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Özcan I, Tursun B. Identifying Molecular Roadblocks for Transcription Factor-Induced Cellular Reprogramming In Vivo by Using C. elegans as a Model Organism. J Dev Biol 2023; 11:37. [PMID: 37754839 PMCID: PMC10531806 DOI: 10.3390/jdb11030037] [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: 06/21/2023] [Revised: 08/18/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023] Open
Abstract
Generating specialized cell types via cellular transcription factor (TF)-mediated reprogramming has gained high interest in regenerative medicine due to its therapeutic potential to repair tissues and organs damaged by diseases or trauma. Organ dysfunction or improper tissue functioning might be restored by producing functional cells via direct reprogramming, also known as transdifferentiation. Regeneration by converting the identity of available cells in vivo to the desired cell fate could be a strategy for future cell replacement therapies. However, the generation of specific cell types via reprogramming is often restricted due to cell fate-safeguarding mechanisms that limit or even block the reprogramming of the starting cell type. Nevertheless, efficient reprogramming to generate homogeneous cell populations with the required cell type's proper molecular and functional identity is critical. Incomplete reprogramming will lack therapeutic potential and can be detrimental as partially reprogrammed cells may acquire undesired properties and develop into tumors. Identifying and evaluating molecular barriers will improve reprogramming efficiency to reliably establish the target cell identity. In this review, we summarize how using the nematode C. elegans as an in vivo model organism identified molecular barriers of TF-mediated reprogramming. Notably, many identified molecular factors have a high degree of conservation and were subsequently shown to block TF-induced reprogramming of mammalian cells.
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Affiliation(s)
- Ismail Özcan
- Department of Biology, Institute of Cell and Systems Biology of Animals, University of Hamburg, 20146 Hamburg, Germany
| | - Baris Tursun
- Department of Biology, Institute of Cell and Systems Biology of Animals, University of Hamburg, 20146 Hamburg, Germany
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2
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Trivedi S, Blazícková J, Silva N. PARG and BRCA1-BARD1 cooperative function regulates DNA repair pathway choice during gametogenesis. Nucleic Acids Res 2022; 50:12291-12308. [PMID: 36478097 PMCID: PMC9757042 DOI: 10.1093/nar/gkac1153] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/09/2022] [Accepted: 11/18/2022] [Indexed: 12/14/2022] Open
Abstract
Meiotic chromosome segregation relies on programmed DNA double-strand break induction. These are in turn repaired by homologous recombination, generating physical attachments between the parental chromosomes called crossovers. A subset of breaks yields recombinant outcomes, while crossover-independent mechanisms repair the majority of lesions. The balance between different repair pathways is crucial to ensure genome integrity. We show that Caenorhabditis elegans BRC-1/BRCA1-BRD-1/BARD1 and PARG-1/PARG form a complex in vivo, essential for accurate DNA repair in the germline. Simultaneous depletion of BRC-1 and PARG-1 causes synthetic lethality due to reduced crossover formation and impaired break repair, evidenced by hindered RPA-1 removal and presence of aberrant chromatin bodies in diakinesis nuclei, whose formation depends on spo-11 function. These factors undergo a similar yet independent loading in developing oocytes, consistent with operating in different pathways. Abrogation of KU- or Theta-mediated end joining elicits opposite effects in brc-1; parg-1 doubles, suggesting a profound impact in influencing DNA repair pathway choice by BRC-1-PARG-1. Importantly, lack of PARG-1 catalytic activity suppresses untimely accumulation of RAD-51 foci in brc-1 mutants but is only partially required for fertility. Our data show that BRC-1/BRD-1-PARG-1 joint function is essential for genome integrity in meiotic cells by regulating multiple DNA repair pathways.
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Affiliation(s)
- Shalini Trivedi
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Jitka Blazícková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Nicola Silva
- To whom correspondence should be addressed. Tel: +420 549 49 8033;
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3
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Zaghet N, Madsen K, Rossi F, Perez DF, Amendola PG, Demharter S, Pfisterer U, Khodosevich K, Pasini D, Salcini AE. Coordinated maintenance of H3K36/K27 methylation by histone demethylases preserves germ cell identity and immortality. Cell Rep 2021; 37:110050. [PMID: 34818537 PMCID: PMC8640224 DOI: 10.1016/j.celrep.2021.110050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/18/2021] [Accepted: 11/02/2021] [Indexed: 12/01/2022] Open
Abstract
Germ cells have evolved unique mechanisms to ensure the transmission of genetically and nongenetically encoded information, whose alteration compromises germ cell immortality. Chromatin factors play fundamental roles in these mechanisms. H3K36 and H3K27 methyltransferases shape and propagate a pattern of histone methylation essential for C. elegans germ cell maintenance, but the role of respective histone demethylases remains unexplored. Here, we show that jmjd-5 regulates H3K36me2 and H3K27me3 levels, preserves germline immortality, and protects germ cell identity by controlling gene expression. The transcriptional and biological effects of jmjd-5 loss can be hindered by the removal of H3K27demethylases, indicating that H3K36/K27 demethylases act in a transcriptional framework and promote the balance between H3K36 and H3K27 methylation required for germ cell immortality. Furthermore, we find that in wild-type, but not in jmjd-5 mutants, alterations of H3K36 methylation and transcription occur at high temperature, suggesting a role for jmjd-5 in adaptation to environmental changes. jmjd-5 is required for germ cell immortality at high temperature jmjd-5 sustains the expression of germline genes and represses somatic fate Mutations in jmjd-5 result in a global increase of H3K36me2 and H3K27me3 Ablation of H3K27 demethylases counteracts the effects of jmjd-5 mutations
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Affiliation(s)
- Nico Zaghet
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Katrine Madsen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Federico Rossi
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Daniel Fernandez Perez
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Pier Giorgio Amendola
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Samuel Demharter
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Ulrich Pfisterer
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Diego Pasini
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy; Department of Health Sciences, University of Milan, Via A. di Rudini 8, 20142 Milan, Italy
| | - Anna Elisabetta Salcini
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark.
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McManus CE, Mazzetto M, Wei G, Han M, Reinke V. The zinc-finger protein OEF-1 stabilizes histone modification patterns and promotes efficient splicing in the C. elegans germ line. G3-GENES GENOMES GENETICS 2021; 11:6370151. [PMID: 34519784 PMCID: PMC8664474 DOI: 10.1093/g3journal/jkab329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/07/2021] [Indexed: 12/03/2022]
Abstract
To ensure stable transmission of genetic information to the next generation, germ cells frequently silence sex chromosomes, as well as autosomal loci that promote inappropriate differentiation programs. In Caenorhabditis elegans, silenced and active genomic domains are established in germ cells by the histone modification complexes MES-2/3/6 and MES-4, which promote silent and active chromatin states, respectively. These states are generally mutually exclusive and modulation of one state influences the pattern of the other. Here, we identify the zinc-finger protein OEF-1 as a novel modifier of this epigenetic balance in the C. elegans germline. Loss of oef-1 genetically enhances mes mutant phenotypes. Moreover, OEF-1 binding correlates with the active modification H3K36me3 and sustains H3K36me3 levels in the absence of MES-4 activity. OEF-1 also promotes efficient mRNA splicing activity, a process that is influenced by H3K36me3 levels. Finally, OEF-1 limits deposition of the silencing modification H3K27me3 on the X chromosome and at repressed autosomal loci. We propose that OEF-1 might act as an intermediary to mediate the downstream effects of H3K36me3 that promote transcript integrity, and indirectly affect gene silencing as a consequence.
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Affiliation(s)
- Catherine E McManus
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mariateresa Mazzetto
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Guifeng Wei
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Mei Han
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Valerie Reinke
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
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5
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Anderson EC, Frankino PA, Higuchi-Sanabria R, Yang Q, Bian Q, Podshivalova K, Shin A, Kenyon C, Dillin A, Meyer BJ. X Chromosome Domain Architecture Regulates Caenorhabditis elegans Lifespan but Not Dosage Compensation. Dev Cell 2019; 51:192-207.e6. [PMID: 31495695 DOI: 10.1016/j.devcel.2019.08.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/26/2019] [Accepted: 08/06/2019] [Indexed: 12/21/2022]
Abstract
Mechanisms establishing higher-order chromosome structures and their roles in gene regulation are elusive. We analyzed chromosome architecture during nematode X chromosome dosage compensation, which represses transcription via a dosage-compensation condensin complex (DCC) that binds hermaphrodite Xs and establishes megabase-sized topologically associating domains (TADs). We show that DCC binding at high-occupancy sites (rex sites) defines eight TAD boundaries. Single rex deletions disrupted boundaries, and single insertions created new boundaries, demonstrating that a rex site is necessary and sufficient to define DCC-dependent boundary locations. Deleting eight rex sites (8rexΔ) recapitulated TAD structure of DCC mutants, permitting analysis when chromosome-wide domain architecture was disrupted but most DCC binding remained. 8rexΔ animals exhibited no changes in X expression and lacked dosage-compensation mutant phenotypes. Hence, TAD boundaries are neither the cause nor the consequence of DCC-mediated gene repression. Abrogating TAD structure did, however, reduce thermotolerance, accelerate aging, and shorten lifespan, implicating chromosome architecture in stress responses and aging.
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Affiliation(s)
- Erika C Anderson
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Phillip A Frankino
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ryo Higuchi-Sanabria
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Qiming Yang
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Qian Bian
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Aram Shin
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Cynthia Kenyon
- Calico Life Sciences, South San Francisco, CA 94080, USA
| | - Andrew Dillin
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Barbara J Meyer
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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6
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Distinct Roles of Two Histone Methyltransferases in Transmitting H3K36me3-Based Epigenetic Memory Across Generations in Caenorhabditis elegans. Genetics 2018; 210:969-982. [PMID: 30217796 PMCID: PMC6218224 DOI: 10.1534/genetics.118.301353] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/04/2018] [Indexed: 02/07/2023] Open
Abstract
Epigenetic information contributes to proper gene expression and development, and can be transmitted not only through mitotic divisions but also from parents to progeny. We investigated the roles in epigenetic inheritance of MES-4 and MET-1, the two Caenorhabditis elegans enzymes that methylate H3K36 (histone H3 Lys 36). Mass spectrometry analysis confirmed immunostaining results showing that both MES-4 and MET-1 catalyze H3K36me3. In the adult germline, MES-4 is enriched in the distal mitotic zone and MET-1 is enriched in the meiotic pachytene zone. Embryos inherit H3K36me3-marked chromosomes from both the oocyte and sperm, and a maternal load of MES-4 and MET-1. Maternal MES-4 quickly associates with sperm chromosomes; that association requires that the sperm chromosomes bear H3K36me3, suggesting that MES-4 is recruited to chromosomes by preexisting H3K36me3. In embryos that inherit H3K36me3-positive oocyte chromosomes and H3K36me3-negative sperm chromosomes, MES-4 and H3K36me3 are maintained on only a subset of chromosomes until at least the 32-cell stage, likely because MES-4 propagates H3K36me3 on regions of the genome with preexisting H3K36me3. In embryos lacking MES-4, H3K36me3 levels on chromosomes drop precipitously postfertilization. In contrast to the relatively high levels of MES-4 in early-stage embryos, MET-1 levels are low at early stages and start increasing by the ∼26-cell stage, consistent with expression from the zygotic genome. Our findings support the model that MET-1 mediates transcription-coupled H3K36me3 in the parental germline and transcriptionally active embryos, and that MES-4 transmits an epigenetic memory of H3K36me3 across generations and through early embryo cell divisions by maintaining inherited patterns of H3K36me3.
