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Atinbayeva N, Valent I, Zenk F, Loeser E, Rauer M, Herur S, Quarato P, Pyrowolakis G, Gomez-Auli A, Mittler G, Cecere G, Erhardt S, Tiana G, Zhan Y, Iovino N. Inheritance of H3K9 methylation regulates genome architecture in Drosophila early embryos. EMBO J 2024; 43:2685-2714. [PMID: 38831123 PMCID: PMC11217351 DOI: 10.1038/s44318-024-00127-z] [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: 02/28/2024] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 06/05/2024] Open
Abstract
Constitutive heterochromatin is essential for transcriptional silencing and genome integrity. The establishment of constitutive heterochromatin in early embryos and its role in early fruitfly development are unknown. Lysine 9 trimethylation of histone H3 (H3K9me3) and recruitment of its epigenetic reader, heterochromatin protein 1a (HP1a), are hallmarks of constitutive heterochromatin. Here, we show that H3K9me3 is transmitted from the maternal germline to the next generation. Maternally inherited H3K9me3, and the histone methyltransferases (HMT) depositing it, are required for the organization of constitutive heterochromatin: early embryos lacking H3K9 methylation display de-condensation of pericentromeric regions, centromere-centromere de-clustering, mitotic defects, and nuclear shape irregularities, resulting in embryo lethality. Unexpectedly, quantitative CUT&Tag and 4D microscopy measurements of HP1a coupled with biophysical modeling revealed that H3K9me2/3 is largely dispensable for HP1a recruitment. Instead, the main function of H3K9me2/3 at this developmental stage is to drive HP1a clustering and subsequent heterochromatin compaction. Our results show that HP1a binding to constitutive heterochromatin in the absence of H3K9me2/3 is not sufficient to promote proper embryo development and heterochromatin formation. The loss of H3K9 HMTs and H3K9 methylation alters genome organization and hinders embryonic development.
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Affiliation(s)
- Nazerke Atinbayeva
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
- Albert-Ludwigs-Universität Freiburg, Fahnenbergplatz, 79085, Freiburg im Breisgau, Germany
| | - Iris Valent
- Karlsruhe Institute of Technology (KIT), Zoological Institute, 76131, Karlsruhe, Germany
| | - Fides Zenk
- Brain Mind Institute, School of Life Sciences EPFL, SV3809, 1015, Lausanne, Switzerland
| | - Eva Loeser
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Michael Rauer
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Shwetha Herur
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Piergiuseppe Quarato
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, 20132, Milan, Italy
| | - Giorgos Pyrowolakis
- Centre for Biological signaling studies, University of Freiburg, 79104, Freiburg im Breisgau, Germany
| | - Alejandro Gomez-Auli
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany
| | - Germano Cecere
- Institute Pasteur, Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, UMR3738, CNRS, 75724, Cedex 15, Paris, France
| | - Sylvia Erhardt
- Karlsruhe Institute of Technology (KIT), Zoological Institute, 76131, Karlsruhe, Germany
| | - Guido Tiana
- Università degli Studi di Milano and INFN, Milan, Italy
| | - Yinxiu Zhan
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milan, Italy.
| | - Nicola Iovino
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg im Breisgau, Germany.
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2
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Koryakov DE. Diversity and functional specialization of H3K9-specific histone methyltransferases. Bioessays 2024; 46:e2300163. [PMID: 38058121 DOI: 10.1002/bies.202300163] [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: 08/29/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023]
Abstract
Histone modifications play a critical role in the control over activities of the eukaryotic genome; among these chemical alterations, the methylation of lysine K9 in histone H3 (H3K9) is one of the most extensively studied. The number of enzymes capable of methylating H3K9 varies greatly across different organisms: in fission yeast, only one such methyltransferase is present, whereas in mammals, 10 are known. If there are several such enzymes, each of them must have some specific function, and they can interact with one another. Thus arises a complex system of interchangeability, "division of labor," and contacts with each other and with diverse proteins. Histone methyltransferases specialize in the number of methyl groups that they attach and have different intracellular localizations as well as different distributions on chromosomes. Each also shows distinct binding to different types of sequences and has a specific set of nonhistone substrates.
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Affiliation(s)
- Dmitry E Koryakov
- Lab of Molecular Cytogenetics, Institute of Molecular and Cellular Biology, Novosibirsk, Russia
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3
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Sarkar K, Kotb NM, Lemus A, Martin ET, McCarthy A, Camacho J, Iqbal A, Valm AM, Sammons MA, Rangan P. A feedback loop between heterochromatin and the nucleopore complex controls germ-cell-to-oocyte transition during Drosophila oogenesis. Dev Cell 2023; 58:2580-2596.e6. [PMID: 37673064 PMCID: PMC11301765 DOI: 10.1016/j.devcel.2023.08.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/12/2023] [Accepted: 08/09/2023] [Indexed: 09/08/2023]
Abstract
Germ cells differentiate into oocytes that launch the next generation upon fertilization. How the highly specialized oocyte acquires this distinct cell fate is poorly understood. During Drosophila oogenesis, H3K9me3 histone methyltransferase SETDB1 translocates from the cytoplasm to the nucleus of germ cells concurrently with oocyte specification. Here, we discovered that nuclear SETDB1 is required for silencing a cohort of differentiation-promoting genes by mediating their heterochromatinization. Intriguingly, SETDB1 is also required for upregulating 18 of the ∼30 nucleoporins (Nups) that compose the nucleopore complex (NPC), promoting NPC formation. NPCs anchor SETDB1-dependent heterochromatin at the nuclear periphery to maintain H3K9me3 and gene silencing in the egg chambers. Aberrant gene expression due to the loss of SETDB1 or Nups results in the loss of oocyte identity, cell death, and sterility. Thus, a feedback loop between heterochromatin and NPCs promotes transcriptional reprogramming at the onset of oocyte specification, which is critical for establishing oocyte identity.
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Affiliation(s)
- Kahini Sarkar
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Noor M Kotb
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA; Department of Biomedical Sciences, School of Public Health, University at Albany SUNY, Albany, NY 12222, USA
| | - Alex Lemus
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Elliot T Martin
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Alicia McCarthy
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Justin Camacho
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Ayman Iqbal
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Alex M Valm
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Morgan A Sammons
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Prashanth Rangan
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA.
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4
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Haddadi M, Ataei R. wde, calpA, if, dap160, and poe genes knock down Drosophila models exhibit neurofunctional deficit. Gene 2022; 829:146499. [PMID: 35447243 DOI: 10.1016/j.gene.2022.146499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/14/2022] [Accepted: 04/14/2022] [Indexed: 11/27/2022]
Abstract
Intellectual disability (ID) is a heterogeneous disorder with high prevalence and remarkable social and cost burdens. Novel genetic variants of ATF7IP, CAPN9, ITGAV, ITSN1, and UBR4 genes are reported to be associated with the ID among Iranian families. However, in vivo validation is required to confirm the functional role of these variants in ID development. Drosophila melanogaster is a convenient model for such functional investigations as its genome bears ortholog of more than 75% of the disease-causing genes in human and represents numerous approaches to study defects in neuronal function. In this connection, RNAi gene silencing was applied to wde, calpA, if, dap160, and poe genes, the Drosophila ortholog of the selected human genes, and then consequent structural and functional changes in neurons were studied by means of immunohistochemistry and confocal microscopy of mushroom bodies (MBs) and validated behavioural assays including larvae and adult conditioning learning and memories, and ethanol sensitivity. Down-regulation of these genes led to neuronal loss which was evident by decline in total fluorescent signal intensity in micrographs of MBs structure. The gene silencing caused neuronal dysfunction and induction of ID-like symptoms manifested by deficits in larval preference learning, and short-term olfactory memory and courtship suppression learning in adults. Moreover, the RNAi flies showed higher sensitivity to ethanol vapour. Interestingly, the poe knock-down flies exhibited the most severe phenotypes among other genes. Altogether, we believe this study is first-of-its-kind and findings are highly applicable to confirm pathogenecity of the selected ID gene variants in Iranian population.
