51
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Braun S, Barrales RR. Beyond Tethering and the LEM domain: MSCellaneous functions of the inner nuclear membrane Lem2. Nucleus 2016; 7:523-531. [PMID: 27797637 DOI: 10.1080/19491034.2016.1252892] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The nuclear envelope plays a pivotal role in the functional organization of chromatin. Various inner nuclear membrane (INM) proteins associate with transcriptionally repressed chromatin, which is often found at the nuclear periphery. A prominent example is the conserved family of LEM (LAP2-Emerin-MAN1) domain proteins that interact with DNA-binding proteins and have been proposed to mediate tethering of chromatin to the nuclear membrane. We recently reported that the fission yeast protein Lem2, a homolog of metazoan LEM proteins, contributes to perinuclear localization and silencing of heterochromatin. 1 We demonstrate that binding and tethering of centromeric chromatin depends on the LEM domain of Lem2. Unexpectedly, this domain is dispensable for heterochromatin silencing, which is instead mediated by a different structural domain of Lem2, the MSC (MAN1-Src1 C-terminal) domain. Hence, silencing and tethering by Lem2 can be mechanistically separated. Notably, the MSC domain has multiple functions beyond heterochromatic silencing. Here we discuss the implications of these novel findings for the understanding of this conserved INM protein.
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Affiliation(s)
- Sigurd Braun
- a Department of Physiological Chemistry , Biomedical Center (BMC), Ludwig-Maximilians-University of Munich , Martinsried , Germany
| | - Ramón Ramos Barrales
- a Department of Physiological Chemistry , Biomedical Center (BMC), Ludwig-Maximilians-University of Munich , Martinsried , Germany.,b Present address: Centro Andaluz de Biología del Desarrollo. Universidad Pablo de Olavide, Sevilla-CSIC-Junta de Andalucía , Sevilla , Spain
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52
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Simmons MJ, Grimes CD, Czora CS. Cytotype Regulation Facilitates Repression of Hybrid Dysgenesis by Naturally Occurring KP Elements in Drosophila melanogaster. G3 (BETHESDA, MD.) 2016; 6:1891-7. [PMID: 27172198 PMCID: PMC4938643 DOI: 10.1534/g3.116.028597] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/22/2016] [Indexed: 11/18/2022]
Abstract
P elements inserted in the Telomere Associated Sequences (TAS) at the left end of the X chromosome are determiners of cytotype regulation of the entire P family of transposons. This regulation is mediated by Piwi-interacting (pi) RNAs derived from the telomeric P elements (TPs). Because these piRNAs are transmitted maternally, cytotype regulation is manifested as a maternal effect of the TPs. When a TP is combined with a transgenic P element inserted at another locus, this maternal effect is strengthened. However, when certain TPs are combined with transgenes that contain the small P element known as KP, stronger regulation arises from a zygotic effect of the KP element. This zygotic effect is observed with transgenic KP elements that are structurally intact, as well as with KP elements that are fused to an ancillary promoter from the hsp70 gene. Zygotic regulation by a KP element occurs only when a TP was present in the maternal germ line, and it is more pronounced when the TP was also present in the grand-maternal germ line. However, this regulation does not require zygotic expression of the TP These observations can be explained if maternally transmitted piRNAs from TPs enable a polypeptide encoded by KP elements to repress P element transposition in zygotes that contain a KP element. In nature, repression by the KP polypeptide may therefore be facilitated by cytotype-mediating piRNAs.