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7
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Huang C, Zhu B. Roles of H3K36-specific histone methyltransferases in transcription: antagonizing silencing and safeguarding transcription fidelity. BIOPHYSICS REPORTS 2018; 4:170-177. [PMID: 30310854 PMCID: PMC6153486 DOI: 10.1007/s41048-018-0063-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/15/2018] [Indexed: 12/20/2022] Open
Abstract
Histone H3K36 methylation is well-known for its role in active transcription. In Saccharomyces cerevisiae, H3K36 methylation is mediated solely by SET2 during transcription elongation. In metazoans, multiple H3K36-specific methyltransferases exist and contribute to distinct biochemical activities and subsequent functions. In this review, we focus on the H3K36-specific histone methyltransferases in metazoans, and discuss their enzymatic activity regulation and their roles in antagonizing Polycomb silencing and safeguarding transcription fidelity.
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Affiliation(s)
- Chang Huang
- 1National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Bing Zhu
- 1National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China.,2College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
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8
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Williams CW, Iyer J, Liu Y, O'Connell KF. CDK-11-Cyclin L is required for gametogenesis and fertility in C. elegans. Dev Biol 2018; 441:52-66. [PMID: 29886128 DOI: 10.1016/j.ydbio.2018.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/05/2018] [Accepted: 06/05/2018] [Indexed: 11/18/2022]
Abstract
CDK11, a member of the cyclin-dependent kinase family, has been implicated in a diverse array of functions including transcription, RNA processing, sister chromatid cohesion, spindle assembly, centriole duplication and apoptosis. Despite its involvement in many essential functions, little is known about the requirements for CDK11 and its partner Cyclin L in a developing multicellular organism. Here we investigate the function of CDK11 and Cyclin L during development of the nematode Caenorhabditis elegans. Worms express two CDK11 proteins encoded by distinct loci: CDK-11.1 is essential for normal male and female fertility and is broadly expressed in the nuclei of somatic and germ line cells, while CDK-11.2 is nonessential and is enriched in hermaphrodite germ line nuclei beginning in mid pachytene. Hermaphrodites lacking CDK-11.1 develop normally but possess fewer mature sperm and oocytes and do not fully activate the RAS-ERK pathway that is required for oocyte production in response to environmental cues. Most of the sperm and eggs that are produced in cdk-11.1 null animals appear to complete development normally but fail to engage in sperm-oocyte signaling suggesting that CDK-11.1 is needed at multiple points in gametogenesis. Finally, we find that CDK-11.1 and CDK-11.2 function redundantly during embryonic and postembryonic development and likely do so in association with Cyclin L. Our results thus define multiple requirements for CDK-11-Cyclin L during animal development.
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Affiliation(s)
- Christopher W Williams
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA
| | - Jyoti Iyer
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA
| | - Yan Liu
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA
| | - Kevin F O'Connell
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA.
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Abstract
Environmental factors, particularly during early life, are important for the later metabolic health of the individual. In our obesogenic environment, it is of major socio-economic importance to investigate the mechanisms that contribute to the risk of metabolic ill health. Increasing evidence from a variety of model organisms suggests that non-genetically determined phenotypes, including metabolic effects such as glucose intolerance and obesity, can be passed between generations, which encourages us to revisit heredity. Inheritance of altered epigenetic information through the germ line has been proposed as one plausible mechanism. Whether the germline epigenome can be altered by environmental conditions such as diet and the extent to which this occurs in humans are the subject of intense current interest and debate, especially given that extensive germline epigenetic reprogramming is known to occur. As epigenetic mechanisms are often highly conserved between organisms, studying epigenetic inheritance in plants and lower metazoans has the potential to inform our investigation in mammals. This Review explores the extent to which epigenetic inheritance contributes to heredity in these different organisms, whether the environment can affect epigenetic inheritance and whether there is any evidence for the inheritance of acquired phenotypes.
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Affiliation(s)
- Elizabeth J Radford
- Department of Paediatrics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
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Lee CYS, Lu T, Seydoux G. Nanos promotes epigenetic reprograming of the germline by down-regulation of the THAP transcription factor LIN-15B. eLife 2017; 6:30201. [PMID: 29111977 PMCID: PMC5734877 DOI: 10.7554/elife.30201] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/06/2017] [Indexed: 12/15/2022] Open
Abstract
Nanos RNA-binding proteins are required for germline development in metazoans, but the underlying mechanisms remain poorly understood. We have profiled the transcriptome of primordial germ cells (PGCs) lacking the nanos homologs nos-1 and nos-2 in C. elegans. nos-1nos-2 PGCs fail to silence hundreds of transcripts normally expressed in oocytes. We find that this misregulation is due to both delayed turnover of maternal transcripts and inappropriate transcriptional activation. The latter appears to be an indirect consequence of delayed turnover of the maternally-inherited transcription factor LIN-15B, a synMuvB class transcription factor known to antagonize PRC2 activity. PRC2 is required for chromatin reprogramming in the germline, and the transcriptome of PGCs lacking PRC2 resembles that of nos-1nos-2 PGCs. Loss of maternal LIN-15B restores fertility to nos-1nos-2 mutants. These findings suggest that Nanos promotes germ cell fate by downregulating maternal RNAs and proteins that would otherwise interfere with PRC2-dependent reprogramming of PGC chromatin.
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Affiliation(s)
- Chih-Yung Sean Lee
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Tu Lu
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Geraldine Seydoux
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
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A Network of Chromatin Factors Is Regulating the Transition to Postembryonic Development in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2017; 7:343-353. [PMID: 28007841 PMCID: PMC5295584 DOI: 10.1534/g3.116.037747] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mi2 proteins are evolutionarily conserved, ATP-dependent chromatin remodelers of the CHD family that play key roles in stem cell differentiation and reprogramming. In Caenorhabditis elegans, the let-418 gene encodes one of the two Mi2 homologs, which is part of at least two chromatin complexes, namely the Nucleosome Remodeling and histone Deacetylase (NuRD) complex and the MEC complex, and functions in larval development, vulval morphogenesis, lifespan regulation, and cell fate determination. To explore the mechanisms involved in the action of LET-418/Mi2, we performed a genome-wide RNA interference (RNAi) screen for suppressors of early larval arrest associated with let-418 mutations. We identified 29 suppressor genes, of which 24 encode chromatin regulators, mostly orthologs of proteins present in transcriptional activator complexes. The remaining five genes vary broadly in their predicted functions. All suppressor genes could suppress multiple aspects of the let-418 phenotype, including developmental arrest and ectopic expression of germline genes in the soma. Analysis of available transcriptomic data and quantitative PCR revealed that LET-418 and the suppressors of early larval arrest are regulating common target genes. These suppressors might represent direct competitors of LET-418 complexes for chromatin regulation of crucial genes involved in the transition to postembryonic development.
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12
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Navratilova P, Danks GB, Long A, Butcher S, Manak JR, Thompson EM. Sex-specific chromatin landscapes in an ultra-compact chordate genome. Epigenetics Chromatin 2017; 10:3. [PMID: 28115992 PMCID: PMC5240408 DOI: 10.1186/s13072-016-0110-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/23/2016] [Indexed: 12/15/2022] Open
Abstract
Background In multicellular organisms, epigenome dynamics are associated with transitions in the cell cycle, development, germline specification, gametogenesis and inheritance. Evolutionarily, regulatory space has increased in complex metazoans to accommodate these functions. In tunicates, the sister lineage to vertebrates, we examine epigenome adaptations to strong secondary genome compaction, sex chromosome evolution and cell cycle modes. Results Across the 70 MB Oikopleura dioica genome, we profiled 19 histone modifications, and RNA polymerase II, CTCF and p300 occupancies, to define chromatin states within two homogeneous tissues with distinct cell cycle modes: ovarian endocycling nurse nuclei and mitotically proliferating germ nuclei in testes. Nurse nuclei had active chromatin states similar to other metazoan epigenomes, with large domains of operon-associated transcription, a general lack of heterochromatin, and a possible role of Polycomb PRC2 in dosage compensation. Testis chromatin states reflected transcriptional activity linked to spermatogenesis and epigenetic marks that have been associated with establishment of transgenerational inheritance in other organisms. We also uncovered an unusual chromatin state specific to the Y-chromosome, which combined active and heterochromatic histone modifications on specific transposable elements classes, perhaps involved in regulating their activity. Conclusions Compacted regulatory space in this tunicate genome is accompanied by reduced heterochromatin and chromatin state domain widths. Enhancers, promoters and protein-coding genes have conserved epigenomic features, with adaptations to the organization of a proportion of genes in operon units. We further identified features specific to sex chromosomes, cell cycle modes, germline identity and dosage compensation, and unusual combinations of histone PTMs with opposing consensus functions. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0110-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pavla Navratilova
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
| | - Gemma Barbara Danks
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
| | - Abby Long
- Departments of Biology and Pediatrics and the Roy J. Carver Center for Genomics, 459 Biology Building, University of Iowa, Iowa City, IA 52242 USA
| | - Stephen Butcher
- Departments of Biology and Pediatrics and the Roy J. Carver Center for Genomics, 459 Biology Building, University of Iowa, Iowa City, IA 52242 USA
| | - John Robert Manak
- Departments of Biology and Pediatrics and the Roy J. Carver Center for Genomics, 459 Biology Building, University of Iowa, Iowa City, IA 52242 USA
| | - Eric M Thompson
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway.,Department of Biology, University of Bergen, 5020 Bergen, Norway
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13
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Akhund-Zade J, Bergland AO, Crowe SO, Unckless RL. The Genetic Basis of Natural Variation in Drosophila (Diptera: Drosophilidae) Virgin Egg Retention. JOURNAL OF INSECT SCIENCE (ONLINE) 2017; 17:iew094. [PMID: 28042107 PMCID: PMC5270406 DOI: 10.1093/jisesa/iew094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Indexed: 06/06/2023]
Abstract
Drosophila melanogaster is able to thrive in harsh northern climates through adaptations in life-history traits and physiological mechanisms that allow for survival through the winter. We examined the genetic basis of natural variation in one such trait, female virgin egg retention, which was previously shown to vary clinally and seasonally. To further our understanding of the genetic basis and evolution of virgin egg retention, we performed a genome-wide association study (GWAS) using the previously sequenced Drosophila Genetic Reference Panel (DGRP) mapping population. We found 29 single nucleotide polymorphisms (SNPs) associated with virgin egg retention and assayed 6 available mutant lines, each harboring a mutation in a candidate gene, for effects on egg retention time. We found that four out of the six mutant lines had defects in egg retention time as compared with the respective controls: mun, T48, Mes-4, and Klp67A Surprisingly, none of these genes has a recognized role in ovulation control, but three of the four genes have known effects on fertility or have high expression in the ovaries. We also found that the SNP set associated with egg retention time was enriched for clinal SNPs. The majority of clinal SNPs had alleles associated with longer egg retention present at higher frequencies in higher latitudes. Our results support previous studies that show higher frequency of long retention times at higher latitude, providing evidence for the adaptive value of virgin egg-retention.