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Affiliation(s)
- Mohammad Haddadi
- Department of Biology, Faculty of Science, University of Zabol, Zabol, Iran.
| | - Reza Ataei
- Department of Biology, Faculty of Science, University of Zabol, Zabol, Iran
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SETDB1-like MET-2 promotes transcriptional silencing and development independently of its H3K9me-associated catalytic activity. Nat Struct Mol Biol 2022; 29:85-96. [PMID: 35102319 PMCID: PMC8850192 DOI: 10.1038/s41594-021-00712-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 12/02/2021] [Indexed: 12/30/2022]
Abstract
Transcriptionally silenced heterochromatin bearing methylation of histone H3 on lysine 9 (H3K9me) is critical for maintaining organismal viability and tissue integrity. Here we show that in addition to ensuring H3K9me, MET-2, the Caenorhabditis elegans homolog of the SETDB1 histone methyltransferase, has a noncatalytic function that contributes to gene repression. Subnuclear foci of MET-2 coincide with H3K9me deposition, yet these foci also form when MET-2 is catalytically deficient and H3K9me is compromised. Whereas met-2 deletion triggers a loss of silencing and increased histone acetylation, foci of catalytically deficient MET-2 maintain silencing of a subset of genes, blocking acetylation on H3K9 and H3K27. In normal development, this noncatalytic MET-2 activity helps to maintain fertility. Under heat stress MET-2 foci disperse, coinciding with increased acetylation and transcriptional derepression. Our study suggests that the noncatalytic, focus-forming function of this SETDB1-like protein and its intrinsically disordered cofactor LIN-65 is physiologically relevant. Genetic and genome-wide analysis of a catalytically deficient SETDB1-like enzyme, MET-2, in Caenorhabditiselegans reveals that MET-2 promotes transcriptional silencing and fertility through both H3K9 methylation and focus formation, which blocks histone acetylation.
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Fabry MH, Falconio FA, Joud F, Lythgoe EK, Czech B, Hannon GJ. Maternally inherited piRNAs direct transient heterochromatin formation at active transposons during early Drosophila embryogenesis. eLife 2021; 10:e68573. [PMID: 34236313 PMCID: PMC8352587 DOI: 10.7554/elife.68573] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
The PIWI-interacting RNA (piRNA) pathway controls transposon expression in animal germ cells, thereby ensuring genome stability over generations. In Drosophila, piRNAs are intergenerationally inherited through the maternal lineage, and this has demonstrated importance in the specification of piRNA source loci and in silencing of I- and P-elements in the germ cells of daughters. Maternally inherited Piwi protein enters somatic nuclei in early embryos prior to zygotic genome activation and persists therein for roughly half of the time required to complete embryonic development. To investigate the role of the piRNA pathway in the embryonic soma, we created a conditionally unstable Piwi protein. This enabled maternally deposited Piwi to be cleared from newly laid embryos within 30 min and well ahead of the activation of zygotic transcription. Examination of RNA and protein profiles over time, and correlation with patterns of H3K9me3 deposition, suggests a role for maternally deposited Piwi in attenuating zygotic transposon expression in somatic cells of the developing embryo. In particular, robust deposition of piRNAs targeting roo, an element whose expression is mainly restricted to embryonic development, results in the deposition of transient heterochromatic marks at active roo insertions. We hypothesize that roo, an extremely successful mobile element, may have adopted a lifestyle of expression in the embryonic soma to evade silencing in germ cells.
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Affiliation(s)
- Martin H Fabry
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Federica A Falconio
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Fadwa Joud
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Emily K Lythgoe
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Benjamin Czech
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Gregory J Hannon
- CRUK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
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7
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Schnabl J, Wang J, Hohmann U, Gehre M, Batki J, Andreev VI, Purkhauser K, Fasching N, Duchek P, Novatchkova M, Mechtler K, Plaschka C, Patel DJ, Brennecke J. Molecular principles of Piwi-mediated cotranscriptional silencing through the dimeric SFiNX complex. Genes Dev 2021; 35:392-409. [PMID: 33574069 PMCID: PMC7919418 DOI: 10.1101/gad.347989.120] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
Nuclear Argonaute proteins, guided by their bound small RNAs to nascent target transcripts, mediate cotranscriptional silencing of transposons and repetitive genomic loci through heterochromatin formation. The molecular mechanisms involved in this process are incompletely understood. Here, we show that the SFiNX complex, a silencing mediator downstream from nuclear Piwi-piRNA complexes in Drosophila, facilitates cotranscriptional silencing as a homodimer. The dynein light chain protein Cut up/LC8 mediates SFiNX dimerization, and its function can be bypassed by a heterologous dimerization domain, arguing for a constitutive SFiNX dimer. Dimeric, but not monomeric SFiNX, is capable of forming molecular condensates in a nucleic acid-stimulated manner. Mutations that prevent SFiNX dimerization result in loss of condensate formation in vitro and the inability of Piwi to initiate heterochromatin formation and silence transposons in vivo. We propose that multivalent SFiNX-nucleic acid interactions are critical for heterochromatin establishment at piRNA target loci in a cotranscriptional manner.
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Affiliation(s)
- Jakob Schnabl
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School at the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Juncheng Wang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ulrich Hohmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Maja Gehre
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Julia Batki
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Veselin I Andreev
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School at the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Kim Purkhauser
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Nina Fasching
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Peter Duchek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Clemens Plaschka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
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8
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Eastwood EL, Jara KA, Bornelöv S, Munafò M, Frantzis V, Kneuss E, Barbar EJ, Czech B, Hannon GJ. Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila. eLife 2021; 10:e65557. [PMID: 33538693 PMCID: PMC7861614 DOI: 10.7554/elife.65557] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022] Open
Abstract
In animal gonads, the PIWI-interacting RNA (piRNA) pathway guards genome integrity in part through the co-transcriptional gene silencing of transposon insertions. In Drosophila ovaries, piRNA-loaded Piwi detects nascent transposon transcripts and instructs heterochromatin formation through the Panoramix-induced co-transcriptional silencing (PICTS) complex, containing Panoramix, Nxf2 and Nxt1. Here, we report that the highly conserved dynein light chain LC8/Cut-up (Ctp) is an essential component of the PICTS complex. Loss of Ctp results in transposon de-repression and a reduction in repressive chromatin marks specifically at transposon loci. In turn, Ctp can enforce transcriptional silencing when artificially recruited to RNA and DNA reporters. We show that Ctp drives dimerisation of the PICTS complex through its interaction with conserved motifs within Panoramix. Artificial dimerisation of Panoramix bypasses the necessity for its interaction with Ctp, demonstrating that conscription of a protein from a ubiquitous cellular machinery has fulfilled a fundamental requirement for a transposon silencing complex.
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Affiliation(s)
- Evelyn L Eastwood
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Kayla A Jara
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Susanne Bornelöv
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Marzia Munafò
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Vasileios Frantzis
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Emma Kneuss
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Benjamin Czech
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeUnited Kingdom
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9
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Tsusaka T, Fukuda K, Shimura C, Kato M, Shinkai Y. The fibronectin type-III (FNIII) domain of ATF7IP contributes to efficient transcriptional silencing mediated by the SETDB1 complex. Epigenetics Chromatin 2020; 13:52. [PMID: 33256805 PMCID: PMC7706265 DOI: 10.1186/s13072-020-00374-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/13/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The histone methyltransferase SETDB1 (also known as ESET) represses genes and various types of transposable elements, such as endogenous retroviruses (ERVs) and integrated exogenous retroviruses, through a deposition of trimethylation on lysine 9 of histone H3 (H3K9me3) in mouse embryonic stem cells (mESCs). ATF7IP (also known as MCAF1 or AM), a binding partner of SETDB1, regulates the nuclear localization and enzymatic activities of SETDB1 and plays a crucial role in SETDB1-mediated transcriptional silencing. In this study, we further dissected the ATF7IP function with its truncated mutants in Atf7ip knockout (KO) mESCs. RESULTS We demonstrated that the SETDB1-interaction region within ATF7IP is essential for ATF7IP-dependent SETDB1 nuclear localization and silencing of both ERVs and integrated retroviral transgenes, whereas its C-terminal fibronectin type-III (FNIII) domain is dispensable for both these functions; rather, it has a role in efficient silencing mediated by the SETDB1 complex. Proteomic analysis identified a number of FNIII domain-interacting proteins, some of which have a consensus binding motif. We showed that one of the FNIII domain-binding proteins, ZMYM2, was involved in the efficient silencing of a transgene by ATF7IP. RNA-seq analysis of Atf7ip KO and WT or the FNIII domain mutant of ATF7IP-rescued Atf7ip KO mESCs showed that the FNIII domain mutant re-silenced most de-repressed SETDB1/ATF7IP-targeted ERVs compared to the WT. However, the silencing activity of the FNIII domain mutant was weaker than that of the ATF7IP WT, and some of the de-repressed germ cell-related genes in Atf7ip KO mESCs were not silenced by the FNIII domain mutant. Such germ cell-related genes are targeted and silenced by the MAX/MGA complex, and MGA was also identified as another potential binding molecule of the ATF7IP FNIII domain in the proteomic analysis. This suggests that the FNIII domain of ATF7IP acts as a binding hub of ATF7IP-interacting molecules possessing a specific interacting motif we named FAM and contributes to one layer of the SETDB1/ATF7IP complex-mediated silencing mechanisms. CONCLUSIONS Our findings contributed to further understanding the function of ATF7IP in the SETDB1 complex, revealed the role of the FNIII domain of ATF7IP in transcriptional silencing, and suggested a potential underlying molecular mechanism for it.