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Affiliation(s)
- Michael J Simmons
- Department of Genetics, Cell Biology, and Development, University of Minnesota, St. Paul, Minnesota 55108-1095
| | - Craig D Grimes
- Department of Genetics, Cell Biology, and Development, University of Minnesota, St. Paul, Minnesota 55108-1095
| | - Cody S Czora
- Department of Genetics, Cell Biology, and Development, University of Minnesota, St. Paul, Minnesota 55108-1095
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53
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Atwood BL, Woolnough JL, Lefevre GM, Saint Just Ribeiro M, Felsenfeld G, Giles KE. Human Argonaute 2 Is Tethered to Ribosomal RNA through MicroRNA Interactions. J Biol Chem 2016; 291:17919-28. [PMID: 27288410 DOI: 10.1074/jbc.m116.725051] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Indexed: 11/06/2022] Open
Abstract
The primary role of the RNAi machinery is to promote mRNA degradation within the cytoplasm in a microRNA-dependent manner. However, both Dicer and the Argonaute protein family have expanded roles in gene regulation within the nucleus. To further our understanding of this role, we have identified chromatin binding sites for AGO2 throughout the 45S region of the human rRNA gene. The location of these sites was mirrored by the positions of AGO2 cross-linking sites identified via PAR-CLIP-seq. AGO2 binding to the rRNA within the nucleus was confirmed by RNA immunoprecipitation and quantitative-PCR. To explore a possible mechanism by which AGO2 could be recruited to the rRNA, we identified 1174 regions within the 45S rRNA transcript that have the ability to form a perfect duplex with position 2-6 (seed sequence) of each microRNA expressed in HEK293T cells. Of these potential AGO2 binding sites, 479 occurred within experimentally verified AGO2-rRNA cross-linking sites. The ability of AGO2 to cross-link to rRNA was almost completely lost in a DICER knock-out cell line. The transfection of miR-92a-2-3p into the noDICE cell line facilitated AGO2 cross-linking at a region of the rRNA that has a perfect seed match at positions 3-8, including a single G-U base pair. Knockdown of AGO2 within HEK293T cells causes a slight, but statistically significant increase in the overall rRNA synthesis rate but did not impact the ratio of processing intermediates or the recruitment of the Pol I transcription factor UBTF.
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Affiliation(s)
- Blake L Atwood
- From the UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35209 and
| | - Jessica L Woolnough
- From the UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35209 and
| | - Gaelle M Lefevre
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland
| | - Mariana Saint Just Ribeiro
- From the UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35209 and
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland
| | - Keith E Giles
- From the UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35209 and
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54
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Interconnections Between RNA-Processing Pathways Revealed by a Sequencing-Based Genetic Screen for Pre-mRNA Splicing Mutants in Fission Yeast. G3-GENES GENOMES GENETICS 2016; 6:1513-23. [PMID: 27172183 PMCID: PMC4889648 DOI: 10.1534/g3.116.027508] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Pre-mRNA splicing is an essential component of eukaryotic gene expression and is highly conserved from unicellular yeasts to humans. Here, we present the development and implementation of a sequencing-based reverse genetic screen designed to identify nonessential genes that impact pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe, an organism that shares many of the complex features of splicing in higher eukaryotes. Using a custom-designed barcoding scheme, we simultaneously queried ∼3000 mutant strains for their impact on the splicing efficiency of two endogenous pre-mRNAs. A total of 61 nonessential genes were identified whose deletions resulted in defects in pre-mRNA splicing; enriched among these were factors encoding known or predicted components of the spliceosome. Included among the candidates identified here are genes with well-characterized roles in other RNA-processing pathways, including heterochromatic silencing and 3ʹ end processing. Splicing-sensitive microarrays confirm broad splicing defects for many of these factors, revealing novel functional connections between these pathways.
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55
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Rando OJ. Intergenerational Transfer of Epigenetic Information in Sperm. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a022988. [PMID: 26801897 DOI: 10.1101/cshperspect.a022988] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The inheritance of information beyond DNA sequence, known as epigenetic inheritance, has been implicated in a multitude of biological processes from control of plant flowering time to cancer in humans. In addition to epigenetic inheritance that occurs in dividing cells of a multicellular organism, it is also increasingly clear that at least some epigenetic information is transmitted via the gametes in a multitude of organisms, including mammals. Here, I review the evidence for epigenetic information carriers in mammalian sperm, and explore the emerging field of intergenerational transfer of environmental information.
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Affiliation(s)
- Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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56
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Götz U, Marker S, Cheaib M, Andresen K, Shrestha S, Durai DA, Nordström KJ, Schulz MH, Simon M. Two sets of RNAi components are required for heterochromatin formation in trans triggered by truncated transgenes. Nucleic Acids Res 2016; 44:5908-23. [PMID: 27085807 PMCID: PMC4937312 DOI: 10.1093/nar/gkw267] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 04/04/2016] [Indexed: 12/13/2022] Open
Abstract
Across kingdoms, RNA interference (RNAi) has been shown to control gene expression at the transcriptional- or the post-transcriptional level. Here, we describe a mechanism which involves both aspects: truncated transgenes, which fail to produce intact mRNA, induce siRNA accumulation and silencing of homologous loci in trans in the ciliate Paramecium. We show that silencing is achieved by co-transcriptional silencing, associated with repressive histone marks at the endogenous gene. This is accompanied by secondary siRNA accumulation, strictly limited to the open reading frame of the remote locus. Our data shows that in this mechanism, heterochromatic marks depend on a variety of RNAi components. These include RDR3 and PTIWI14 as well as a second set of components, which are also involved in post-transcriptional silencing: RDR2, PTIWI13, DCR1 and CID2. Our data indicates differential processing of nascent un-spliced and long, spliced transcripts thus suggesting a hitherto-unrecognized functional interaction between post-transcriptional and co-transcriptional RNAi. Both sets of RNAi components are required for efficient trans-acting RNAi at the chromatin level and our data indicates similar mechanisms contributing to genome wide regulation of gene expression by epigenetic mechanisms.