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Affiliation(s)
- Jamilla Akhund-Zade
- Department of Biology, Stanford University, 371 Serra Street, Palo Alto, CA 94305
- Department of Organismal and Evolutionary Biology, Harvard University, Northwest Labs 248, Cambridge, MA 02138
| | - Alan O Bergland
- Department of Biology, Stanford University, 371 Serra Street, Palo Alto, CA 94305
- Department of Biology, University of Virginia, 063A Gilmer Hall, Charlottesville, VA 22903
| | - Sarah O Crowe
- Department of Entomology, Cornell University, 3125 Comstock Hall, Ithaca, 14853 NY
| | - Robert L Unckless
- Department of Entomology, Cornell University, 3125 Comstock Hall, Ithaca, 14853 NY
- Department of Molecular Biosciences, University of Kansas, 4055 Haworth Hall, Lawrence, KS 66045
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14
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Seelk S, Adrian-Kalchhauser I, Hargitai B, Hajduskova M, Gutnik S, Tursun B, Ciosk R. Increasing Notch signaling antagonizes PRC2-mediated silencing to promote reprograming of germ cells into neurons. eLife 2016; 5. [PMID: 27602485 PMCID: PMC5045294 DOI: 10.7554/elife.15477] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 09/06/2016] [Indexed: 12/12/2022] Open
Abstract
Cell-fate reprograming is at the heart of development, yet very little is known about the molecular mechanisms promoting or inhibiting reprograming in intact organisms. In the C. elegans germline, reprograming germ cells into somatic cells requires chromatin perturbation. Here, we describe that such reprograming is facilitated by GLP-1/Notch signaling pathway. This is surprising, since this pathway is best known for maintaining undifferentiated germline stem cells/progenitors. Through a combination of genetics, tissue-specific transcriptome analysis, and functional studies of candidate genes, we uncovered a possible explanation for this unexpected role of GLP-1/Notch. We propose that GLP-1/Notch promotes reprograming by activating specific genes, silenced by the Polycomb repressive complex 2 (PRC2), and identify the conserved histone demethylase UTX-1 as a crucial GLP-1/Notch target facilitating reprograming. These findings have wide implications, ranging from development to diseases associated with abnormal Notch signaling. DOI:http://dx.doi.org/10.7554/eLife.15477.001 The DNA in genes encodes the basic information needed to build an organism or control its day-to-day operations. Most cells in an organism contain the same genetic information, but different types of cell use the information differently. For example, many of the genes that are active in a muscle cell are different from those that are active in a skin cell. These different patterns of gene activation largely determine a cell’s identity and are brought about by DNA-binding proteins or chemical modifications to the DNA (which are both forms of so-called epigenetic regulation). Nevertheless, cells occasionally change their identities – a phenomenon that is referred to as reprograming. This process allows tissues to be regenerated after wounding, but, due to technical difficulties, reprograming has been often studied in isolated cells grown in a dish. Seelk, Adrian-Kalchhauser et al. set out to understand how being surrounded by intact tissue influences reprograming. The experiments made use of C. elegans worms, because disturbing how this worm’s DNA is packaged can trigger its cells to undergo reprograming. Seelk, Adrian-Kalchhauser et al. show that a signaling pathway that is found in many different animals enhances this kind of reprograming in C. elegans. On the one hand, these findings help in understanding how epigenetic regulation can be altered by a specific tissue environment. On the other hand, the findings also suggest that abnormal signaling can result in altered epigenetic control of gene expression and lead to cells changing their identity. Indeed, increased signaling is linked to a major epigenetic mechanism seen in specific blood tumors, suggesting that the regulatory principles uncovered using this simple worm model could eventually provide insights into a human disease. A future challenge will be to determine precisely how the studied signaling pathway interacts with the epigenetic regulator that controls reprograming. Understanding this interaction in molecular detail could help to devise strategies for controlling reprograming. These strategies could in turn lead to treatments for people with conditions that cause specific cells types to be lost, such as Alzheimer’s disease or injuries. DOI:http://dx.doi.org/10.7554/eLife.15477.002
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Affiliation(s)
- Stefanie Seelk
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | | | - Balázs Hargitai
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Martina Hajduskova
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Silvia Gutnik
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Baris Tursun
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Rafal Ciosk
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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15
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Frøkjær-Jensen C, Jain N, Hansen L, Davis MW, Li Y, Zhao D, Rebora K, Millet JRM, Liu X, Kim SK, Dupuy D, Jorgensen EM, Fire AZ. An Abundant Class of Non-coding DNA Can Prevent Stochastic Gene Silencing in the C. elegans Germline. Cell 2016; 166:343-357. [PMID: 27374334 PMCID: PMC4947018 DOI: 10.1016/j.cell.2016.05.072] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 03/31/2016] [Accepted: 05/18/2016] [Indexed: 11/30/2022]
Abstract
Cells benefit from silencing foreign genetic elements but must simultaneously avoid inactivating endogenous genes. Although chromatin modifications and RNAs contribute to maintenance of silenced states, the establishment of silenced regions will inevitably reflect underlying DNA sequence and/or structure. Here we demonstrate that a pervasive non-coding DNA feature in Caenorhabditis elegans, characterized by 10-basepair periodic An/Tn-clusters (PATCs), can license transgenes for germline expression within repressive chromatin domains. Transgenes containing natural or synthetic PATCs are resistant to position effect variegation and stochastic silencing in the germline. Among endogenous genes, intron length and PATC-character undergo dramatic changes as orthologs move from active to repressive chromatin over evolutionary time, indicating a dynamic character to the An/Tn periodicity. We propose that PATCs form the basis of a cellular immune system, identifying certain endogenous genes in heterochromatic contexts as privileged while foreign DNA can be suppressed with no requirement for a cellular memory of prior exposure.
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Affiliation(s)
- Christian Frøkjær-Jensen
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT 84112, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Sciences and Danish National Research Foundation Centre for Cardiac Arrhythmia, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Nimit Jain
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Loren Hansen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - M Wayne Davis
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Yongbin Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Di Zhao
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Karine Rebora
- IECB, University of Bordeaux, Laboratoire ARNA-INSERM, U869, 33600 Pessac, France
| | - Jonathan R M Millet
- IECB, University of Bordeaux, Laboratoire ARNA-INSERM, U869, 33600 Pessac, France
| | - Xiao Liu
- Department of Developmental Biology, Stanford University Medical Center, Stanford, CA 94305, USA; School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Stuart K Kim
- Department of Developmental Biology, Stanford University Medical Center, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Denis Dupuy
- IECB, University of Bordeaux, Laboratoire ARNA-INSERM, U869, 33600 Pessac, France
| | - Erik M Jorgensen
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT 84112, USA.
| | - Andrew Z Fire
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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16
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Butuči M, Wong MM, Michael WM. Trouble in transitioning: activation of zygotic transcription can lead to DNA breakage and genome instability. WORM 2015; 4:e1115946. [PMID: 27123372 DOI: 10.1080/21624054.2015.1115946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 10/29/2015] [Indexed: 10/22/2022]
Abstract
Recent work from our laboratory has identified zygotic genome activation as a source of intrinsic DNA damage during germline development in C. elegans. More specifically, we have found that the primordial germ cells Z2 and Z3 experience DNA damage and damage checkpoint activation shortly after RNA polymerase II is activated by a nutrient-dependent signal in L1 stage animals. In this Commentary we review these data, put them into context with other examples of programmed DNA double-strand breaks (DSBs) during gene activation, and speculate as to how a DSB would facilitate signal-dependent activation of gene expression.
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Affiliation(s)
- Melina Butuči
- Molecular and Computational Biology Section; Department of Biological Sciences; University of Southern California ; Los Angeles, CA USA
| | - Matthew M Wong
- Molecular and Computational Biology Section; Department of Biological Sciences; University of Southern California ; Los Angeles, CA USA
| | - W Matthew Michael
- Molecular and Computational Biology Section; Department of Biological Sciences; University of Southern California ; Los Angeles, CA USA
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17
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Miwa T, Takasaki T, Inoue K, Sakamoto H. Restricted distribution of mrg-1 mRNA in C. elegans primordial germ cells through germ granule-independent regulation. Genes Cells 2015; 20:932-42. [PMID: 26537333 DOI: 10.1111/gtc.12285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/02/2015] [Indexed: 11/27/2022]
Abstract
The chromodomain protein MRG-1 is an essential maternal factor for proper germline development that protects germ cells from cell death in C. elegans. Unlike germ granules, which are exclusively segregated to the germline blastomeres at each cell division from the first cleavage of the embryo, MRG-1 is abundant in all cells in early embryos and is then gradually restricted to the primordial germ cells (PGCs) by the morphogenesis stage. Here, we show that this characteristic spatiotemporal expression pattern is dictated by the mrg-1 3'UTR and is differentially regulated at the RNA level between germline and somatic cells. Asymmetric segregation of germ granules is not necessary to localize MRG-1 to the PGCs. We found that MES-4, an essential chromatin regulator in germ cells, also accumulates in the PGCs in a germ granule-independent manner. We propose that C.elegans PGCs have a novel mechanism to accumulate at least some chromatin-associated proteins that are essential for germline immortality.
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Affiliation(s)
- Takashi Miwa
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
| | - Teruaki Takasaki
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
| | - Kunio Inoue
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
| | - Hiroshi Sakamoto
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
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18
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Butuči M, Williams AB, Wong MM, Kramer B, Michael WM. Zygotic Genome Activation Triggers Chromosome Damage and Checkpoint Signaling in C. elegans Primordial Germ Cells. Dev Cell 2015; 34:85-95. [PMID: 26073019 DOI: 10.1016/j.devcel.2015.04.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 03/17/2015] [Accepted: 04/24/2015] [Indexed: 01/05/2023]
Abstract
Recent findings have identified highly transcribed genes as a source of genome instability; however, the degree to which large-scale shifts in transcriptional activity cause DNA damage was not known. One example of a large-scale shift in transcriptional activity occurs during development, when maternal regulators are destroyed and zygotic genome activation (ZGA) occurs. Here, we show that ZGA triggers widespread chromosome damage in the primordial germ cells of the nematode C. elegans. We show that ZGA-induced DNA damage activates a checkpoint response, the damage is repaired by factors required for inter-sister homologous recombination, and topoisomerase II plays a role in generating the damage. These findings identify ZGA as a source of intrinsic genome instability in the germline and suggest that genome destabilization may be a general consequence of extreme shifts in cellular transcriptional load.