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Affiliation(s)
- Takeshi Tsusaka
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Orthopedic Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Kei Fukuda
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan
| | - Chikako Shimura
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan
| | - Masaki Kato
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan. .,Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, 230-0045, Japan.
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, 351-0198, Japan.
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10
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Villagra C, Frías-Lasserre D. Epigenetic Molecular Mechanisms in Insects. NEOTROPICAL ENTOMOLOGY 2020; 49:615-642. [PMID: 32514997 DOI: 10.1007/s13744-020-00777-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
Insects are the largest animal group on Earth both in biomass and diversity. Their outstanding success has inspired genetics and developmental research, allowing the discovery of dynamic process explaining extreme phenotypic plasticity and canalization. Epigenetic molecular mechanisms (EMMs) are vital for several housekeeping functions in multicellular organisms, regulating developmental, ontogenetic trajectories and environmental adaptations. In Insecta, EMMs are involved in the development of extreme phenotypic divergences such as polyphenisms and eusocial castes. Here, we review the history of this research field and how the main EMMs found in insects help to understand their biological processes and diversity. EMMs in insects confer them rapid response capacity allowing insect either to change with plastic divergence or to keep constant when facing different stressors or stimuli. EMMs function both at intra as well as transgenerational scales, playing important roles in insect ecology and evolution. We discuss on how EMMs pervasive influences in Insecta require not only the control of gene expression but also the dynamic interplay of EMMs with further regulatory levels, including genetic, physiological, behavioral, and environmental among others, as was earlier proposed by the Probabilistic Epigenesis model and Developmental System Theory.
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Affiliation(s)
- C Villagra
- Instituto de Entomología, Univ Metropolitana de Ciencias de la Educación, Santiago, Chile.
| | - D Frías-Lasserre
- Instituto de Entomología, Univ Metropolitana de Ciencias de la Educación, Santiago, Chile
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11
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Fukuda K, Shinkai Y. SETDB1-Mediated Silencing of Retroelements. Viruses 2020; 12:E596. [PMID: 32486217 PMCID: PMC7354471 DOI: 10.3390/v12060596] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 12/11/2022] Open
Abstract
SETDB1 (SET domain bifurcated histone lysine methyltransferase 1) is a protein lysine methyltransferase and methylates histone H3 at lysine 9 (H3K9). Among other H3K9 methyltransferases, SETDB1 and SETDB1-mediated H3K9 trimethylation (H3K9me3) play pivotal roles for silencing of endogenous and exogenous retroelements, thus contributing to genome stability against retroelement transposition. Furthermore, SETDB1 is highly upregulated in various tumor cells. In this article, we describe recent advances about how SETDB1 activity is regulated, how SETDB1 represses various types of retroelements such as L1 and class I, II, and III endogenous retroviruses (ERVs) in concert with other epigenetic factors such as KAP1 and the HUSH complex and how SETDB1-mediated H3K9 methylation can be maintained during replication.
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Affiliation(s)
- Kei Fukuda
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako 351-0198, Japan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako 351-0198, Japan
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12
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SATO K, SIOMI MC. The piRNA pathway in Drosophila ovarian germ and somatic cells. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2020; 96:32-42. [PMID: 31932527 PMCID: PMC6974405 DOI: 10.2183/pjab.96.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 10/28/2019] [Indexed: 05/30/2023]
Abstract
RNA silencing refers to gene silencing pathways mediated by small non-coding RNAs, including microRNAs. Piwi-interacting RNAs (piRNAs) constitute the largest class of small non-coding RNAs in animal gonads, which repress transposons to protect the germline genome from the selfish invasion of transposons. Deterioration of the system causes DNA damage, leading to severe defects in gametogenesis and infertility. Studies using Drosophila ovaries show that piRNAs originate from specific genomic loci, termed piRNA clusters, and that in piRNA biogenesis, cluster transcripts are processed into mature piRNAs via three distinct pathways: initiator or responder for ping-pong piRNAs and trailing for phased piRNAs. piRNAs then assemble with PIWI members of the Argonaute family of proteins to form piRNA-induced RNA silencing complexes (piRISCs), the core engine of the piRNA-mediated silencing pathway. Upon piRISC assembly, the PIWI member, Piwi, is translocated to the nucleus and represses transposons co-transcriptionally by inducing local heterochromatin formation at target transposon loci.
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Affiliation(s)
- Kaoru SATO
- 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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13
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The SUMO Ligase Su(var)2-10 Controls Hetero- and Euchromatic Gene Expression via Establishing H3K9 Trimethylation and Negative Feedback Regulation. Mol Cell 2019; 77:571-585.e4. [PMID: 31901448 DOI: 10.1016/j.molcel.2019.09.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/11/2019] [Accepted: 09/26/2019] [Indexed: 02/07/2023]
Abstract
Сhromatin is critical for genome compaction and gene expression. On a coarse scale, the genome is divided into euchromatin, which harbors the majority of genes and is enriched in active chromatin marks, and heterochromatin, which is gene-poor but repeat-rich. The conserved molecular hallmark of heterochromatin is the H3K9me3 modification, which is associated with gene silencing. We found that in Drosophila, deposition of most of the H3K9me3 mark depends on SUMO and the SUMO ligase Su(var)2-10, which recruits the histone methyltransferase complex SetDB1/Wde. In addition to repressing repeats, H3K9me3 influences expression of both hetero- and euchromatic host genes. High H3K9me3 levels in heterochromatin are required to suppress spurious transcription and ensure proper gene expression. In euchromatin, a set of conserved genes is repressed by Su(var)2-10/SetDB1-induced H3K9 trimethylation, ensuring tissue-specific gene expression. Several components of heterochromatin are themselves repressed by this pathway, providing a negative feedback mechanism to ensure chromatin homeostasis.
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14
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Ninova M, Chen YCA, Godneeva B, Rogers AK, Luo Y, Fejes Tóth K, Aravin AA. Su(var)2-10 and the SUMO Pathway Link piRNA-Guided Target Recognition to Chromatin Silencing. Mol Cell 2019; 77:556-570.e6. [PMID: 31901446 DOI: 10.1016/j.molcel.2019.11.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/11/2019] [Accepted: 11/08/2019] [Indexed: 01/14/2023]
Abstract
Regulation of transcription is the main mechanism responsible for precise control of gene expression. Whereas the majority of transcriptional regulation is mediated by DNA-binding transcription factors that bind to regulatory gene regions, an elegant alternative strategy employs small RNA guides, Piwi-interacting RNAs (piRNAs) to identify targets of transcriptional repression. Here, we show that in Drosophila the small ubiquitin-like protein SUMO and the SUMO E3 ligase Su(var)2-10 are required for piRNA-guided deposition of repressive chromatin marks and transcriptional silencing of piRNA targets. Su(var)2-10 links the piRNA-guided target recognition complex to the silencing effector by binding the piRNA/Piwi complex and inducing SUMO-dependent recruitment of the SetDB1/Wde histone methyltransferase effector. We propose that in Drosophila, the nuclear piRNA pathway has co-opted a conserved mechanism of SUMO-dependent recruitment of the SetDB1/Wde chromatin modifier to confer repression of genomic parasites.
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Affiliation(s)
- Maria Ninova
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, Pasadena, CA 91125, USA
| | - Yung-Chia Ariel Chen
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, Pasadena, CA 91125, USA
| | - Baira Godneeva
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, Pasadena, CA 91125, USA; Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Alicia K Rogers
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, Pasadena, CA 91125, USA
| | - Yicheng Luo
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, Pasadena, CA 91125, USA
| | - Katalin Fejes Tóth
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, Pasadena, CA 91125, USA.
| | - Alexei A Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, 147-75, Pasadena, CA 91125, USA.
