2, are not involved in the repression of neuronal genes. Taken together, these results suggest that an unknown protein or protein complex binds to the C-terminal region of Su(Hw) and is responsible for the direct repression activity of Su(Hw).
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12
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Association of SHMT1, MAZ, ERG, and L3MBTL3 Gene Polymorphisms with Susceptibility to Multiple Sclerosis. Biochem Genet 2018; 57:355-370. [PMID: 30456721 DOI: 10.1007/s10528-018-9894-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 11/07/2018] [Indexed: 01/08/2023]
Abstract
Multiple sclerosis (MS) is the most common inflammatory and chronic disease of the central nervous system (CNS). A complex interaction between genetic, environmental, and epigenetic factors is involved in the pathogenesis of MS. With the advancement of GWAS, various variants associated with MS have been identified. This study aimed to evaluate the association of single-nucleotide polymorphisms (SNPs) rs4925166 and rs1979277 in the SHMT1, MAZ rs34286592, ERG rs2836425, and L3MBTL3 rs4364506 with MS. In this case-control study, the association of five SNPs in SHMT1, MAZ, ERG, and L3MBTL3 genes with relapsing-remitting MS (RR-MS) was investigated in 190 patients and 200 healthy individuals. Four SNPs including SHMT1 rs4925166, SHMT1 rs1979277, MAZ rs34286592, and L3MBTL3 rs4364506 were genotyped using PCR-RFLP and genotyping of ERG rs2836425 was performed by tetra-primer ARMS PCR. Our findings showed a significant difference in the allelic frequencies for the four SNPs of SHMT1 rs4925166, SHMT1 rs1979277, MAZ rs34286592, and ERG rs2836425, while there were no differences in the allele and genotype frequencies for L3MBTL3 rs4364506. These significant associations were observed for the following genotypes: TT and GG genotypes of SHMT1 rs4925166 (OR 0.47 and 1.90, respectively) genotype GG of SHMT1 rs1979277 (OR 0.63), genotype GG of MAZ rs34286592 (OR 0.61), TC and CC genotypes of ERG rs2836425 (OR 1.89 and 0.50, respectively). Our study highlighted that people who are carrying genotypes including GG (SHMT1 rs4925166) and TC (ERG rs2836425) have the highest susceptibility chance for MS, respectively. However, genotypes TT (SHMT1 rs4925166), CC (ERG rs2836425), GG (MAZ rs34286592), and GG (SHMT1 rs1979277) had the highest negative association (protective effect) with MS, respectively. L3MBTL3 rs4364506 was found neither as a predisposing nor a protective variant.
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13
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Rossi F, Molnar C, Hashiyama K, Heinen JP, Pampalona J, Llamazares S, Reina J, Hashiyama T, Rai M, Pollarolo G, Fernández-Hernández I, Gonzalez C. An in vivo genetic screen in Drosophila identifies the orthologue of human cancer/testis gene SPO11 among a network of targets to inhibit lethal(3)malignant brain tumour growth. Open Biol 2018; 7:rsob.170156. [PMID: 28855394 PMCID: PMC5577452 DOI: 10.1098/rsob.170156] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 07/27/2017] [Indexed: 12/31/2022] Open
Abstract
Using transgenic RNAi technology, we have screened over 4000 genes to identify targets to inhibit malignant growth caused by the loss of function of lethal(3)malignant brain tumour in Drosophila in vivo. We have identified 131 targets, which belong to a wide range of gene ontologies. Most of these target genes are not significantly overexpressed in mbt tumours hence showing that, rather counterintuitively, tumour-linked overexpression is not a good predictor of functional requirement. Moreover, we have found that most of the genes upregulated in mbt tumours remain overexpressed in tumour-suppressed double-mutant conditions, hence revealing that most of the tumour transcriptome signature is not necessarily correlated with malignant growth. One of the identified target genes is meiotic W68 (mei-W68), the Drosophila orthologue of the human cancer/testis gene Sporulation-specific protein 11 (SPO11), the enzyme that catalyses the formation of meiotic double-strand breaks. We show that Drosophila mei-W68/SPO11 drives oncogenesis by causing DNA damage in a somatic tissue, hence providing the first instance in which a SPO11 orthologue is unequivocally shown to have a pro-tumoural role. Altogether, the results from this screen point to the possibility of investigating the function of human cancer relevant genes in a tractable experimental model organism like Drosophila.