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Affiliation(s)
- Melina Butuči
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ashley B Williams
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Matthew M Wong
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Brendan Kramer
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - W Matthew Michael
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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19
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Gao J, Kim HM, Elia AE, Elledge SJ, Colaiácovo MP. NatB domain-containing CRA-1 antagonizes hydrolase ACER-1 linking acetyl-CoA metabolism to the initiation of recombination during C. elegans meiosis. PLoS Genet 2015; 11:e1005029. [PMID: 25768301 PMCID: PMC4359108 DOI: 10.1371/journal.pgen.1005029] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/27/2015] [Indexed: 11/18/2022] Open
Abstract
The formation of DNA double-strand breaks (DSBs) must take place during meiosis to ensure the formation of crossovers, which are required for accurate chromosome segregation, therefore avoiding aneuploidy. However, DSB formation must be tightly regulated to maintain genomic integrity. How this regulation operates in the context of different chromatin architectures and accessibility, and how it is linked to metabolic pathways, is not understood. We show here that global histone acetylation levels undergo changes throughout meiotic progression. Moreover, perturbations to global histone acetylation levels are accompanied by changes in the frequency of DSB formation in C. elegans. We provide evidence that the regulation of histone acetylation requires CRA-1, a NatB domain-containing protein homologous to human NAA25, which controls the levels of acetyl-Coenzyme A (acetyl-CoA) by antagonizing ACER-1, a previously unknown and conserved acetyl-CoA hydrolase. CRA-1 is in turn negatively regulated by XND-1, an AT-hook containing protein. We propose that this newly defined protein network links acetyl-CoA metabolism to meiotic DSB formation via modulation of global histone acetylation. Achieving accurate chromosome segregation is a critical outcome for any cell division process. Programmed DNA double-strand break formation is a central mechanism set in place to promote faithful chromosome segregation during meiosis. A subset of these DSBs is repaired as crossovers via reciprocal exchange of genetic information between homologous chromosomes resulting in physical attachments (chiasmata) between homologs, which ensure proper chromosome alignment at the metaphase plate at meiosis I, and also promote genetic diversity. How this regulation operates in the context of different chromatin architectures and accessibility, and how it is linked to metabolic pathways, is not understood. In this study, we found that CRA-1, a NatB domain-containing protein, promotes histone acetylation by maintaining the levels of acetyl-Coenzyme A (acetyl-CoA) through antagonizing ACER-1, a previously unknown and conserved acetyl-CoA hydrolase. CRA-1 is in turn negatively regulated by XND-1, an AT-hook containing protein. We leveraged this discovery to find a connection between the levels of acetyl-CoA, histone acetylation and DSB formation. We identified a novel protein network that links the regulation of DSB formation to the modulation of global levels of histone acetylation, and revealed a link between metabolism and the regulation of DSB formation.
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Affiliation(s)
- Jinmin Gao
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Hyun-Min Kim
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Andrew E. Elia
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Stephen J. Elledge
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Monica P. Colaiácovo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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20
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Veitia RA, Veyrunes F, Bottani S, Birchler JA. X chromosome inactivation and active X upregulation in therian mammals: facts, questions, and hypotheses. J Mol Cell Biol 2015; 7:2-11. [PMID: 25564545 DOI: 10.1093/jmcb/mjv001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
X chromosome inactivation is a mechanism that modulates the expression of X-linked genes in eutherian females (XX). Ohno proposed that to achieve a proper balance between X-linked and autosomal genes, those on the active X should also undergo a 2-fold upregulation. Although some support for Ohno's hypothesis has been provided through the years, recent genomic studies testing this hypothesis have brought contradictory results and fueled debate. Thus far, there are as many results in favor as against Ohno's hypothesis, depending on the nature of the datasets and the various assumptions and thresholds involved in the analyses. However, they have confirmed the importance of dosage balance between X-linked and autosomal genes involved in stoichiometric relationships. These facts as well as questions and hypotheses are discussed below.
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Affiliation(s)
- Reiner A Veitia
- Institut Jacques Monod, Paris, France Université Paris Diderot, Paris, France
| | - Frédéric Veyrunes
- Institut des Sciences de l'Evolution de Montpellier, CNRS/Université Montpellier II, Montpellier, France
| | - Samuel Bottani
- Université Paris Diderot, Paris, France Matière et Systèmes Complexes, Paris, France
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
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21
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Beadell AV, Haag ES. Evolutionary Dynamics of GLD-1-mRNA complexes in Caenorhabditis nematodes. Genome Biol Evol 2014; 7:314-35. [PMID: 25502909 PMCID: PMC4316625 DOI: 10.1093/gbe/evu272] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2014] [Indexed: 12/17/2022] Open
Abstract
Given the large number of RNA-binding proteins and regulatory RNAs within genomes, posttranscriptional regulation may be an underappreciated aspect of cis-regulatory evolution. Here, we focus on nematode germ cells, which are known to rely heavily upon translational control to regulate meiosis and gametogenesis. GLD-1 belongs to the STAR-domain family of RNA-binding proteins, conserved throughout eukaryotes, and functions in Caenorhabditis elegans as a germline-specific translational repressor. A phylogenetic analysis across opisthokonts shows that GLD-1 is most closely related to Drosophila How and deuterostome Quaking, both implicated in alternative splicing. We identify messenger RNAs associated with C. briggsae GLD-1 on a genome-wide scale and provide evidence that many participate in aspects of germline development. By comparing our results with published C. elegans GLD-1 targets, we detect nearly 100 that are conserved between the two species. We also detected several hundred Cbr-GLD-1 targets whose homologs have not been reported to be associated with C. elegans GLD-1 in either of two independent studies. Low expression in C. elegans may explain the failure to detect most of them, but a highly expressed subset are strong candidates for Cbr-GLD-1-specific targets. We examine GLD-1-binding motifs among targets conserved in C. elegans and C. briggsae and find that most, but not all, display evidence of shared ancestral binding sites. Our work illustrates both the conservative and the dynamic character of evolution at the posttranslational level of gene regulation, even between congeners.
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Affiliation(s)
- Alana V Beadell
- Program in Behavior, Evolution, Ecology, and Systematics, University of Maryland, College Park Present address: Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL
| | - Eric S Haag
- Program in Behavior, Evolution, Ecology, and Systematics, University of Maryland, College Park Department of Biology, University of Maryland, College Park
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22
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Xu D, Wei G, Lu P, Luo J, Chen X, Skogerbø G, Chen R. Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy. Protein Cell 2014; 5:770-82. [PMID: 24844773 PMCID: PMC4180458 DOI: 10.1007/s13238-014-0071-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 04/09/2014] [Indexed: 11/28/2022] Open
Abstract
In recent years, large numbers of non-coding RNAs (ncRNAs) have been identified in C. elegans but their functions are still not well studied. In C. elegans, CEP-1 is the sole homolog of the p53 family of genes. In order to obtain transcription profiles of ncRNAs regulated by CEP-1 under normal and UV stressed conditions, we applied the 'not-so-random' hexamers priming strategy to RNA sequencing in C. elegans, This NSR-seq strategy efficiently depleted rRNA transcripts from the samples and showed high technical replicability. We identified more than 1,000 ncRNAs whose apparent expression was repressed by CEP-1, while around 200 were activated. Around 40% of the CEP-1 activated ncRNAs promoters contain a putative CEP-1-binding site. CEP-1 regulated ncRNAs were frequently clustered and concentrated on the X chromosome. These results indicate that numerous ncRNAs are involved in CEP-1 transcriptional network and that these are especially enriched on the X chromosome in C. elegans.
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Affiliation(s)
- Derong Xu
- Laboratory of Non-coding RNA, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, 100101 China
- Graduate University of Chinese Academy of Sciences, Beijing, 100080 China
| | - Guifeng Wei
- Laboratory of Non-coding RNA, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, 100101 China
- Graduate University of Chinese Academy of Sciences, Beijing, 100080 China
| | - Ping Lu
- Key Laboratory of Forest Protection, State Forestry
Administration/Research Institute of Forest Ecology, Environment and
Protection, Chinese Academy of Forestry, Beijing, 100091 China
| | - Jianjun Luo
- Laboratory of Non-coding RNA, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Xiaomin Chen
- Laboratory of Non-coding RNA, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Geir Skogerbø
- Laboratory of Non-coding RNA, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Runsheng Chen
- Laboratory of Non-coding RNA, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, 100101 China
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23
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Birchler JA. Facts and artifacts in studies of gene expression in aneuploids and sex chromosomes. Chromosoma 2014; 123:459-69. [DOI: 10.1007/s00412-014-0478-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 12/18/2022]
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24
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Abstract
Studies of X chromosome evolution in various organisms have indicated that sex-biased genes are nonrandomly distributed between the X and autosomes. Here, to extend these studies to nematodes, we annotated and analyzed X chromosome gene content in four Caenorhabditis species and in Pristionchus pacificus. Our gene expression analyses comparing young adult male and female mRNA-seq data indicate that, in general, nematode X chromosomes are enriched for genes with high female-biased expression and depleted of genes with high male-biased expression. Genes with low sex-biased expression do not show the same trend of X chromosome enrichment and depletion. Combined with the observation that highly sex-biased genes are primarily expressed in the gonad, differential distribution of sex-biased genes reflects differences in evolutionary pressures linked to tissue-specific regulation of X chromosome transcription. Our data also indicate that X dosage imbalance between males (XO) and females (XX) is influential in shaping both expression and gene content of the X chromosome. Predicted upregulation of the single male X to match autosomal transcription (Ohno's hypothesis) is supported by our observation that overall transcript levels from the X and autosomes are similar for highly expressed genes. However, comparison of differentially located one-to-one orthologs between C. elegans and P. pacificus indicates lower expression of X-linked orthologs, arguing against X upregulation. These contradicting observations may be reconciled if X upregulation is not a global mechanism but instead acts locally on a subset of tissues and X-linked genes that are dosage sensitive.
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25
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Strome S, Kelly WG, Ercan S, Lieb JD. Regulation of the X chromosomes in Caenorhabditis elegans. Cold Spring Harb Perspect Biol 2014; 6:6/3/a018366. [PMID: 24591522 DOI: 10.1101/cshperspect.a018366] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Dosage compensation, which regulates the expression of genes residing on the sex chromosomes, has provided valuable insights into chromatin-based mechanisms of gene regulation. The nematode Caenorhabditis elegans has adopted various strategies to down-regulate and even nearly silence the X chromosomes. This article discusses the different chromatin-based strategies used in somatic tissues and in the germline to modulate gene expression from the C. elegans X chromosomes and compares these strategies to those used by other organisms to cope with similar X-chromosome dosage differences.