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15
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Abstract
Transposon silencing requires the histone methyltransferase SETDB1. In this issue of EMBO Reports, Tsusaka et al [1] and Osumi et al [2] illustrate how the cofactor ATF7IP and its fly homolog Windei (Wde) regulate the methyltransferase function of SETDB1 through its nuclear licensing. The new insight gained from these two articles will shift how we think about epigenetic regulation and its multiple layers of control.
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Affiliation(s)
- Poppy A Gould
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | - Helen M Rowe
- Division of Infection and ImmunityUniversity College LondonLondonUK
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16
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Meisel RP, Delclos PJ, Wexler JR. The X chromosome of the German cockroach, Blattella germanica, is homologous to a fly X chromosome despite 400 million years divergence. BMC Biol 2019; 17:100. [PMID: 31806031 PMCID: PMC6894488 DOI: 10.1186/s12915-019-0721-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/11/2019] [Indexed: 12/30/2022] Open
Abstract
Background Sex chromosome evolution is a dynamic process that can proceed at varying rates across lineages. For example, different chromosomes can be sex-linked between closely related species, whereas other sex chromosomes have been conserved for > 100 million years. Cases of long-term sex chromosome conservation could be informative of factors that constrain sex chromosome evolution. Cytological similarities between the X chromosomes of the German cockroach (Blattella germanica) and most flies suggest that they may be homologous—possibly representing an extreme case of long-term conservation. Results To test the hypothesis that the cockroach and fly X chromosomes are homologous, we analyzed whole-genome sequence data from cockroaches. We found evidence in both sequencing coverage and heterozygosity that a significant excess of the same genes are on both the cockroach and fly X chromosomes. We also present evidence that the candidate X-linked cockroach genes may be dosage compensated in hemizygous males. Consistent with this hypothesis, three regulators of transcription and chromatin on the fly X chromosome are conserved in the cockroach genome. Conclusions Our results support our hypothesis that the German cockroach shares the same X chromosome as most flies. This may represent the convergent evolution of the X chromosome in the lineages leading to cockroaches and flies. Alternatively, the common ancestor of most insects may have had an X chromosome that resembled the extant cockroach and fly X. Cockroaches and flies diverged ∼ 400 million years ago, which would be the longest documented conservation of a sex chromosome. Cockroaches and flies have different mechanisms of sex determination, raising the possibility that the X chromosome was conserved despite the evolution of the sex determination pathway.
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Affiliation(s)
- Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd., Houston, 77204, TX, USA.
| | - Pablo J Delclos
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd., Houston, 77204, TX, USA
| | - Judith R Wexler
- Department of Ecology and Evolution, University of California, Davis, One Shields Ave, Davis, 95616, CA, USA.,Department of Entomology, University of Maryland, 4112 Plant Sciences Building, College Park, 20742, MD, USA
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17
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Paddibhatla I, Gautam DK, Mishra RK. SETDB1 modulates the differentiation of both the crystal cells and the lamellocytes in Drosophila. Dev Biol 2019; 456:74-85. [DOI: 10.1016/j.ydbio.2019.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 01/10/2023]
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18
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Tsusaka T, Shimura C, Shinkai Y. ATF7IP regulates SETDB1 nuclear localization and increases its ubiquitination. EMBO Rep 2019; 20:e48297. [PMID: 31576654 DOI: 10.15252/embr.201948297] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 09/02/2019] [Accepted: 09/11/2019] [Indexed: 12/17/2022] Open
Abstract
Understanding of the appropriate regulation of enzymatic activities of histone-modifying enzymes remains poor. The lysine methyltransferase, SETDB1, is one of the enzymes responsible for the methylation of histone H3 at lysine 9 (H3K9) and plays a key role in H3K9 trimethylation-mediated silencing of genes and retrotransposons. Here, we reported that how SETDB1's enzymatic activities can be regulated by the nuclear protein, ATF7IP, a known binding partner of SETDB1. Mechanistically, ATF7IP mediates SETDB1 retention inside the nucleus, presumably by inhibiting its nuclear export by binding to the N-terminal region of SETDB1, which harbors the nuclear export signal motifs, and also by promoting its nuclear import. The nuclear localization of SETDB1 increases its ubiquitinated, enzymatically more active form. Our results provided an insight as to how ATF7IP can regulate the histone methyltransferase activity of SETDB1 accompanied by its nuclear translocation.
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Affiliation(s)
- Takeshi Tsusaka
- Cellular Memory Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Japan
| | - Chikako Shimura
- Cellular Memory Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Japan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Japan
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19
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Osumi K, Sato K, Murano K, Siomi H, Siomi MC. Essential roles of Windei and nuclear monoubiquitination of Eggless/SETDB1 in transposon silencing. EMBO Rep 2019; 20:e48296. [PMID: 31576653 DOI: 10.15252/embr.201948296] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 09/02/2019] [Accepted: 09/11/2019] [Indexed: 11/09/2022] Open
Abstract
Eggless/SETDB1 (Egg), the only essential histone methyltransferase (HMT) in Drosophila, plays a role in gene repression, including piRNA-mediated transposon silencing in the ovaries. Previous studies suggested that Egg is post-translationally modified and showed that Windei (Wde) regulates Egg nuclear localization through protein-protein interaction. Monoubiquitination of mammalian SETDB1 is necessary for the HMT activity. Here, using cultured ovarian somatic cells, we show that Egg is monoubiquitinated and phosphorylated but that only monoubiquitination is required for piRNA-mediated transposon repression. Egg monoubiquitination occurs in the nucleus. Egg has its own nuclear localization signal, and the nuclear import of Egg is Wde-independent. Wde recruits Egg to the chromatin at target gene silencing loci, but their interaction is monoubiquitin-independent. The abundance of nuclear Egg is governed by that of nuclear Wde. These results illuminate essential roles of nuclear monoubiquitination of Egg and the role of Wde in piRNA-mediated transposon repression.
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Affiliation(s)
- Ken Osumi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kaoru Sato
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kensaku Murano
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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20
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Sin JH, Zuckerman C, Cortez JT, Eckalbar WL, Erle DJ, Anderson MS, Waterfield MR. The epigenetic regulator ATF7ip inhibits Il2 expression, regulating Th17 responses. J Exp Med 2019; 216:2024-2037. [PMID: 31217192 PMCID: PMC6719416 DOI: 10.1084/jem.20182316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/19/2019] [Accepted: 05/22/2019] [Indexed: 12/24/2022] Open
Abstract
T helper 17 cells (Th17) are critical for fighting infections at mucosal surfaces; however, they have also been found to contribute to the pathogenesis of multiple autoimmune diseases and have been targeted therapeutically. Due to the role of Th17 cells in autoimmune pathogenesis, it is important to understand the factors that control Th17 development. Here we identify the activating transcription factor 7 interacting protein (ATF7ip) as a critical regulator of Th17 differentiation. Mice with T cell-specific deletion of Atf7ip have impaired Th17 differentiation secondary to the aberrant overproduction of IL-2 with T cell receptor (TCR) stimulation and are resistant to colitis in vivo. ChIP-seq studies identified ATF7ip as an inhibitor of Il2 gene expression through the deposition of the repressive histone mark H3K9me3 in the Il2-Il21 intergenic region. These results demonstrate a new epigenetic pathway by which IL-2 production is constrained, and this may open up new avenues for modulating its production.
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Affiliation(s)
- Jun Hyung Sin
- Diabetes Center, University of California, San Francisco, San Francisco, CA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA
| | - Cassandra Zuckerman
- Diabetes Center, University of California, San Francisco, San Francisco, CA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA
| | - Jessica T Cortez
- Diabetes Center, University of California, San Francisco, San Francisco, CA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA
| | - Walter L Eckalbar
- Department of Medicine, University of California San Francisco, San Francisco, CA
- The Lung Biology Center and Functional Genomics Core, University of California San Francisco, San Francisco, CA
| | - David J Erle
- Department of Medicine, University of California San Francisco, San Francisco, CA
- The Lung Biology Center and Functional Genomics Core, University of California San Francisco, San Francisco, CA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA
- Department of Medicine, University of California San Francisco, San Francisco, CA
| | - Michael R Waterfield
- Diabetes Center, University of California, San Francisco, San Francisco, CA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA
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21
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Seller CA, Cho CY, O'Farrell PH. Rapid embryonic cell cycles defer the establishment of heterochromatin by Eggless/SetDB1 in Drosophila. Genes Dev 2019; 33:403-417. [PMID: 30808658 PMCID: PMC6446540 DOI: 10.1101/gad.321646.118] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/14/2019] [Indexed: 12/15/2022]
Abstract
Acquisition of chromatin modifications during embryogenesis distinguishes different regions of an initially naïve genome. In many organisms, repetitive DNA is packaged into constitutive heterochromatin that is marked by di/trimethylation of histone H3K9 and the associated protein HP1a. These modifications enforce the unique epigenetic properties of heterochromatin. However, in the early Drosophila melanogaster embryo, the heterochromatin lacks these modifications, which appear only later, when rapid embryonic cell cycles slow down at the midblastula transition (MBT). Here we focus on the initial steps restoring heterochromatic modifications in the embryo. We describe the JabbaTrap, a technique for inactivating maternally provided proteins in embryos. Using the JabbaTrap, we reveal a major requirement for the methyltransferase Eggless/SetDB1 in the establishment of heterochromatin. In contrast, other methyltransferases contribute minimally. Live imaging reveals that endogenous Eggless gradually accumulates on chromatin in interphase but then dissociates in mitosis, and its accumulation must restart in the next cell cycle. Cell cycle slowing as the embryo approaches the MBT permits increasing accumulation and action of Eggless at its targets. Experimental manipulation of interphase duration shows that cell cycle speed regulates Eggless. We propose that developmental slowing of the cell cycle times embryonic heterochromatin formation.