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Affiliation(s)
- Fabrizio Rossi
- Cell Division Group, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Cristina Molnar
- Cell Division Group, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Kazuya Hashiyama
- Cell Division Group, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Jan P Heinen
- Cell Division Group, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Judit Pampalona
- Cell Division Group, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Salud Llamazares
- Cell Division Group, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - José Reina
- Cell Division Group, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Tomomi Hashiyama
- Cell Division Group, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Madhulika Rai
- Cell Division Group, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Giulia Pollarolo
- Cell Division Group, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Ismael Fernández-Hernández
- Cell Division Group, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Cayetano Gonzalez
- Cell Division Group, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 08010 Barcelona, Spain
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14
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Coux RX, Teixeira FK, Lehmann R. L(3)mbt and the LINT complex safeguard cellular identity in the Drosophila ovary. Development 2018; 145:dev.160721. [PMID: 29511022 PMCID: PMC5963868 DOI: 10.1242/dev.160721] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/19/2018] [Indexed: 01/10/2023]
Abstract
Maintenance of cellular identity is essential for tissue development and homeostasis. At the molecular level, cell identity is determined by the coordinated activation and repression of defined sets of genes. The tumor suppressor L(3)mbt has been shown to secure cellular identity in Drosophila larval brains by repressing germline-specific genes. Here, we interrogate the temporal and spatial requirements for L(3)mbt in the Drosophila ovary, and show that it safeguards the integrity of both somatic and germline tissues. l(3)mbt mutant ovaries exhibit multiple developmental defects, which we find to be largely caused by the inappropriate expression of a single gene, nanos, a key regulator of germline fate, in the somatic ovarian cells. In the female germline, we find that L(3)mbt represses testis-specific and neuronal genes. At the molecular level, we show that L(3)mbt function in the ovary is mediated through its co-factor Lint-1 but independently of the dREAM complex. Together, our work uncovers a more complex role for L(3)mbt than previously understood and demonstrates that L(3)mbt secures tissue identity by preventing the simultaneous expression of original identity markers and tissue-specific misexpression signatures. Highlighted Article: Characterization of the developmental defects of l(3)mbt mutant ovaries shows that L(3)mbt regulates tissue-specific gene signatures to secure the identity of somatic ovarian and germline tissues.
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Affiliation(s)
- Rémi-Xavier Coux
- Howard Hughes Medical Institute (HHMI) and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Felipe Karam Teixeira
- Howard Hughes Medical Institute (HHMI) and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Ruth Lehmann
- Howard Hughes Medical Institute (HHMI) and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
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15
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Xu T, Park SS, Giaimo BD, Hall D, Ferrante F, Ho DM, Hori K, Anhezini L, Ertl I, Bartkuhn M, Zhang H, Milon E, Ha K, Conlon KP, Kuick R, Govindarajoo B, Zhang Y, Sun Y, Dou Y, Basrur V, Elenitoba-Johnson KS, Nesvizhskii AI, Ceron J, Lee CY, Borggrefe T, Kovall RA, Rual JF. RBPJ/CBF1 interacts with L3MBTL3/MBT1 to promote repression of Notch signaling via histone demethylase KDM1A/LSD1. EMBO J 2017; 36:3232-3249. [PMID: 29030483 PMCID: PMC5666606 DOI: 10.15252/embj.201796525] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 08/31/2017] [Accepted: 09/12/2017] [Indexed: 12/21/2022] Open
Abstract
Notch signaling is an evolutionarily conserved signal transduction pathway that is essential for metazoan development. Upon ligand binding, the Notch intracellular domain (NOTCH ICD) translocates into the nucleus and forms a complex with the transcription factor RBPJ (also known as CBF1 or CSL) to activate expression of Notch target genes. In the absence of a Notch signal, RBPJ acts as a transcriptional repressor. Using a proteomic approach, we identified L3MBTL3 (also known as MBT1) as a novel RBPJ interactor. L3MBTL3 competes with NOTCH ICD for binding to RBPJ. In the absence of NOTCH ICD, RBPJ recruits L3MBTL3 and the histone demethylase KDM1A (also known as LSD1) to the enhancers of Notch target genes, leading to H3K4me2 demethylation and to transcriptional repression. Importantly, in vivo analyses of the homologs of RBPJ and L3MBTL3 in Drosophila melanogaster and Caenorhabditis elegans demonstrate that the functional link between RBPJ and L3MBTL3 is evolutionarily conserved, thus identifying L3MBTL3 as a universal modulator of Notch signaling in metazoans.