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Affiliation(s)
- Susan Strome
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California 95064
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26
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Opposing activities of DRM and MES-4 tune gene expression and X-chromosome repression in Caenorhabditis elegans germ cells. G3-GENES GENOMES GENETICS 2014; 4:143-53. [PMID: 24281426 PMCID: PMC3887530 DOI: 10.1534/g3.113.007849] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During animal development, gene transcription is tuned to tissue-appropriate levels. Here we uncover antagonistic regulation of transcript levels in the germline of Caenorhabditis elegans hermaphrodites. The histone methyltransferase MES-4 (Maternal Effect Sterile-4) marks genes expressed in the germline with methylated lysine on histone H3 (H3K36me) and promotes their transcription; MES-4 also represses genes normally expressed in somatic cells and genes on the X chromosome. The DRM transcription factor complex, named for its Dp/E2F, Retinoblastoma-like, and MuvB subunits, affects germline gene expression and prevents excessive repression of X-chromosome genes. Using genome-scale analyses of germline tissue, we show that common germline-expressed genes are activated by MES-4 and repressed by DRM, and that MES-4 and DRM co-bind many germline-expressed genes. Reciprocally, MES-4 represses and DRM activates a set of autosomal soma-expressed genes and overall X-chromosome gene expression. Mutations in mes-4 and the DRM subunit lin-54 oppositely skew the transcript levels of their common targets and cause sterility. A double mutant restores target gene transcript levels closer to wild type, and the concomitant loss of lin-54 suppresses the severe germline proliferation defect observed in mes-4 single mutants. Together, “yin-yang” regulation by MES-4 and DRM ensures transcript levels appropriate for germ-cell function, elicits robust but not excessive dampening of X-chromosome-wide transcription, and may poise genes for future expression changes. Our study reveals that conserved transcriptional regulators implicated in development and cancer counteract each other to fine-tune transcript dosage.
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27
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Custer LM, Snyder MJ, Flegel K, Csankovszki G. The onset of C. elegans dosage compensation is linked to the loss of developmental plasticity. Dev Biol 2013; 385:279-90. [PMID: 24252776 DOI: 10.1016/j.ydbio.2013.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 09/17/2013] [Accepted: 11/03/2013] [Indexed: 12/29/2022]
Abstract
Dosage compensation (DC) equalizes X-linked gene expression between sexes. In Caenorhabditis elegans, the dosage compensation complex (DCC) localizes to both X chromosomes in hermaphrodites and downregulates gene expression 2-fold. The DCC first localizes to hermaphrodite X chromosomes at the 30-cell stage, coincident with a developmental transition from plasticity to differentiation. To test whether DC onset is linked to loss of developmental plasticity, we established a timeline for the accumulation of DC-mediated chromatin features on X (depletion of histone H4 lysine 16 acetylation (H4K16ac) and enrichment of H4K20 monomethylation (H4K20me1)) in both wild type and developmentally delayed embryos. Surprisingly, we found that H4K16ac is depleted from the X even before the 30-cell stage in a DCC-independent manner. This depletion requires the activities of MES-2, MES-3, and MES-6 (a complex similar to the Polycomb Repressive Complex 2), and MES-4. By contrast, H4K20me1 becomes enriched on X chromosomes several cell cycles after DCC localization to the X, suggesting that it is a late mark in DC. MES-2 also promotes differentiation, and mes-2 mutant embryos exhibit prolonged developmental plasticity. Consistent with the hypothesis that the onset of DC is linked to differentiation, DCC localization and H4K20me1 accumulation on the X chromosomes are delayed in mes mutant hermaphrodite embryos. Furthermore, the onset of hermaphrodite-specific transcription of sdc-2 (which triggers DC) is delayed in mes-2 mutants. We propose that as embryonic blastomeres lose their developmental plasticity, hermaphrodite X chromosomes transition from a MES protein-regulated state to DCC-mediated repression.
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Affiliation(s)
- Laura M Custer
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University Ave., Ann Arbor, MI 48109-1048, USA
| | - Martha J Snyder
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University Ave., Ann Arbor, MI 48109-1048, USA
| | - Kerry Flegel
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University Ave., Ann Arbor, MI 48109-1048, USA
| | - Györgyi Csankovszki
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University Ave., Ann Arbor, MI 48109-1048, USA.
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'Escaping' the X chromosome leads to increased gene expression in the male germline of Drosophila melanogaster. Heredity (Edinb) 2013; 112:149-55. [PMID: 24022496 DOI: 10.1038/hdy.2013.86] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/27/2013] [Accepted: 07/29/2013] [Indexed: 01/17/2023] Open
Abstract
Genomic analyses of Drosophila species suggest that the X chromosome presents an unfavourable environment for the expression of genes in the male germline. A previous study in D. melanogaster used a reporter gene driven by a testis-specific promoter to show that expression was greatly reduced when the gene was inserted onto the X chromosome as compared with the autosomes. However, a limitation of this study was that only the expression regulated by a single, autosomal-derived promoter was investigated. To test for an increase in expression associated with 'escaping' the X chromosome, we analysed reporter gene expression driven by the promoters of three X-linked, testis-expressed genes (CG10920, CG12681 and CG1314) that were inserted randomly throughout the D. melanogaster genome. In all cases, insertions on the autosomes showed significantly higher expression than those on the X chromosome. Thus, even genes whose regulation has adapted to the X-chromosomal environment show increased male germline expression when relocated to an autosome. Our results provide direct experimental evidence for the suppression of X-linked gene expression in the Drosophila male germline that is independent of gene dose.
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29
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Venkatesh S, Workman JL. Set2 mediated H3 lysine 36 methylation: regulation of transcription elongation and implications in organismal development. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2013; 2:685-700. [PMID: 24014454 DOI: 10.1002/wdev.109] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Set2 is a RNA polymerase II (RNAPII) associated histone methyltransferase involved in the cotranscriptional methylation of the H3 K36 residue (H3K36me). It is responsible for multiple degrees of methylation (mono-, di-, and trimethylation), each of which has a distinct functional consequence. The extent of methylation and its genomic distribution is determined by different factors that coordinate to achieve a functional outcome. In yeast, the Set2-mediated H3K36me is involved in suppressing histone exchange, preventing hyperacetylation and promoting maintenance of well-spaced chromatin structure over the coding regions. In metazoans, separation of this enzymatic activity affords greater functional diversity extending beyond the control of transcription elongation to developmental gene regulation. This review focuses on the molecular aspects of the Set2 distribution and function, and discusses the role played by H3 K36 methyl mark in organismal development.
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30
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Van Wynsberghe PM, Maine EM. Epigenetic control of germline development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 757:373-403. [PMID: 22872484 DOI: 10.1007/978-1-4614-4015-4_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Dynamic regulation of histone modifications and small noncoding RNAs is observed throughout the development of the C. elegans germ line. Histone modifications are differentially regulated in the mitotic vs meiotic germ line, on X chromosomes vs autosomes and on paired chromosomes vs unpaired chromosomes. Small RNAs function in transposon silencing and developmental gene regulation. Histone modifications and small RNAs produced in the germ line can be inherited and impact embryonic development. Disruption of histone-modifying enzymes or small RNA machinery in the germ line can result in sterility due to degeneration of the germ line and/or an inability to produce functional gametes.
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31
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Wang JT, Seydoux G. Germ cell specification. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 757:17-39. [PMID: 22872473 DOI: 10.1007/978-1-4614-4015-4_2] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The germline of Caenorhabditis elegans derives from a single founder cell, the germline blastomere P(4). P(4) is the product of four asymmetric cleavages that divide the zygote into distinct somatic and germline (P) lineages. P(4) inherits a specialized cytoplasm ("germ plasm") containing maternally encoded proteins and RNAs. The germ plasm has been hypothesized to specify germ cell fate, but the mechanisms involved remain unclear. Three processes stand out: (1) inhibition of mRNA transcription to prevent activation of somatic development, (2) translational regulation of the nanos homolog nos-2 and of other germ plasm mRNAs, and (3) establishment of a unique, partially repressive chromatin. Together, these processes ensure that the daughters of P(4), the primordial germ cells Z2 and Z3, gastrulate inside the embryo, associate with the somatic gonad, initiate the germline transcriptional program, and proliferate during larval development to generate ∼2,000 germ cells by adulthood.
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Affiliation(s)
- Jennifer T Wang
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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Lamelza P, Bhalla N. Histone methyltransferases MES-4 and MET-1 promote meiotic checkpoint activation in Caenorhabditis elegans. PLoS Genet 2012; 8:e1003089. [PMID: 23166523 PMCID: PMC3499413 DOI: 10.1371/journal.pgen.1003089] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 09/28/2012] [Indexed: 11/18/2022] Open
Abstract
Chromosomes that fail to synapse during meiosis become enriched for chromatin marks associated with heterochromatin assembly. This response, called meiotic silencing of unsynapsed or unpaired chromatin (MSUC), is conserved from fungi to mammals. In Caenorhabditis elegans, unsynapsed chromosomes also activate a meiotic checkpoint that monitors synapsis. The synapsis checkpoint signal is dependent on cis-acting loci called Pairing Centers (PCs). How PCs signal to activate the synapsis checkpoint is currently unknown. We show that a chromosomal duplication with PC activity is sufficient to activate the synapsis checkpoint and that it undergoes heterochromatin assembly less readily than a duplication of a non-PC region, suggesting that the chromatin state of these loci is important for checkpoint function. Consistent with this hypothesis, MES-4 and MET-1, chromatin-modifying enzymes associated with transcriptional activity, are required for the synapsis checkpoint. In addition, a duplication with PC activity undergoes heterochromatin assembly when mes-4 activity is reduced. MES-4 function is required specifically for the X chromosome, while MES-4 and MET-1 act redundantly to monitor autosomal synapsis. We propose that MES-4 and MET-1 antagonize heterochromatin assembly at PCs of unsynapsed chromosomes by promoting a transcriptionally permissive chromatin environment that is required for meiotic checkpoint function. Moreover, we suggest that different genetic requirements to monitor the behavior of sex chromosomes and autosomes allow for the lone unsynapsed X present in male germlines to be shielded from inappropriate checkpoint activation.
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Affiliation(s)
| | - Needhi Bhalla
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
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33
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Wasson JA, Ruppersburg CC, Katz DJ. Restoring totipotency through epigenetic reprogramming. Brief Funct Genomics 2012; 12:118-28. [PMID: 23117862 DOI: 10.1093/bfgp/els042] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Epigenetic modifications are implicated in the maintenance and regulation of transcriptional memory by marking genes that were previously transcribed to facilitate transmission of these expression patterns through cell division. During germline specification and maintenance, extensive epigenetic modifications are acquired. Yet somehow at fertilization, the fusion of the highly differentiated sperm and egg results in formation of the totipotent zygote. This massive change in cell fate implies that the selective erasure and maintenance of epigenetic modifications at fertilization may be critical for the re-establishment of totipotency. In this review, we discuss recent studies that provide insight into the extensive epigenetic reprogramming that occurs around fertilization and the mechanisms that may be involved in the re-establishment of totipotency in the embryo.