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Affiliation(s)
- Charles A Seller
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94143, USA
| | - Chun-Yi Cho
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94143, USA
| | - Patrick H O'Farrell
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94143, USA
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22
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Delaney CE, Methot SP, Guidi M, Katic I, Gasser SM, Padeken J. Heterochromatic foci and transcriptional repression by an unstructured MET-2/SETDB1 co-factor LIN-65. J Cell Biol 2019; 218:820-838. [PMID: 30737265 PMCID: PMC6400574 DOI: 10.1083/jcb.201811038] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/22/2019] [Accepted: 01/25/2019] [Indexed: 12/14/2022] Open
Abstract
The segregation of the genome into accessible euchromatin and histone H3K9-methylated heterochromatin helps silence repetitive elements and tissue-specific genes. In Caenorhabditis elegans, MET-2, the homologue of mammalian SETDB1, catalyzes H3K9me1 and me2, yet like SETDB1, its regulation is enigmatic. Contrary to the cytosolic enrichment of overexpressed MET-2, we show that endogenous MET-2 is nuclear throughout development, forming perinuclear foci in a cell cycle-dependent manner. Mass spectrometry identified two cofactors that bind MET-2: LIN-65, a highly unstructured protein, and ARLE-14, a conserved GTPase effector. All three factors colocalize in heterochromatic foci. Ablation of lin-65, but not arle-14, mislocalizes and destabilizes MET-2, resulting in decreased H3K9 dimethylation, dispersion of heterochromatic foci, and derepression of MET-2 targets. Mutation of met-2 or lin-65 also disrupts the perinuclear anchoring of genomic heterochromatin. Loss of LIN-65, like that of MET-2, compromises temperature stress resistance and germline integrity, which are both linked to promiscuous repeat transcription and gene expression.
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Affiliation(s)
- Colin E Delaney
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Stephen P Methot
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Micol Guidi
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Iskra Katic
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Faculty of Natural Sciences, Basel, Switzerland
| | - Jan Padeken
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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23
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Yang B, Xu X, Russell L, Sullenberger MT, Yanowitz JL, Maine EM. A DNA repair protein and histone methyltransferase interact to promote genome stability in the Caenorhabditis elegans germ line. PLoS Genet 2019; 15:e1007992. [PMID: 30794539 PMCID: PMC6402707 DOI: 10.1371/journal.pgen.1007992] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 03/06/2019] [Accepted: 01/28/2019] [Indexed: 12/29/2022] Open
Abstract
Histone modifications regulate gene expression and chromosomal events, yet how histone-modifying enzymes are targeted is poorly understood. Here we report that a conserved DNA repair protein, SMRC-1, associates with MET-2, the C. elegans histone methyltransferase responsible for H3K9me1 and me2 deposition. We used molecular, genetic, and biochemical methods to investigate the biological role of SMRC-1 and to explore its relationship with MET-2. SMRC-1, like its mammalian ortholog SMARCAL1, provides protection from DNA replication stress. SMRC-1 limits accumulation of DNA damage and promotes germline and embryonic viability. MET-2 and SMRC-1 localize to mitotic and meiotic germline nuclei, and SMRC-1 promotes an increase in MET-2 abundance in mitotic germline nuclei upon replication stress. In the absence of SMRC-1, germline H3K9me2 generally decreases after multiple generations at high culture temperature. Genetic data are consistent with MET-2 and SMRC-1 functioning together to limit replication stress in the germ line and in parallel to promote other germline processes. We hypothesize that loss of SMRC-1 activity causes chronic replication stress, in part because of insufficient recruitment of MET-2 to nuclei.
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Affiliation(s)
- Bing Yang
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Xia Xu
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Logan Russell
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | | | - Judith L. Yanowitz
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Eleanor M. Maine
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
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24
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Yang F, Quan Z, Huang H, He M, Liu X, Cai T, Xi R. Ovaries absent links dLsd1 to HP1a for local H3K4 demethylation required for heterochromatic gene silencing. eLife 2019; 8:40806. [PMID: 30648969 PMCID: PMC6335052 DOI: 10.7554/elife.40806] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 12/20/2018] [Indexed: 12/30/2022] Open
Abstract
Heterochromatin Protein 1 (HP1) is a conserved chromosomal protein in eukaryotic cells that has a major role in directing heterochromatin formation, a process that requires co-transcriptional gene silencing mediated by small RNAs and their associated argonaute proteins. Heterochromatin formation requires erasing the active epigenetic mark, such as H3K4me2, but the molecular link between HP1 and H3K4 demethylation remains unclear. In a fertility screen in female Drosophila, we identified ovaries absent (ova), which functions in the stem cell niche, downstream of Piwi, to support germline stem cell differentiation. Moreover, ova acts as a suppressor of position effect variegation, and is required for silencing telomeric transposons in the germline. Biochemically, Ova acts to link the H3K4 demethylase dLsd1 to HP1a for local histone modifications. Therefore, our study provides a molecular connection between HP1a and local H3K4 demethylation during HP1a-mediated gene silencing that is required for ovary development, transposon silencing, and heterochromatin formation. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter). The complete set of genetic material within a cell is known as a genome. The genomes of human and other animal cells have regions of active genes interspersed with ‘dark’ regions known as heterochromatin, which contain genes and other types of genetic material that have been inactivated. Heterochromatin commonly contains sections of genetic material known as transposons. When a transposon is active it is able to move around the genome, therefore, inactivating (or ‘silencing’) transposons helps to maintain the integrity of the genetic material in a cell. It is particularly important to silence transposons in the stem cells that produce sperm and egg cells – known as germline stem cells – to ensure genetic information is faithfully passed on to the next generation. A protein called HP1a plays a major role in directing where heterochromatin forms in the genome. This process requires an enzyme called dLsd1 to remove a small tag from the genetic material but it is not clear how HP1a regulates the activity of dLsd1. To address this question, Yang et al. studied how egg cells form in fruit flies, which are often used as models of animal biology in experiments. The team screened a population of fruit flies that carried mutations in many different genes to identify genes that affect the fertility of female flies. This revealed a gene named as ovaries absent (or ova for short) is required for egg cells to form. In germline stem cells ova silences transposons and in the surrounding tissue it represses a specific signal that usually maintains stem cells to allow the stem cells to divide to make egg cells. Further experiments using biochemical techniques found that the protein encoded by ova acts as a bridge to bring HP1a and dLsd1 together to silence genes in heterochromatin. The next step would be to identify the functional counterpart of the ova gene in mammals, including humans, which may help to discover causes of infertility and develop new fertility treatment.