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Affiliation(s)
- Tao Xu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sung-Soo Park
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Daniel Hall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Diana M Ho
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Kazuya Hori
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Lucas Anhezini
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Iris Ertl
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Marek Bartkuhn
- Institute for Genetics, University of Giessen, Giessen, Germany
| | - Honglai Zhang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Eléna Milon
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kimberly Ha
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kevin P Conlon
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Rork Kuick
- Center for Cancer Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Brandon Govindarajoo
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yang Zhang
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yuqing Sun
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yali Dou
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.,Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Julian Ceron
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Cheng-Yu Lee
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Giessen, Germany
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jean-François Rual
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
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16
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Kreher J, Kovač K, Bouazoune K, Mačinković I, Ernst AL, Engelen E, Pahl R, Finkernagel F, Murawska M, Ullah I, Brehm A. EcR recruits dMi-2 and increases efficiency of dMi-2-mediated remodelling to constrain transcription of hormone-regulated genes. Nat Commun 2017; 8:14806. [PMID: 28378812 PMCID: PMC5382322 DOI: 10.1038/ncomms14806] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 01/30/2017] [Indexed: 12/27/2022] Open
Abstract
Gene regulation by steroid hormones plays important roles in health and disease. In Drosophila, the hormone ecdysone governs transitions between key developmental stages. Ecdysone-regulated genes are bound by a heterodimer of ecdysone receptor (EcR) and Ultraspiracle. According to the bimodal switch model, steroid hormone receptors recruit corepressors in the absence of hormone and coactivators in its presence. Here we show that the nucleosome remodeller dMi-2 is recruited to ecdysone-regulated genes to limit transcription. Contrary to the prevalent model, recruitment of the dMi-2 corepressor increases upon hormone addition to constrain gene activation through chromatin remodelling. Furthermore, EcR and dMi-2 form a complex that is devoid of Ultraspiracle. Unexpectedly, EcR contacts the dMi-2 ATPase domain and increases the efficiency of dMi-2-mediated nucleosome remodelling. This study identifies a non-canonical EcR-corepressor complex with the potential for a direct regulation of ATP-dependent nucleosome remodelling by a nuclear hormone receptor.
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Affiliation(s)
- Judith Kreher
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
| | - Kristina Kovač
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
| | - Karim Bouazoune
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
| | - Igor Mačinković
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
| | - Anna Luise Ernst
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
| | - Erik Engelen
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
| | - Roman Pahl
- Institute of Medical Biometry and Epidemiology, Philipps University Marburg, Marburg 35037, Germany
| | - Florian Finkernagel
- Center for Tumour Biology and Immunology, Philipps University Marburg, Marburg 35043, Germany
| | - Magdalena Murawska
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
| | - Ikram Ullah
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
| | - Alexander Brehm
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
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17
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Fagegaltier D, Falciatori I, Czech B, Castel S, Perrimon N, Simcox A, Hannon GJ. Oncogenic transformation of Drosophila somatic cells induces a functional piRNA pathway. Genes Dev 2016; 30:1623-35. [PMID: 27474441 PMCID: PMC4973292 DOI: 10.1101/gad.284927.116] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/07/2016] [Indexed: 12/21/2022]
Abstract
Germline genes often become re-expressed in soma-derived human cancers as "cancer/testis antigens" (CTAs), and piRNA (PIWI-interacting RNA) pathway proteins are found among CTAs. However, whether and how the piRNA pathway contributes to oncogenesis in human neoplasms remain poorly understood. We found that oncogenic Ras combined with loss of the Hippo tumor suppressor pathway reactivates a primary piRNA pathway in Drosophila somatic cells coincident with oncogenic transformation. In these cells, Piwi becomes loaded with piRNAs derived from annotated generative loci, which are normally restricted to either the germline or the somatic follicle cells. Negating the pathway leads to increases in the expression of a wide variety of transposons and also altered expression of some protein-coding genes. This correlates with a reduction in the proliferation of the transformed cells in culture, suggesting that, at least in this context, the piRNA pathway may play a functional role in cancer.