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Affiliation(s)
- Jadiel A Wasson
- Department of Cell Biology, Emory University, Atlanta, GA 30322, USA
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Gaydos LJ, Rechtsteiner A, Egelhofer TA, Carroll CR, Strome S. Antagonism between MES-4 and Polycomb repressive complex 2 promotes appropriate gene expression in C. elegans germ cells. Cell Rep 2012; 2:1169-77. [PMID: 23103171 DOI: 10.1016/j.celrep.2012.09.019] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/12/2012] [Accepted: 09/14/2012] [Indexed: 12/12/2022] Open
Abstract
The Caenorhabditis elegans MES proteins are key chromatin regulators of the germline. MES-2, MES-3, and MES-6 form the C. elegans Polycomb repressive complex 2 and generate repressive H3K27me3. MES-4 generates H3K36me3 on germline-expressed genes. Transcript profiling of dissected mutant germlines revealed that MES-2/3/6 and MES-4 cooperate to promote the expression of germline genes and repress the X chromosomes and somatic genes. Results from genome-wide chromatin immunoprecipitation showed that H3K27me3 and H3K36me3 occupy mutually exclusive domains on the autosomes and that H3K27me3 is enriched on the X. Loss of MES-4 from germline genes causes H3K27me3 to spread to germline genes, resulting in reduced H3K27me3 elsewhere on the autosomes and especially on the X. Our findings support a model in which H3K36me3 repels H3K27me3 from germline genes and concentrates it on other regions of the genome. This antagonism ensures proper patterns of gene expression for germ cells, which includes repression of somatic genes and the X chromosomes.
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Affiliation(s)
- Laura J Gaydos
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
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35
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Vielle A, Lang J, Dong Y, Ercan S, Kotwaliwale C, Rechtsteiner A, Appert A, Chen QB, Dose A, Egelhofer T, Kimura H, Stempor P, Dernburg A, Lieb JD, Strome S, Ahringer J. H4K20me1 contributes to downregulation of X-linked genes for C. elegans dosage compensation. PLoS Genet 2012; 8:e1002933. [PMID: 23028348 PMCID: PMC3441679 DOI: 10.1371/journal.pgen.1002933] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 07/02/2012] [Indexed: 01/02/2023] Open
Abstract
The Caenorhabditis elegans dosage compensation complex (DCC) equalizes X-chromosome gene dosage between XO males and XX hermaphrodites by two-fold repression of X-linked gene expression in hermaphrodites. The DCC localizes to the X chromosomes in hermaphrodites but not in males, and some subunits form a complex homologous to condensin. The mechanism by which the DCC downregulates gene expression remains unclear. Here we show that the DCC controls the methylation state of lysine 20 of histone H4, leading to higher H4K20me1 and lower H4K20me3 levels on the X chromosomes of XX hermaphrodites relative to autosomes. We identify the PR-SET7 ortholog SET-1 and the Suv4-20 ortholog SET-4 as the major histone methyltransferases for monomethylation and di/trimethylation of H4K20, respectively, and provide evidence that X-chromosome enrichment of H4K20me1 involves inhibition of SET-4 activity on the X. RNAi knockdown of set-1 results in synthetic lethality with dosage compensation mutants and upregulation of X-linked gene expression, supporting a model whereby H4K20me1 functions with the condensin-like C. elegans DCC to repress transcription of X-linked genes. H4K20me1 is important for mitotic chromosome condensation in mammals, suggesting that increased H4K20me1 on the X may restrict access of the transcription machinery to X-linked genes via chromatin compaction. In many animals, males have one X chromosome and females have two. However, the same amount of gene expression from X chromosomes is needed in the two sexes. The process of dosage compensation (DC) globally regulates X-chromosome gene expression to make it equal between the sexes, and it occurs in different ways in different animals. In mammals, one X chromosome in females is randomly inactivated, leaving one active X chromosome. In contrast, in the nematode worm C. elegans, the two X chromosomes in hermaphrodites are repressed two-fold to match gene expression to the single X chromosome in males. Previous work in C. elegans identified proteins required for DC that bind to the X chromosome, but their mode of action is not known. Here we show that DC proteins lead to higher levels of histone H4 lysine 20 monomethylation (H4K20me1) on hermaphrodite X chromosomes and that H4K20me1 functions in repressing X-chromosome gene expression. This shows that histone modification is an important aspect of the mechanism of dosage compensation. Together with previous work linking H4K20me1 to chromatin structure regulation, our results suggest that dosage compensation might lower gene expression on hermaphrodite X chromosomes by compacting them.
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Affiliation(s)
- Anne Vielle
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jackie Lang
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Yan Dong
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Sevinc Ercan
- Department of Biology, Carolina Center for the Genome Sciences, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Chitra Kotwaliwale
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Andreas Rechtsteiner
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Alex Appert
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Q. Brent Chen
- Department of Biology, Carolina Center for the Genome Sciences, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Andrea Dose
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Thea Egelhofer
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Hiroshi Kimura
- Graduate School for Frontier Biosciences, Osaka University, Osaka, Japan
| | - Przemyslaw Stempor
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Abby Dernburg
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Jason D. Lieb
- Department of Biology, Carolina Center for the Genome Sciences, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Susan Strome
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Julie Ahringer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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36
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Wagner DE, Ho JJ, Reddien PW. Genetic regulators of a pluripotent adult stem cell system in planarians identified by RNAi and clonal analysis. Cell Stem Cell 2012; 10:299-311. [PMID: 22385657 DOI: 10.1016/j.stem.2012.01.016] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 12/30/2011] [Accepted: 01/23/2012] [Indexed: 12/24/2022]
Abstract
Pluripotency is a central, well-studied feature of embryonic development, but the role of pluripotent cell regulation in somatic tissue regeneration remains poorly understood. In planarians, regeneration of entire animals from tissue fragments is promoted by the activity of adult pluripotent stem cells (cNeoblasts). We utilized transcriptional profiling to identify planarian genes expressed in adult proliferating, regenerative cells (neoblasts). We also developed quantitative clonal analysis methods for expansion and differentiation of cNeoblast descendants that, together with RNAi, revealed gene roles in stem cell biology. Genes encoding two zinc finger proteins, Vasa, a LIM domain protein, Sox and Jun-like transcription factors, two candidate RNA-binding proteins, a Setd8-like protein, and PRC2 (Polycomb) were required for proliferative expansion and/or differentiation of cNeoblast-derived clones. These findings suggest that planarian stem cells utilize molecular mechanisms found in germ cells and other pluripotent cell types and identify genetic regulators of the planarian stem cell system.
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Affiliation(s)
- Daniel E Wagner
- Howard Hughes Medical Institute, MIT Biology, Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
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37
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Hajduskova M, Ahier A, Daniele T, Jarriault S. Cell plasticity in Caenorhabditis elegans: from induced to natural cell reprogramming. Genesis 2011; 50:1-17. [PMID: 21932439 DOI: 10.1002/dvg.20806] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 08/29/2011] [Accepted: 08/30/2011] [Indexed: 01/17/2023]
Abstract
Achieving controlled reprogramming of differentiated cells into a desired cell type would open new opportunities in stem-cell biology and regenerative medicine. Experimentation on cell reprogramming requires a model in which cell conversion can be induced and tracked individually. The tiny nematode, Caenorhabditis elegans, owing to its known cellular lineage, allows the study of direct cell type conversion with a single-cell resolution. Indeed, recent advances have shown that despite its invariant cell lineage, cellular identities can be reprogrammed, leading to cell conversion in vivo. In addition, natural transdifferentiation events occur in the worm, providing a powerful model for the study of cellular plasticity in a physiological cellular microenvironment. Here, we review pioneer studies on induced and naturally occurring reprogramming events in C. elegans and the new notions that have emerged.
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Affiliation(s)
- Martina Hajduskova
- Development and Stem Cells Programme, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch CU Strasbourg, France
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38
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Checchi PM, Engebrecht J. Caenorhabditis elegans histone methyltransferase MET-2 shields the male X chromosome from checkpoint machinery and mediates meiotic sex chromosome inactivation. PLoS Genet 2011; 7:e1002267. [PMID: 21909284 PMCID: PMC3164706 DOI: 10.1371/journal.pgen.1002267] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 07/12/2011] [Indexed: 11/23/2022] Open
Abstract
Meiosis is a specialized form of cellular division that results in the precise halving of the genome to produce gametes for sexual reproduction. Checkpoints function during meiosis to detect errors and subsequently to activate a signaling cascade that prevents the formation of aneuploid gametes. Indeed, asynapsis of a homologous chromosome pair elicits a checkpoint response that can in turn trigger germline apoptosis. In a heterogametic germ line, however, sex chromosomes proceed through meiosis with unsynapsed regions and are not recognized by checkpoint machinery. We conducted a directed RNAi screen in Caenorhabditis elegans to identify regulatory factors that prevent recognition of heteromorphic sex chromosomes as unpaired and uncovered a role for the SET domain histone H3 lysine 9 histone methyltransferase (HMTase) MET-2 and two additional HMTases in shielding the male X from checkpoint machinery. We found that MET-2 also mediates the transcriptional silencing program of meiotic sex chromosome inactivation (MSCI) but not meiotic silencing of unsynapsed chromatin (MSUC), suggesting that these processes are distinct. Further, MSCI and checkpoint shielding can be uncoupled, as double-strand breaks targeted to an unpaired, transcriptionally silenced extra-chromosomal array induce checkpoint activation in germ lines depleted for met-2. In summary, our data uncover a mechanism by which repressive chromatin architecture enables checkpoint proteins to distinguish between the partnerless male X chromosome and asynapsed chromosomes thereby shielding the lone X from inappropriate activation of an apoptotic program. Meiosis results in the generation of non-identical haploid gametes and maintenance of chromosome number during sexual reproduction. Precise meiotic chromosome segregation is essential for life, and in humans errors in this process contribute to aneuploidy or failure in meiosis, which manifests as spontaneous abortions or infertility. Cellular surveillance pathways monitor the steps of meiosis; and, if homologous chromosomes fail to pair and recombine, checkpoint machinery responds by eliciting signals to induce apoptosis. However, in many species males possess a single X chromosome that is transcriptionally silenced, accumulates repressive histone marks, and is not recognized as partnerless by meiotic checkpoints. Here, we used C. elegans to investigate how the male X is precluded from checkpoint signaling and uncovered a role for conserved chromatin-remodeling proteins that block checkpoints and mediate meiotic silencing. Our data elucidate the molecular mechanisms by which chromatin architecture influences both transcriptional silencing and checkpoint response to breaks on unpaired sex chromosomes, and we propose a model by which repressive chromatin modifiers directly block meiotic checkpoints from accessing the male X chromosome.