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Affiliation(s)
- Fu Yang
- National Institute of Biological Sciences, Beijing, China
| | - Zhenghui Quan
- National Institute of Biological Sciences, Beijing, China
| | - Huanwei Huang
- National Institute of Biological Sciences, Beijing, China
| | - Minghui He
- National Institute of Biological Sciences, Beijing, China
| | - Xicheng Liu
- National Institute of Biological Sciences, Beijing, China
| | - Tao Cai
- National Institute of Biological Sciences, Beijing, China
| | - Rongwen Xi
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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25
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Novel roles of Drosophila FUS and Aub responsible for piRNA biogenesis in neuronal disorders. Brain Res 2018; 1708:207-219. [PMID: 30578769 DOI: 10.1016/j.brainres.2018.12.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 11/16/2018] [Accepted: 12/19/2018] [Indexed: 02/08/2023]
Abstract
piRNAs, small non-coding RNAs, were considered to be restricted to germline cells. Although they have recently been detected in somatic cells including neurons, it remains unclear how piRNA biogenesis is involved in neuronal diseases. We herein examined the possible roles of Aubergine (Aub), a Piwi-family protein (PIWI) responsible for piRNA biogenesis, in the neuronal disorders, using the Cabeza (Caz) knockdown Drosophila. Caz is a Drosophila homologue of FUS, which is one of the genes causing amyotrophic lateral sclerosis (ALS). Aub overexpression enhanced the mobility defects accompanied by anatomical defects in motoneurons at neuromuscular junctions induced by the neuron-specific knockdown of Caz. In order to elucidate the underlying mechanisms, we examined pre-piRNA and mature-size piRNA levels under these conditions. qRT-PCR and RNA-seq analyses revealed that the Caz knockdown increased pre-piRNA levels, but reduced mature-size piRNA levels in the central nervous system (CNS), suggesting a role in the pre-piRNAs production. Aub overexpression did not increase mature-size piRNA levels. These results suggest that the accumulated pre-piRNAs are abnormal abortive pre-piRNAs that cannot be further processed by slicers, including Aub. We also demonstrated a relationship between Caz and pre-piRNAs in the CNS by RNA immunoprecipitation. Aub overexpression induced the abnormal cytoplasmic localization of Caz. Based on these results, we propose a model in which Caz knockdown-induced abnormal pre-piRNAs associate with Caz, then translocate and accumulate in the cytoplasm, a process that may be mediated by Aub. The novel roles for Caz and Aub demonstrated herein using the Caz-knockdown fly will contribute to a deeper understanding of the pathogenesis of ALS.
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26
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Riddle NC, Elgin SCR. The Drosophila Dot Chromosome: Where Genes Flourish Amidst Repeats. Genetics 2018; 210:757-772. [PMID: 30401762 PMCID: PMC6218221 DOI: 10.1534/genetics.118.301146] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/17/2018] [Indexed: 11/18/2022] Open
Abstract
The F element of the Drosophila karyotype (the fourth chromosome in Drosophila melanogaster) is often referred to as the "dot chromosome" because of its appearance in a metaphase chromosome spread. This chromosome is distinct from other Drosophila autosomes in possessing both a high level of repetitious sequences (in particular, remnants of transposable elements) and a gene density similar to that found in the other chromosome arms, ∼80 genes distributed throughout its 1.3-Mb "long arm." The dot chromosome is notorious for its lack of recombination and is often neglected as a consequence. This and other features suggest that the F element is packaged as heterochromatin throughout. F element genes have distinct characteristics (e.g, low codon bias, and larger size due both to larger introns and an increased number of exons), but exhibit expression levels comparable to genes found in euchromatin. Mapping experiments show the presence of appropriate chromatin modifications for the formation of DNaseI hypersensitive sites and transcript initiation at the 5' ends of active genes, but, in most cases, high levels of heterochromatin proteins are observed over the body of these genes. These various features raise many interesting questions about the relationships of chromatin structures with gene and chromosome function. The apparent evolution of the F element as an autosome from an ancestral sex chromosome also raises intriguing questions. The findings argue that the F element is a unique chromosome that occupies its own space in the nucleus. Further study of the F element should provide new insights into chromosome structure and function.
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Affiliation(s)
- Nicole C Riddle
- Department of Biology, The University of Alabama at Birmingham, Alabama 35294
| | - Sarah C R Elgin
- Department of Biology, Washington University in St. Louis, Missouri 63130
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The H3K9 methyltransferase SETDB1 maintains female identity in Drosophila germ cells. Nat Commun 2018; 9:4155. [PMID: 30297796 PMCID: PMC6175928 DOI: 10.1038/s41467-018-06697-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 09/19/2018] [Indexed: 12/17/2022] Open
Abstract
The preservation of germ cell sexual identity is essential for gametogenesis. Here we show that H3K9me3-mediated gene silencing is integral to female fate maintenance in Drosophila germ cells. Germ cell specific loss of the H3K9me3 pathway members, the H3K9 methyltransferase SETDB1, WDE, and HP1a, leads to ectopic expression of genes, many of which are normally expressed in testis. SETDB1 controls the accumulation of H3K9me3 over a subset of these genes without spreading into neighboring loci. At phf7, a regulator of male germ cell sexual fate, the H3K9me3 peak falls over the silenced testis-specific transcription start site. Furthermore, H3K9me3 recruitment to phf7 and repression of testis-specific transcription is dependent on the female sex determination gene Sxl. Thus, female identity is secured by an H3K9me3 epigenetic pathway in which Sxl is the upstream female-specific regulator, SETDB1 is the required chromatin writer, and phf7 is one of the critical SETDB1 target genes. Epigenetic regulation is critical for the maintenance of germ cell identity. Here the authors show that H3K9me3-mediated gene silencing is critical for repression of testis-specific transcription in Drosophila female germ cells, indicating H3K9me3 maintains female germ cell sexual identity.
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Yamashiro H, Siomi MC. PIWI-Interacting RNA in Drosophila: Biogenesis, Transposon Regulation, and Beyond. Chem Rev 2017; 118:4404-4421. [PMID: 29281264 DOI: 10.1021/acs.chemrev.7b00393] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
PIWI-interacting RNAs (piRNAs) are germline-enriched small RNAs that control transposons to maintain genome integrity. To achieve this, upon being processed from piRNA precursors, most of which are transcripts of intergenic piRNA clusters, piRNAs bind PIWI proteins, germline-specific Argonaute proteins, to form effector complexes. The mechanism of this piRNA-mediated transposon silencing pathway is fundamentally similar to that of siRNA/miRNA-dependent gene silencing in that a small RNA guides its partner Argonaute protein to target gene transcripts for repression via RNA-RNA base pairing. However, the uniqueness of this piRNA pathway has emerged through intensive genetic, biochemical, bioinformatic, and structural investigations. Here, we review the studies that elucidated the piRNA pathway, mainly in Drosophila, by describing both historical and recent progress. Studies in other species that have made important contributions to the field are also described.
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Affiliation(s)
- Haruna Yamashiro
- Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Tokyo 113-0032 , Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science , The University of Tokyo , Tokyo 113-0032 , Japan
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29
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Timms RT, Tchasovnikarova IA, Antrobus R, Dougan G, Lehner PJ. ATF7IP-Mediated Stabilization of the Histone Methyltransferase SETDB1 Is Essential for Heterochromatin Formation by the HUSH Complex. Cell Rep 2017; 17:653-659. [PMID: 27732843 PMCID: PMC5081395 DOI: 10.1016/j.celrep.2016.09.050] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/19/2016] [Accepted: 09/15/2016] [Indexed: 12/27/2022] Open
Abstract
The histone methyltransferase SETDB1 plays a central role in repressive chromatin processes, but the functional requirement for its binding partner ATF7IP has remained enigmatic. Here, we show that ATF7IP is essential for SETDB1 stability: nuclear SETDB1 protein is degraded by the proteasome upon ablation of ATF7IP. As a result, ATF7IP is critical for repression that requires H3K9 trimethylation by SETDB1, including transgene silencing by the HUSH complex. Furthermore, we show that loss of ATF7IP phenocopies loss of SETDB1 in genome-wide assays. ATF7IP and SETDB1 knockout cells exhibit near-identical defects in the global deposition of H3K9me3, which results in similar dysregulation of the transcriptome. Overall, these data identify a critical functional role for ATF7IP in heterochromatin formation by regulating SETDB1 abundance in the nucleus. The SETDB1-interacting partner ATF7IP is critical for HUSH-mediated silencing ATF7IP shields SETDB1 from proteasomal degradation in the nucleus Loss of ATF7IP phenocopies loss of SETDB1 in genome-wide assays
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Affiliation(s)
- Richard T Timms
- Department of Medicine, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Iva A Tchasovnikarova
- Department of Medicine, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Robin Antrobus
- Department of Medicine, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Paul J Lehner
- Department of Medicine, Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK.