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Affiliation(s)
- Delphine Fagegaltier
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ilaria Falciatori
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Benjamin Czech
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | | | - Norbert Perrimon
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Amanda Simcox
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Gregory J Hannon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom; The New York Genome Center, New York, New York 10011, USA
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18
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Kang H, McElroy KA, Jung YL, Alekseyenko AA, Zee BM, Park PJ, Kuroda MI. Sex comb on midleg (Scm) is a functional link between PcG-repressive complexes in Drosophila. Genes Dev 2015; 29:1136-50. [PMID: 26063573 PMCID: PMC4470282 DOI: 10.1101/gad.260562.115] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this study, Kang et al. investigate how PcG complexes form repressive chromatin domains. The findings show that Scm, a transcriptional repressor, is an important regulator of PRC1, PRC2, and transcriptional silencing and suggest that Scm coordinates PcG complexes and polymerizes, resulting in PcG silencing. The Polycomb group (PcG) proteins are key regulators of development in Drosophila and are strongly implicated in human health and disease. How PcG complexes form repressive chromatin domains remains unclear. Using cross-linked affinity purifications of BioTAP-Polycomb (Pc) or BioTAP-Enhancer of zeste [E(z)], we captured all PcG-repressive complex 1 (PRC1) or PRC2 core components and Sex comb on midleg (Scm) as the only protein strongly enriched with both complexes. Although previously not linked to PRC2, we confirmed direct binding of Scm and PRC2 using recombinant protein expression and colocalization of Scm with PRC1, PRC2, and H3K27me3 in embryos and cultured cells using ChIP-seq (chromatin immunoprecipitation [ChIP] combined with deep sequencing). Furthermore, we found that RNAi knockdown of Scm and overexpression of the dominant-negative Scm-SAM (sterile α motif) domain both affected the binding pattern of E(z) on polytene chromosomes. Aberrant localization of the Scm-SAM domain in long contiguous regions on polytene chromosomes revealed its independent ability to spread on chromatin, consistent with its previously described ability to oligomerize in vitro. Pull-downs of BioTAP-Scm captured PRC1 and PRC2 and additional repressive complexes, including PhoRC, LINT, and CtBP. We propose that Scm is a key mediator connecting PRC1, PRC2, and transcriptional silencing. Combined with previous structural and genetic analyses, our results strongly suggest that Scm coordinates PcG complexes and polymerizes to produce broad domains of PcG silencing.
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Affiliation(s)
- Hyuckjoon Kang
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kyle A McElroy
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Youngsook Lucy Jung
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Artyom A Alekseyenko
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Barry M Zee
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter J Park
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mitzi I Kuroda
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;
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19
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Mazumdar S, Arendt LM, Phillips S, Sedic M, Kuperwasser C, Gill G. CoREST1 promotes tumor formation and tumor stroma interactions in a mouse model of breast cancer. PLoS One 2015; 10:e0121281. [PMID: 25793264 PMCID: PMC4368644 DOI: 10.1371/journal.pone.0121281] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/29/2015] [Indexed: 01/14/2023] Open
Abstract
Regulators of chromatin structure and gene expression contribute to tumor formation and progression. The co-repressor CoREST1 regulates the localization and activity of associated histone modifying enzymes including lysine specific demethylase 1 (LSD1) and histone deacetylase 1 (HDAC1). Although several CoREST1 associated proteins have been reported to enhance breast cancer progression, the role of CoREST1 in breast cancer is currently unclear. Here we report that knockdown of CoREST1 in the basal-type breast cancer cell line, MDA-MB-231, led to significantly reduced incidence and diminished size of tumors compared to controls in mouse xenograft studies. Notably, CoREST1-depleted cells gave rise to tumors with a marked decrease in angiogenesis. CoREST1 knockdown led to a decrease in secreted angiogenic and inflammatory factors, and mRNA analysis suggests that CoREST1 promotes expression of genes related to angiogenesis and inflammation including VEGF-A and CCL2. CoREST1 knockdown decreased the ability of MDA-MB-231 conditioned media to promote endothelial cell tube formation and migration. Further, tumors derived from CoREST1-depleted cells had reduced macrophage infiltration and the secretome of CoREST1 knockdown cells was deficient in promoting macrophage migration and macrophage-mediated angiogenesis. Taken together, these findings reveal that the epigenetic regulator CoREST1 promotes tumorigenesis in a breast cancer model at least in part through regulation of gene expression patterns in tumor cells that have profound non-cell autonomous effects on endothelial and inflammatory cells in the tumor microenvironment.