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Affiliation(s)
- Paula M. Checchi
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California, United States of America
| | - JoAnne Engebrecht
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California, United States of America
- * E-mail:
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39
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Wenzel D, Palladino F, Jedrusik-Bode M. Epigenetics in C. elegans: facts and challenges. Genesis 2011; 49:647-61. [PMID: 21538806 DOI: 10.1002/dvg.20762] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 04/14/2011] [Accepted: 04/15/2011] [Indexed: 12/31/2022]
Abstract
Epigenetics is defined as the study of heritable changes in gene expression that are not accompanied by changes in the DNA sequence. Epigenetic mechanisms include histone post-translational modifications, histone variant incorporation, non-coding RNAs, and nucleosome remodeling and exchange. In addition, the functional compartmentalization of the nucleus also contributes to epigenetic regulation of gene expression. Studies on the molecular mechanisms underlying epigenetic phenomena and their biological function have relied on various model systems, including yeast, plants, flies, and cultured mammalian cells. Here we will expose the reader to the current understanding of epigenetic regulation in the roundworm C. elegans. We will review recent models of nuclear organization and its impact on gene expression, the biological role of enzymes modifying core histones, and the function of chromatin-associated factors, with special emphasis on Polycomb (PcG) and Trithorax (Trx-G) group proteins. We will discuss how the C. elegans model has provided novel insight into mechanisms of epigenetic regulation as well as suggest directions for future research.
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Affiliation(s)
- Dirk Wenzel
- Electron Microscopy Group 3 Epigenetics in C. elegans Group, Max Planck Institute for Biophysical Chemistry, Am Faβberg 11, 37077 Göttingen, Germany
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40
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Tabuchi TM, Deplancke B, Osato N, Zhu LJ, Barrasa MI, Harrison MM, Horvitz HR, Walhout AJM, Hagstrom KA. Chromosome-biased binding and gene regulation by the Caenorhabditis elegans DRM complex. PLoS Genet 2011; 7:e1002074. [PMID: 21589891 PMCID: PMC3093354 DOI: 10.1371/journal.pgen.1002074] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 03/25/2011] [Indexed: 01/28/2023] Open
Abstract
DRM is a conserved transcription factor complex that includes E2F/DP and pRB
family proteins and plays important roles in development and cancer. Here we
describe new aspects of DRM binding and function revealed through genome-wide
analyses of the Caenorhabditis elegans DRM subunit LIN-54. We
show that LIN-54 DNA-binding activity recruits DRM to promoters enriched for
adjacent putative E2F/DP and LIN-54 binding sites, suggesting that these two
DNA–binding moieties together direct DRM to its target genes. Chromatin
immunoprecipitation and gene expression profiling reveals conserved roles for
DRM in regulating genes involved in cell division, development, and
reproduction. We find that LIN-54 promotes expression of reproduction genes in
the germline, but prevents ectopic activation of germline-specific genes in
embryonic soma. Strikingly, C. elegans DRM does not act
uniformly throughout the genome: the DRM recruitment motif, DRM binding, and
DRM-regulated embryonic genes are all under-represented on the X chromosome.
However, germline genes down-regulated in lin-54 mutants are
over-represented on the X chromosome. We discuss models for how loss of
autosome-bound DRM may enhance germline X chromosome silencing. We propose that
autosome-enriched binding of DRM arose in C. elegans as a
consequence of germline X chromosome silencing and the evolutionary
redistribution of germline-expressed and essential target genes to autosomes.
Sex chromosome gene regulation may thus have profound evolutionary effects on
genome organization and transcriptional regulatory networks. X chromosomes differ in number between the sexes and differ from autosomes in
their associated proteins and gene regulatory properties. In C.
elegans both X chromosomes are partially silenced in hermaphrodite
germlines. Germline-expressed and essential genes are autosome-enriched and are
thought to have fled the X chromosome during evolution because silencing these
genes would result in sterility or lethality. We discovered that the C.
elegans DRM complex, which controls transcription of genes
implicated in development and cancer, avoids the X chromosome. We first describe
how DNA–binding components of the DRM complex together recognize DNA
sequences upstream of its target genes, and we describe that DRM controls
different target genes in the germline versus the soma. We show that the DRM
binding motif, the genes bound by DRM, and the embryonic genes regulated by DRM
are all under-represented on the X chromosome. Interestingly, compromising DRM
function in the germline enhances X chromosome silencing, and we discuss how
autosome-bound DRM might regulate X-linked genes in trans. We
propose that autosome-enriched binding of DRM co-evolved with the redistribution
of its germline-expressed and essential target genes to autosomes. Our data
highlight how X chromosome gene regulation may impact both the genomic
distribution of gene sets and their transcriptional regulators.
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Affiliation(s)
- Tomoko M. Tabuchi
- Program in Molecular Medicine and Program in Cell Dynamics, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
| | - Bart Deplancke
- Program in Gene Function and Expression and Program in Molecular
Medicine, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
| | - Naoki Osato
- Program in Gene Function and Expression and Program in Molecular
Medicine, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
| | - Lihua J. Zhu
- Program in Gene Function and Expression and Program in Molecular
Medicine, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
| | - M. Inmaculada Barrasa
- Program in Gene Function and Expression and Program in Molecular
Medicine, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
| | - Melissa M. Harrison
- Howard Hughes Medical Institute, Department of Biology, Massachusetts
Institute of Technology, Cambridge, Massachusetts, United States of
America
| | - H. Robert Horvitz
- Howard Hughes Medical Institute, Department of Biology, Massachusetts
Institute of Technology, Cambridge, Massachusetts, United States of
America
| | - Albertha J. M. Walhout
- Program in Gene Function and Expression and Program in Molecular
Medicine, University of Massachusetts Medical School, Worcester, Massachusetts,
United States of America
- * E-mail: (KAH); (AJMW)
| | - Kirsten A. Hagstrom
- Program in Molecular Medicine and Program in Cell Dynamics, University of
Massachusetts Medical School, Worcester, Massachusetts, United States of
America
- * E-mail: (KAH); (AJMW)
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41
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Abstract
The RB1 gene is the first tumor suppressor gene identified whose mutational inactivation is the cause of a human cancer, the pediatric cancer retinoblastoma. The 25 years of research since its discovery has not only illuminated a general role for RB1 in human cancer, but also its critical importance in normal development. Understanding the molecular function of the RB1 encoded protein, pRb, is a long-standing goal that promises to inform our understanding of cancer, its relationship to normal development, and possible therapeutic strategies to combat this disease. Achieving this goal has been difficult, complicated by the complexity of pRb and related proteins. The goal of this review is to explore the hypothesis that, at its core, the molecular function of pRb is to dynamically regulate the location-specific assembly or disassembly of protein complexes on the DNA in response to the output of various signaling pathways. These protein complexes participate in a variety of molecular processes relevant to DNA including gene transcription, DNA replication, DNA repair, and mitosis. Through regulation of these processes, RB1 plays a uniquely prominent role in normal development and cancer.
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Affiliation(s)
- Meenalakshmi Chinnam
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York, USA
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42
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xnd-1 regulates the global recombination landscape in Caenorhabditis elegans. Nature 2010; 467:839-43. [PMID: 20944745 PMCID: PMC3045774 DOI: 10.1038/nature09429] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 08/18/2010] [Indexed: 01/14/2023]
Abstract
Meiotic crossover (CO) recombination establishes physical linkages between homologous chromosomes that are required for their proper segregation into developing gametes, and promotes genetic diversity by shuffling genetic material between parental chromosomes. COs require the formation of double strand breaks (DSBs) to create the substrate for strand exchange. DSBs occur in small intervals called hotspots and significant variation in hotspot usage exists between and among individuals. This variation is thought to reflect differences in sequence identity and chromatin structure, DNA topology and/ or chromosome domain organization. Chromosomes show different frequencies of nondisjunction (NDJ), reflecting inherent differences in meiotic crossover control, yet the underlying basis of these differences remains elusive. Here we show that a novel chromatin factor, X non-disjunction factor 1 (xnd-1), is responsible for the global distribution of COs in C. elegans. xnd-1 is also required for formation of double-strand breaks (DSBs) on the X, but surprisingly XND-1 protein is autosomally enriched. We show that xnd-1 functions independently of genes required for X chromosome-specific gene silencing, revealing a novel pathway that distinguishes the X from autosomes in the germ line, and further show that xnd-1 exerts its effects on COs, at least in part, by modulating levels of H2A lysine 5 acetylation.
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43
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Furuhashi H, Kelly WG. The epigenetics of germ-line immortality: lessons from an elegant model system. Dev Growth Differ 2010; 52:527-32. [PMID: 20646025 DOI: 10.1111/j.1440-169x.2010.01179.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Epigenetic mechanisms are thought to help regulate the unique transcription program that is established in germ cell development. During the germline cycle of many organisms, the epigenome undergoes waves of extensive resetting events, while a part of epigenetic modification remains faithful to specific loci. Little is known about the mechanisms underlying these events, how loci are selected for, or avoid, reprogramming, or even why these events are required. In particular, although the significance of genomic imprinting phenomena involving DNA methylation in mammals is now well accepted, the role of histone modification as a transgenerational epigenetic mechanism has been the subject of debate. Such epigenetic mechanisms may help regulate transcription programs and/or the pluripotent status conferred on germ cells, and contribute to germ line continuity across generations. Recent studies provide new evidence for heritability of histone modifications through germ line cells and its potential effects on transcription regulation both in the soma and germ line of subsequent generations. Unraveling transgenerational epigenetic mechanisms involving highly conserved histone modifications in elegant model systems will accelerate the generation of new paradigms and inspire research in a wide variety of fields, including basic developmental studies and clinical stem cell research.
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Affiliation(s)
- Hirofumi Furuhashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.