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Czech B, Hannon GJ. One Loop to Rule Them All: The Ping-Pong Cycle and piRNA-Guided Silencing. Trends Biochem Sci 2016; 41:324-337. [PMID: 26810602 PMCID: PMC4819955 DOI: 10.1016/j.tibs.2015.12.008] [Citation(s) in RCA: 300] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 01/06/2023]
Abstract
The PIWI-interacting RNA (piRNA) pathway is a conserved defense mechanism that protects the genetic information of animal germ cells from the deleterious effects of molecular parasites, such as transposons. Discovered nearly a decade ago, this small RNA silencing system comprises PIWI-clade Argonaute proteins and their associated RNA-binding partners, the piRNAs. In this review, we highlight recent work that has advanced our understanding of how piRNAs preserve genome integrity across generations. We discuss the mechanism of piRNA biogenesis, give an overview of common themes as well as differences in piRNA-mediated silencing between species, and end by highlighting known and emerging functions of piRNAs.
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Affiliation(s)
- Benjamin Czech
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
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31
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Thompson PJ, Dulberg V, Moon KM, Foster LJ, Chen C, Karimi MM, Lorincz MC. hnRNP K coordinates transcriptional silencing by SETDB1 in embryonic stem cells. PLoS Genet 2015; 11:e1004933. [PMID: 25611934 PMCID: PMC4303303 DOI: 10.1371/journal.pgen.1004933] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 12/02/2014] [Indexed: 01/23/2023] Open
Abstract
Retrotransposition of endogenous retroviruses (ERVs) poses a substantial threat to genome stability. Transcriptional silencing of a subset of these parasitic elements in early mouse embryonic and germ cell development is dependent upon the lysine methyltransferase SETDB1, which deposits H3K9 trimethylation (H3K9me3) and the co-repressor KAP1, which binds SETDB1 when SUMOylated. Here we identified the transcription co-factor hnRNP K as a novel binding partner of the SETDB1/KAP1 complex in mouse embryonic stem cells (mESCs) and show that hnRNP K is required for ERV silencing. RNAi-mediated knockdown of hnRNP K led to depletion of H3K9me3 at ERVs, concomitant with de-repression of proviral reporter constructs and specific ERV subfamilies, as well as a cohort of germline-specific genes directly targeted by SETDB1. While hnRNP K recruitment to ERVs is dependent upon KAP1, SETDB1 binding at these elements requires hnRNP K. Furthermore, an intact SUMO conjugation pathway is necessary for SETDB1 recruitment to proviral chromatin and depletion of hnRNP K resulted in reduced SUMOylation at ERVs. Taken together, these findings reveal a novel regulatory hierarchy governing SETDB1 recruitment and in turn, transcriptional silencing in mESCs. Retroelements, including endogenous retroviruses (ERVs), pose a significant threat to genome stability. In mouse embryonic stem (ES) cells, the enzyme SETDB1 safeguards the genome against transcription of specific ERVs by depositing a repressive mark H3K9 trimethylation (H3K9me3). Although SETDB1 is recruited to ERVs by its binding partner KAP1, the molecular basis of this silencing pathway is not clear. Using biochemical and genetic approaches, we identified hnRNP K as a novel component of this silencing pathway that facilitates the recruitment of SETDB1 to ERVs to promote their repression. HnRNP K binds to ERV sequences via KAP1 and subsequently promotes SETDB1 binding. Together, our results reveal a novel function for hnRNP K in transcriptional silencing of ERVs and demonstrate a new regulatory mechanism governing the deposition of H3K9me3 by SETDB1 in ES cells.
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Affiliation(s)
- Peter J. Thompson
- Life Sciences Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vered Dulberg
- Life Sciences Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kyung-Mee Moon
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Leonard J. Foster
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carol Chen
- Life Sciences Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mohammad M. Karimi
- Life Sciences Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew C. Lorincz
- Life Sciences Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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32
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Iovino N. Drosophila epigenome reorganization during oocyte differentiation and early embryogenesis. Brief Funct Genomics 2014; 13:246-53. [PMID: 24665128 DOI: 10.1093/bfgp/elu007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In sexually reproducing organisms, propagation of the species relies on specialized haploid cells (gametes) produced by germ cells. During their development in the adult germline, the female and male gametes undergo a complex differentiation process that requires transcriptional regulation and chromatin reorganization. After fertilization, the gametes then go through extensive epigenetic reprogramming, which resets the cells to a totipotent state essential for the development of the embryo. Several histone modifications characterize distinct developmental stages of gamete formation and early embryonic development, but it is unknown whether these modifications have any physiological role. Furthermore, accumulating evidence suggests that environmentally induced chromatin changes can be inherited, yet the mechanisms underlying zygotic inheritance of the gamete epigenome remain unclear. This review gives a brief overview of the mechanisms of transgenerational epigenetic inheritance and examines the function of epigenetics during oogenesis and early embryogenesis with a focus on histone posttranslational modifications.
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33
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Stathopoulos S, Neafsey DE, Lawniczak MKN, Muskavitch MAT, Christophides GK. Genetic dissection of Anopheles gambiae gut epithelial responses to Serratia marcescens. PLoS Pathog 2014; 10:e1003897. [PMID: 24603764 PMCID: PMC3946313 DOI: 10.1371/journal.ppat.1003897] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 12/09/2013] [Indexed: 12/29/2022] Open
Abstract
Genetic variation in the mosquito Anopheles gambiae profoundly influences its ability to transmit malaria. Mosquito gut bacteria are shown to influence the outcome of infections with Plasmodium parasites and are also thought to exert a strong drive on genetic variation through natural selection; however, a link between antibacterial effects and genetic variation is yet to emerge. Here, we combined SNP genotyping and expression profiling with phenotypic analyses of candidate genes by RNAi-mediated silencing and 454 pyrosequencing to investigate this intricate biological system. We identified 138 An. gambiae genes to be genetically associated with the outcome of Serratia marcescens infection, including the peptidoglycan recognition receptor PGRPLC that triggers activation of the antibacterial IMD/REL2 pathway and the epidermal growth factor receptor EGFR. Silencing of three genes encoding type III fibronectin domain proteins (FN3Ds) increased the Serratia load and altered the gut microbiota composition in favor of Enterobacteriaceae. These data suggest that natural genetic variation in immune-related genes can shape the bacterial population structure of the mosquito gut with high specificity. Importantly, FN3D2 encodes a homolog of the hypervariable pattern recognition receptor Dscam, suggesting that pathogen-specific recognition may involve a broader family of immune factors. Additionally, we showed that silencing the gene encoding the gustatory receptor Gr9 that is also associated with the Serratia infection phenotype drastically increased Serratia levels. The Gr9 antibacterial activity appears to be related to mosquito feeding behavior and to mostly rely on changes of neuropeptide F expression, together suggesting a behavioral immune response following Serratia infection. Our findings reveal that the mosquito response to oral Serratia infection comprises both an epithelial and a behavioral immune component. In malaria vector mosquitoes, the presence of bacteria and malaria parasites is tightly linked. Bacteria that are part of the mosquito gut ecosystem are critical modulators of the immune response elicited during infection with malaria parasites. Furthermore, responses against oral bacterial infections can affect malaria parasites. Here, we combined mosquito gut infections with the enterobacterium Serratia marcescens with genome-wide discovery and phenotypic analysis of genes involved in antibacterial responses to characterize molecular processes that control gut bacterial infections thus possibly affecting the mosquito susceptibility to infection by malaria parasites. Our data reveal complex genetic networks controlling the gut bacterial infection load and ecosystem homeostasis. These networks appear to exhibit much higher specificity toward specific classes of bacteria than previously thought and include behavioral response circuits involved in antibacterial immunity.
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Affiliation(s)
| | | | | | | | - George K. Christophides
- Department of Life Sciences, Imperial College London, London, United Kingdom
- The Cyprus Institute, Nicosia, Cyprus
- * E-mail:
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34
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Chorion formation in panoistic ovaries requires windei and trimethylation of histone 3 lysine 9. Exp Cell Res 2014; 320:46-53. [DOI: 10.1016/j.yexcr.2013.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/09/2013] [Accepted: 07/10/2013] [Indexed: 02/05/2023]
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35
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Muerdter F, Guzzardo PM, Gillis J, Luo Y, Yu Y, Chen C, Fekete R, Hannon GJ. A genome-wide RNAi screen draws a genetic framework for transposon control and primary piRNA biogenesis in Drosophila. Mol Cell 2013; 50:736-48. [PMID: 23665228 DOI: 10.1016/j.molcel.2013.04.006] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 04/04/2013] [Accepted: 04/05/2013] [Indexed: 01/19/2023]
Abstract
A large fraction of our genome consists of mobile genetic elements. Governing transposons in germ cells is critically important, and failure to do so compromises genome integrity, leading to sterility. In animals, the piRNA pathway is the key to transposon constraint, yet the precise molecular details of how piRNAs are formed and how the pathway represses mobile elements remain poorly understood. In an effort to identify general requirements for transposon control and components of the piRNA pathway, we carried out a genome-wide RNAi screen in Drosophila ovarian somatic sheet cells. We identified and validated 87 genes necessary for transposon silencing. Among these were several piRNA biogenesis factors. We also found CG3893 (asterix) to be essential for transposon silencing, most likely by contributing to the effector step of transcriptional repression. Asterix loss leads to decreases in H3K9me3 marks on certain transposons but has no effect on piRNA levels.