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Affiliation(s)
- Sohini Mazumdar
- Department of Developmental, Molecular and Chemical Biology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Genetics Program, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Lisa M. Arendt
- Department of Developmental, Molecular and Chemical Biology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, Massachusetts, United States of America
| | - Sarah Phillips
- Department of Developmental, Molecular and Chemical Biology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Genetics Program, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, Massachusetts, United States of America
| | - Maja Sedic
- Department of Developmental, Molecular and Chemical Biology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Cellular, Molecular and Developmental Biology Program, Sackler School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, Massachusetts, United States of America
| | - Charlotte Kuperwasser
- Department of Developmental, Molecular and Chemical Biology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, Massachusetts, United States of America
| | - Grace Gill
- Department of Developmental, Molecular and Chemical Biology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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20
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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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Chromatin reader L(3)mbt requires the Myb-MuvB/DREAM transcriptional regulatory complex for chromosomal recruitment. Proc Natl Acad Sci U S A 2014; 111:E4234-43. [PMID: 25249635 DOI: 10.1073/pnas.1416321111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Lethal malignant brain tumors (lmbt) result from the loss of the conserved transcriptional repressor l(3)mbt, in Drosophila melanogaster. Similar mutations in the human homolog L3MBTL1 correlate with some cancers. The protein's C-terminal MBT repeats bind mono and dimethylated histones in vitro, which could influence recruitment of L3MBTL1 to its target sites. The L(3)mbt chromatin targeting mechanism, however, is controversial and several studies suggest insufficiency or a minor role for histone methylation in determining the site specificity for recruitment. We report that L(3)mbt colocalizes with core members of the Myb-MuvB/DREAM (MMB/DREAM) transcriptional regulatory complex genome-wide, and that L(3)mbt-mediated repression requires this complex in salivary glands and larval brains. Loss of l(3)mbt or of MMB components through mutation cause similar spurious expression of genes, including the transposon regulatory gene piwi, in terminally differentiated cells. The DNA-binding MMB core component Mip120 (Lin54) is required for L(3)mbt recruitment to chromosomes, whereas Mip130 (Lin9) (an MMB core protein) and E2f2 (an MMB transcriptional repressor) are not, but are essential for repression. Cytolocalization experiments suggest the presence of site-specific differential composition of MMB in polytene chromosomes where some loci were bound by a Myb-containing or alternatively, an E2f2 and L(3)mbt form of the complex.
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22
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Feichtinger J, Larcombe L, McFarlane RJ. Meta-analysis of expression of l(3)mbt tumor-associated germline genes supports the model that a soma-to-germline transition is a hallmark of human cancers. Int J Cancer 2014; 134:2359-65. [PMID: 24243547 PMCID: PMC4166677 DOI: 10.1002/ijc.28577] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/27/2013] [Accepted: 10/18/2013] [Indexed: 12/14/2022]
Abstract
Evidence is starting to emerge indicating that tumorigenesis in metazoans involves a soma-to-germline transition, which may contribute to the acquisition of neoplastic characteristics. Here, we have meta-analyzed gene expression profiles of the human orthologs of Drosophila melanogaster germline genes that are ectopically expressed in l(3)mbt brain tumors using gene expression datasets derived from a large cohort of human tumors. We find these germline genes, some of which drive oncogenesis in D. melanogaster, are similarly ectopically activated in a wide range of human cancers. Some of these genes normally have expression restricted to the germline, making them of particular clinical interest. Importantly, these analyses provide additional support to the emerging model that proposes a soma-to-germline transition is a general hallmark of a wide range of human tumors. This has implications for our understanding of human oncogenesis and the development of new therapeutic and biomarker targets with clinical potential.
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Affiliation(s)
- Julia Feichtinger
- North West Cancer Research Institute, Bangor University, Brambell Building, Bangor, Gwynedd, United Kingdom; Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
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23
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Soshnev AA, Baxley RM, Manak JR, Tan K, Geyer PK. The insulator protein Suppressor of Hairy-wing is an essential transcriptional repressor in the Drosophila ovary. Development 2013; 140:3613-23. [PMID: 23884443 DOI: 10.1242/dev.094953] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Suppressor of Hairy-wing [Su(Hw)] is a DNA-binding factor required for gypsy insulator function and female germline development in Drosophila. The insulator function of the gypsy retrotransposon depends on Su(Hw) binding to clustered Su(Hw) binding sites (SBSs) and recruitment of the insulator proteins Centrosomal Protein 190 kD (CP190) and Modifier of mdg4 67.2 kD (Mod67.2). By contrast, the Su(Hw) germline function involves binding to non-clustered SBSs and does not require CP190 or Mod67.2. Here, we identify Su(Hw) target genes, using genome-wide analyses in the ovary to uncover genes with an ovary-bound SBS that are misregulated upon Su(Hw) loss. Most Su(Hw) target genes demonstrate enriched expression in the wild-type CNS. Loss of Su(Hw) leads to increased expression of these CNS-enriched target genes in the ovary and other tissues, suggesting that Su(Hw) is a repressor of neural genes in non-neural tissues. Among the Su(Hw) target genes is RNA-binding protein 9 (Rbp9), a member of the ELAV/Hu gene family. Su(Hw) regulation of Rbp9 appears to be insulator independent, as Rbp9 expression is unchanged in a genetic background that compromises the functions of the CP190 and Mod67.2 insulator proteins, even though both localize to Rbp9 SBSs. Rbp9 misregulation is central to su(Hw)(-/-) sterility, as Rbp9(+/-), su(Hw)(-/-) females are fertile. Eggs produced by Rbp9(+/-), su(Hw)(-/-) females show patterning defects, revealing a somatic requirement for Su(Hw) in the ovary. Our studies demonstrate that Su(Hw) is a versatile transcriptional regulatory protein with an essential developmental function involving transcriptional repression.