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44
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Rechtsteiner A, Ercan S, Takasaki T, Phippen TM, Egelhofer TA, Wang W, Kimura H, Lieb JD, Strome S. The histone H3K36 methyltransferase MES-4 acts epigenetically to transmit the memory of germline gene expression to progeny. PLoS Genet 2010; 6:e1001091. [PMID: 20824077 PMCID: PMC2932692 DOI: 10.1371/journal.pgen.1001091] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 07/26/2010] [Indexed: 11/25/2022] Open
Abstract
Methylation of histone H3K36 in higher eukaryotes is mediated by multiple methyltransferases. Set2-related H3K36 methyltransferases are targeted to genes by association with RNA Polymerase II and are involved in preventing aberrant transcription initiation within the body of genes. The targeting and roles of the NSD family of mammalian H3K36 methyltransferases, known to be involved in human developmental disorders and oncogenesis, are not known. We used genome-wide chromatin immunoprecipitation (ChIP) to investigate the targeting and roles of the Caenorhabditis elegans NSD homolog MES-4, which is maternally provided to progeny and is required for the survival of nascent germ cells. ChIP analysis in early C. elegans embryos revealed that, consistent with immunostaining results, MES-4 binding sites are concentrated on the autosomes and the leftmost ∼2% (300 kb) of the X chromosome. MES-4 overlies the coding regions of approximately 5,000 genes, with a modest elevation in the 5′ regions of gene bodies. Although MES-4 is generally found over Pol II-bound genes, analysis of gene sets with different temporal-spatial patterns of expression revealed that Pol II association with genes is neither necessary nor sufficient to recruit MES-4. In early embryos, MES-4 associates with genes that were previously expressed in the maternal germ line, an interaction that does not require continued association of Pol II with those loci. Conversely, Pol II association with genes newly expressed in embryos does not lead to recruitment of MES-4 to those genes. These and other findings suggest that MES-4, and perhaps the related mammalian NSD proteins, provide an epigenetic function for H3K36 methylation that is novel and likely to be unrelated to ongoing transcription. We propose that MES-4 transmits the memory of gene expression in the parental germ line to offspring and that this memory role is critical for the PGCs to execute a proper germline program. Germ cells transmit the genome from one generation to the next. The identity and immortality of germ cells are crucial for the perpetuation of species, yet the mechanisms that regulate these properties remain elusive. In C.elegans, a histone methyltransferase MES-4 is required for survival of the primordial germ cells. MES-4 methylates histone H3 at lysine 36 (H3K36), a modification previously linked to transcription elongation and involved in preventing aberrant transcription initiation within the body of genes. Surprisingly, our genome-wide analysis of MES-4 binding sites in C. elegans embryos revealed that MES-4 is capable of associating with genes that were expressed in the germ line of the parent worms but are no longer being actively transcribed in embryos. To our knowledge, this is the first example of transcription-uncoupled H3K36 methylation. We suggest that MES-4-generated H3K36 methylation serves an “epigenetic role,” by marking germline-expressed genes and by carrying the memory of gene expression from one generation of germ cells to the next.
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Affiliation(s)
- Andreas Rechtsteiner
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Sevinc Ercan
- Department of Biology, Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Teruaki Takasaki
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Taryn M. Phippen
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Thea A. Egelhofer
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Wenchao Wang
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Hiroshi Kimura
- Graduate School for Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Jason D. Lieb
- Department of Biology, Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail: (SS); (JDL)
| | - Susan Strome
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (SS); (JDL)
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45
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Furuhashi H, Takasaki T, Rechtsteiner A, Li T, Kimura H, Checchi PM, Strome S, Kelly WG. Trans-generational epigenetic regulation of C. elegans primordial germ cells. Epigenetics Chromatin 2010; 3:15. [PMID: 20704745 PMCID: PMC3146070 DOI: 10.1186/1756-8935-3-15] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Accepted: 08/12/2010] [Indexed: 12/21/2022] Open
Abstract
Background The processes through which the germline maintains its continuity across generations has long been the focus of biological research. Recent studies have suggested that germline continuity can involve epigenetic regulation, including regulation of histone modifications. However, it is not clear how histone modifications generated in one generation can influence the transcription program and development of germ cells of the next. Results We show that the histone H3K36 methyltransferase maternal effect sterile (MES)-4 is an epigenetic modifier that prevents aberrant transcription activity in Caenorhabditis elegans primordial germ cells (PGCs). In mes-4 mutant PGCs, RNA Pol II activation is abnormally regulated and the PGCs degenerate. Genetic and genomewide analyses of MES-4-mediated H3K36 methylation suggest that MES-4 activity can operate independently of ongoing transcription, and may be predominantly responsible for maintenance methylation of H3K36 in germline-expressed loci. Conclusions Our data suggest a model in which MES-4 helps to maintain an 'epigenetic memory' of transcription that occurred in germ cells of previous generations, and that MES-4 and its epigenetic product are essential for normal germ cell development.
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46
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Maine EM. Meiotic silencing in Caenorhabditis elegans. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 282:91-134. [PMID: 20630467 DOI: 10.1016/s1937-6448(10)82002-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In many animals and some fungi, mechanisms have been described that target unpaired chromosomes and chromosomal regions for silencing during meiotic prophase. These phenomena, collectively called "meiotic silencing," target sex chromosomes in the heterogametic sex, for example, the X chromosome in male nematodes and the XY-body in male mice, and also target any other chromosomes that fail to synapse due to mutation or chromosomal rearrangement. Meiotic silencing phenomena are hypothesized to maintain genome integrity and perhaps function in setting up epigenetic control of embryogenesis. This review focuses on meiotic silencing in the nematode, Caenorhabditis elegans, including its mechanism and function(s), and its relationship to other gene silencing processes in the germ line. One hallmark of meiotic silencing in C. elegans is that unpaired/unsynapsed chromosomes and chromosomal regions become enriched for a repressive histone modification, dimethylation of histone H3 on lysine 9 (H3K9me2). Accumulation and proper targeting of H3K9me2 rely on activity of an siRNA pathway, suggesting that histone methyltransferase activity may be targeted/regulated by a small RNA-based transcriptional silencing mechanism.
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Affiliation(s)
- Eleanor M Maine
- Department of Biology, Syracuse University, Syracuse, New York, USA
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47
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Abstract
Although now dogma, the idea that nonvertebrate organisms such as yeast, worms, and flies could inform, and in some cases even revolutionize, our understanding of oncogenesis in humans was not immediately obvious. Aided by the conservative nature of evolution and the persistence of a cohort of devoted researchers, the role of model organisms as a key tool in solving the cancer problem has, however, become widely accepted. In this review, we focus on the nematode Caenorhabditis elegans and its diverse and sometimes surprising contributions to our understanding of the tumorigenic process. Specifically, we discuss findings in the worm that address a well-defined set of processes known to be deregulated in cancer cells including cell cycle progression, growth factor signaling, terminal differentiation, apoptosis, the maintenance of genome stability, and developmental mechanisms relevant to invasion and metastasis.
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Affiliation(s)
- Natalia V. Kirienko
- University of Wyoming, College of Agriculture, Department of Molecular Biology, Dept 3944, 1000 E. University Avenue, Laramie, WY 82071
| | - Kumaran Mani
- University of Wyoming, College of Agriculture, Department of Molecular Biology, Dept 3944, 1000 E. University Avenue, Laramie, WY 82071
| | - David S. Fay
- University of Wyoming, College of Agriculture, Department of Molecular Biology, Dept 3944, 1000 E. University Avenue, Laramie, WY 82071
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48
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Korta DZ, Hubbard EJA. Soma-germline interactions that influence germline proliferation in Caenorhabditis elegans. Dev Dyn 2010; 239:1449-59. [PMID: 20225254 PMCID: PMC3323287 DOI: 10.1002/dvdy.22268] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Caenorhabditis elegans boasts a short lifecycle and high fecundity, two features that make it an attractive and powerful genetic model organism. Several recent studies indicate that germline proliferation, a prerequisite to optimal fecundity, is tightly controlled over the course of development. Cell proliferation control includes regulation of competence to proliferate, a poorly understood aspect of cell fate specification, as well as cell-cycle control. Furthermore, dynamic regulation of cell proliferation occurs in response to multiple external signals. The C. elegans germ line is proving a valuable model for linking genetic, developmental, systemic, and environmental control of cell proliferation. Here, we consider recent studies that contribute to our understanding of germ cell proliferation in C. elegans. We focus primarily on somatic control of germline proliferation, how it differs at different life stages, and how it can be altered in the context of the life cycle and changes in environmental status.
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Affiliation(s)
- Dorota Z. Korta
- Developmental Genetics Program, Department of Pathology, Helen and Martin Kimmel Center for Stem Cell Biology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York
| | - E. Jane Albert Hubbard
- Developmental Genetics Program, Department of Pathology, Helen and Martin Kimmel Center for Stem Cell Biology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York
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49
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Petty EL, Collette KS, Cohen AJ, Snyder MJ, Csankovszki G. Restricting dosage compensation complex binding to the X chromosomes by H2A.Z/HTZ-1. PLoS Genet 2009; 5:e1000699. [PMID: 19851459 PMCID: PMC2760203 DOI: 10.1371/journal.pgen.1000699] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Accepted: 09/23/2009] [Indexed: 01/15/2023] Open
Abstract
Dosage compensation ensures similar levels of X-linked gene products in males (XY or XO) and females (XX), despite their different numbers of X chromosomes. In mammals, flies, and worms, dosage compensation is mediated by a specialized machinery that localizes to one or both of the X chromosomes in one sex resulting in a change in gene expression from the affected X chromosome(s). In mammals and flies, dosage compensation is associated with specific histone posttranslational modifications and replacement with variant histones. Until now, no specific histone modifications or histone variants have been implicated in Caenorhabditis elegans dosage compensation. Taking a candidate approach, we have looked at specific histone modifications and variants on the C. elegans dosage compensated X chromosomes. Using RNAi-based assays, we show that reducing levels of the histone H2A variant, H2A.Z (HTZ-1 in C. elegans), leads to partial disruption of dosage compensation. By immunofluorescence, we have observed that HTZ-1 is under-represented on the dosage compensated X chromosomes, but not on the non-dosage compensated male X chromosome. We find that reduction of HTZ-1 levels by RNA interference (RNAi) and mutation results in only a very modest change in dosage compensation complex protein levels. However, in these animals, the X chromosome-specific localization of the complex is partially disrupted, with some nuclei displaying DCC localization beyond the X chromosome territory. We propose a model in which HTZ-1, directly or indirectly, serves to restrict the dosage compensation complex to the X chromosome by acting as or regulating the activity of an autosomal repellant.
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Affiliation(s)
- Emily L. Petty
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Karishma S. Collette
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alysse J. Cohen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Martha J. Snyder
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Györgyi Csankovszki
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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50
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Simon JA, Kingston RE. Mechanisms of polycomb gene silencing: knowns and unknowns. Nat Rev Mol Cell Biol 2009; 10:697-708. [PMID: 19738629 DOI: 10.1038/nrm2763] [Citation(s) in RCA: 1004] [Impact Index Per Article: 66.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Polycomb proteins form chromatin-modifying complexes that implement transcriptional silencing in higher eukaryotes. Hundreds of genes are silenced by Polycomb proteins, including dozens of genes that encode crucial developmental regulators in organisms ranging from plants to humans. Two main families of complexes, called Polycomb repressive complex 1 (PRC1) and PRC2, are targeted to repressed regions. Recent studies have advanced our understanding of these complexes, including their potential mechanisms of gene silencing, the roles of chromatin modifications, their means of delivery to target genes and the functional distinctions among variant complexes. Emerging concepts include the existence of a Polycomb barrier to transcription elongation and the involvement of non-coding RNAs in the targeting of Polycomb complexes. These findings have an impact on the epigenetic programming of gene expression in many biological systems.
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Affiliation(s)
- Jeffrey A Simon
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis 55455, USA.
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