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Affiliation(s)
- Felix Muerdter
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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36
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37
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Figueiredo MLA, Philip P, Stenberg P, Larsson J. HP1a recruitment to promoters is independent of H3K9 methylation in Drosophila melanogaster. PLoS Genet 2012; 8:e1003061. [PMID: 23166515 PMCID: PMC3499360 DOI: 10.1371/journal.pgen.1003061] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 09/19/2012] [Indexed: 11/19/2022] Open
Abstract
Heterochromatin protein 1 (HP1) proteins, recognized readers of the heterochromatin mark methylation of histone H3 lysine 9 (H3K9me), are important regulators of heterochromatin-mediated gene silencing and chromosome structure. In Drosophila melanogaster three histone lysine methyl transferases (HKMTs) are associated with the methylation of H3K9: Su(var)3-9, Setdb1, and G9a. To probe the dependence of HP1a binding on H3K9me, its dependence on these three HKMTs, and the division of labor between the HKMTs, we have examined correlations between HP1a binding and H3K9me patterns in wild type and null mutants of these HKMTs. We show here that Su(var)3-9 controls H3K9me-dependent binding of HP1a in pericentromeric regions, while Setdb1 controls it in cytological region 2L:31 and (together with POF) in chromosome 4. HP1a binds to the promoters and within bodies of active genes in these three regions. More importantly, however, HP1a binding at promoters of active genes is independent of H3K9me and POF. Rather, it is associated with heterochromatin protein 2 (HP2) and open chromatin. Our results support a hypothesis in which HP1a nucleates with high affinity independently of H3K9me in promoters of active genes and then spreads via H3K9 methylation and transient looping contacts with those H3K9me target sites. HP1 is a key protein in heterochromatin and epigenetic silencing, a phenomenon involving chromatin condensation. It is generally accepted that HP1 forms a dimer that links two adjacent nucleosomes through interactions with histone 3 methylated at lysine 9 (H3K9me). Since HP1 also interacts with the histone lysine methyltransferases (HKMTs) generating this modification, histone H3 becomes methylated and HP1 spreading is propagated. Here, we show that HP1a in Drosophila binds to promoters of active genes on chromosome 4 and pericentromeric regions. In contrast to current dogma, this binding is independent of H3K9me. In the presence of the HKMTs and H3K9me, HP1a is also enriched within the bodies of the bound genes. These findings shed new light on the role of HP1a and the epigenetic nature of this chromatin mark. We propose that HP1a interacts independently of H3K9me with the nucleosome with high affinity, probably via the H3 histone-fold. This interaction is followed by a more transient interaction between HP1a and H3K9me, which results in spreading of the HP1a enrichment into gene bodies. Overall, the presented results and hypothesized model provide an explanation for this epigenetic mark and possibly more general insights into the relationships between chromo-domain proteins and methylated histones.
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Affiliation(s)
| | - Philge Philip
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Per Stenberg
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Jan Larsson
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- * E-mail:
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38
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Takács S, Biessmann H, Reddy HM, Mason JM, Török T. Protein interactions on telomeric retrotransposons in Drosophila. Int J Biol Sci 2012; 8:1055-61. [PMID: 22949888 PMCID: PMC3432853 DOI: 10.7150/ijbs.4460] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 07/04/2012] [Indexed: 12/02/2022] Open
Abstract
Telomere length in Drosophila is maintained by targeted transposition of three non-LTR retrotransposons: HeT-A, TART and TAHRE (HTT), but understanding the regulation of this process is hindered by our poor knowledge of HTT associated proteins. We have identified new protein components of the HTT array: Chromator (Chro), the TRF2/DREF complex and the sumoylation machinery. Chro was localized on telomeric HTT arrays by immunostaining, where it may interact with Prod directly, as indicated by yeast two-hybrid interaction, co-IP, and colocalization on polytene chromosomes. The TRF2/DREF complex may promote the open structure of HTT chromatin. The protein interactions controlling HTT chromatin structure and telomere length may be modulated by sumoylation.
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Affiliation(s)
- Sándor Takács
- Department of Genetics, University of Szeged, H-6701 Szeged, Hungary
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Wang X, Pan L, Wang S, Zhou J, McDowell W, Park J, Haug J, Staehling K, Tang H, Xie T. Histone H3K9 trimethylase Eggless controls germline stem cell maintenance and differentiation. PLoS Genet 2011; 7:e1002426. [PMID: 22216012 PMCID: PMC3245301 DOI: 10.1371/journal.pgen.1002426] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 11/04/2011] [Indexed: 11/18/2022] Open
Abstract
Epigenetic regulation plays critical roles in the regulation of cell proliferation, fate determination, and survival. It has been shown to control self-renewal and lineage differentiation of embryonic stem cells. However, epigenetic regulation of adult stem cell function remains poorly defined. Drosophila ovarian germline stem cells (GSCs) are a productive adult stem cell system for revealing regulatory mechanisms controlling self-renewal and differentiation. In this study, we show that Eggless (Egg), a H3K9 methyltransferase in Drosophila, is required in GSCs for controlling self-renewal and in escort cells for regulating germ cell differentiation. egg mutant ovaries primarily exhibit germ cell differentiation defects in young females and gradually lose GSCs with time, indicating that Egg regulates both germ cell maintenance and differentiation. Marked mutant egg GSCs lack expression of trimethylated H3K9 (H3k9me3) and are rapidly lost from the niche, but their mutant progeny can still differentiate into 16-cell cysts, indicating that Egg is required intrinsically to control GSC self-renewal but not differentiation. Interestingly, BMP-mediated transcriptional repression of differentiation factor bam in marked egg mutant GSCs remains normal, indicating that Egg is dispensable for BMP signaling in GSCs. Normally, Bam and Bgcn interact with each other to promote GSC differentiation. Interestingly, marked double mutant egg bgcn GSCs are still lost, but their progeny are able to differentiate into 16-cell cysts though bgcn mutant GSCs normally do not differentiate, indicating that Egg intrinsically controls GSC self-renewal through repressing a Bam/Bgcn-independent pathway. Surprisingly, RNAi-mediated egg knockdown in escort cells leads to their gradual loss and a germ cell differentiation defect. The germ cell differentiation defect is at least in part attributed to an increase in BMP signaling in the germ cell differentiation niche. Therefore, this study has revealed the essential roles of histone H3K9 trimethylation in controlling stem cell maintenance and differentiation through distinct mechanisms.
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Affiliation(s)
- Xiaoxi Wang
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Lei Pan
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- The Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Su Wang
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Anatomy and Cell Biology, University of Kansas School of Medicine, Kansas City, Kansas, United States of America
| | - Jian Zhou
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - William McDowell
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Jungeun Park
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Jeff Haug
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Karen Staehling
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Hong Tang
- The Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ting Xie
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Anatomy and Cell Biology, University of Kansas School of Medicine, Kansas City, Kansas, United States of America
- * E-mail:
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40
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Epigenetic regulation of germ cell differentiation. Curr Opin Cell Biol 2010; 22:737-43. [PMID: 20951019 DOI: 10.1016/j.ceb.2010.09.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 08/13/2010] [Accepted: 09/16/2010] [Indexed: 11/22/2022]
Abstract
Germ cells and somatic cells have the identical genome. However, unlike the mortal fate of somatic cells, germ cells have the unique ability to differentiate into gametes that retain totipotency and produce an entire organism upon fertilization. The processes by which germ cells differentiate into gametes, and those by which gametes become embryos, involve dramatic cellular differentiation accompanied by drastic changes in gene expression, which are tightly regulated by genetic circuitries as well as epigenetic mechanisms. Epigenetic regulation refers to heritable changes in gene expression that are not due to changes in primary DNA sequence. The past decade has witnessed an ever-increasing understanding of epigenetic regulation in many different cell types/tissues during embryonic development and adult homeostasis. In this review, we focus on recent discoveries of epigenetic regulation of germ cell differentiation in various metazoan model organisms, including worms, flies, and mammals.
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