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Affiliation(s)
- Alexey A Soshnev
- Interdisciplinary Graduate Program in Molecular and Cellular Biology, University of Iowa, Iowa City, IA 52242, USA
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24
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Zhang J, Bonasio R, Strino F, Kluger Y, Holloway JK, Modzelewski AJ, Cohen PE, Reinberg D. SFMBT1 functions with LSD1 to regulate expression of canonical histone genes and chromatin-related factors. Genes Dev 2013; 27:749-66. [PMID: 23592795 DOI: 10.1101/gad.210963.112] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
SFMBT1 (Scm [Sex comb on midleg] with four MBT [malignant brain tumor] domains 1) is a poorly characterized mammalian MBT domain-containing protein homologous to Drosophila SFMBT, a Polycomb group protein involved in epigenetic regulation of gene expression. Here, we show that SFMBT1 regulates transcription in somatic cells and during spermatogenesis through the formation of a stable complex with LSD1 and CoREST. When bound to its gene targets, SFMBT1 recruits its associated proteins and causes chromatin compaction and transcriptional repression. SFMBT1, LSD1, and CoREST share a large fraction of target genes, including those encoding replication-dependent histones. Simultaneous occupancy of histone genes by SFMBT1, LSD1, and CoREST is regulated during the cell cycle and correlates with the loss of RNA polymerase II at these promoters during G2, M, and G1. The interplay between the repressive SFMBT1-LSD1-CoREST complex and RNA polymerase II contributes to the timely transcriptional regulation of histone genes in human cells. SFMBT1, LSD1, and CoREST also form a stable complex in germ cells, and their chromatin binding activity is regulated during spermatogenesis.
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Affiliation(s)
- Jin Zhang
- Howard Hughes Medical Institute, Department of Biochemistry, New York University School of Medicine, New York, New York 10016, USA
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25
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Gonzalez C. Drosophila melanogaster: a model and a tool to investigate malignancy and identify new therapeutics. Nat Rev Cancer 2013; 13:172-83. [PMID: 23388617 DOI: 10.1038/nrc3461] [Citation(s) in RCA: 204] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
For decades, lower-model organisms such as Drosophila melanogaster have often provided the first glimpse into the mechanism of action of human cancer-related proteins, thus making a substantial contribution to elucidating the molecular basis of the disease. More recently, D. melanogaster strains that are engineered to recapitulate key aspects of specific types of human cancer have been paving the way for the future role of this 'workhorse' of biomedical research, helping to further investigate the process of malignancy, and serving as platforms for therapeutic drug discovery.
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Affiliation(s)
- Cayetano Gonzalez
- IRB-Barcelona, c/Baldiri Reixac 10-12, Barcelona, Spain. gonzalez@ irbbarcelona.org
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26
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Kallio A, Elo LL. Optimizing detection of transcription factor-binding sites in ChIP-seq experiments. Methods Mol Biol 2013; 1038:181-191. [PMID: 23872976 DOI: 10.1007/978-1-62703-514-9_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) offers a powerful means to study transcription factor binding on a genome-wide scale. While a number of advanced software packages have already become available for identifying ChIP-seq-binding sites, it has become evident that the choice of the package together with its adjustable parameters can considerably affect the biological conclusions made from the data. Therefore, to aid these choices, we have recently introduced a reproducibility-optimization procedure, which computationally adjusts the parameters of the popular peak detection algorithms for each ChIP-seq data separately. Here, we provide a detailed description of the procedure together with practical guidelines on how to apply its implementation, the peakROTS R-package, in a given ChIP-seq experiment.
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