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Affiliation(s)
- Ulrike Götz
- Molecular Cell Dynamics Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany Department of Biology, University of Kaiserslautern, Erwin-Schrödinger Straße, Building Nr. 14, 67663 Kaiserslautern, Germany
| | - Simone Marker
- Molecular Cell Dynamics Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany
| | - Miriam Cheaib
- Molecular Cell Dynamics Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany Department of Biology, University of Kaiserslautern, Erwin-Schrödinger Straße, Building Nr. 14, 67663 Kaiserslautern, Germany
| | - Karsten Andresen
- Institute of Biotechnology and Drug Research, Erwin-Schrödinger-Str. 56, 67663 Kaiserslautern, Germany
| | - Simon Shrestha
- Molecular Cell Dynamics Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany Department of Biology, University of Kaiserslautern, Erwin-Schrödinger Straße, Building Nr. 14, 67663 Kaiserslautern, Germany
| | - Dilip A Durai
- Cluster of Excellence, Multimodal Computing and Interaction and Max Planck Institute for Informatics Saarland University, Department for Computational Biology and Applied Algorithmics, Campus E1 4, 66123 Saarbrücken, Germany
| | - Karl J Nordström
- Department for Genetics, Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany
| | - Marcel H Schulz
- Cluster of Excellence, Multimodal Computing and Interaction and Max Planck Institute for Informatics Saarland University, Department for Computational Biology and Applied Algorithmics, Campus E1 4, 66123 Saarbrücken, Germany
| | - Martin Simon
- Molecular Cell Dynamics Saarland University, Centre for Human and Molecular Biology, Campus A2 4, 66123 Saarbrücken, Germany
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57
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Tasselli L, Xi Y, Zheng W, Tennen RI, Odrowaz Z, Simeoni F, Li W, Chua KF. SIRT6 deacetylates H3K18ac at pericentric chromatin to prevent mitotic errors and cellular senescence. Nat Struct Mol Biol 2016; 23:434-40. [PMID: 27043296 PMCID: PMC5826646 DOI: 10.1038/nsmb.3202] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 03/11/2016] [Indexed: 12/12/2022]
Abstract
Pericentric heterochromatin silencing at mammalian centromeres is essential for mitotic fidelity and genomic stability. Defective pericentric silencing has been observed in senescent cells, aging tissues, and mammalian tumors, but the underlying mechanisms and functional consequences of these defects are unclear. Here, we uncover an essential role of the human SIRT6 enzyme in pericentric transcriptional silencing, and we show that this function protects against mitotic defects, genomic instability, and cellular senescence. At pericentric heterochromatin, SIRT6 promotes deacetylation of a new substrate, residue K18 of histone H3 (H3K18), and inactivation of SIRT6 in cells leads to H3K18 hyperacetylation and aberrant accumulation of pericentric transcripts. Strikingly, depletion of these transcripts through RNA interference rescues the mitotic and senescence phenotypes of SIRT6-deficient cells. Together, our findings reveal a new function for SIRT6 and regulation of acetylated H3K18 at heterochromatin, and demonstrate the pathogenic role of deregulated pericentric transcription in aging- and cancer-related cellular dysfunction.
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Affiliation(s)
- Luisa Tasselli
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Geriatric Research, Education, and Clinical Center, Veterans Affairs, Palo Alto Health Care System, Palo Alto, California, USA
| | - Yuanxin Xi
- Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Wei Zheng
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Geriatric Research, Education, and Clinical Center, Veterans Affairs, Palo Alto Health Care System, Palo Alto, California, USA
| | - Ruth I Tennen
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Zaneta Odrowaz
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Geriatric Research, Education, and Clinical Center, Veterans Affairs, Palo Alto Health Care System, Palo Alto, California, USA
| | - Federica Simeoni
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Geriatric Research, Education, and Clinical Center, Veterans Affairs, Palo Alto Health Care System, Palo Alto, California, USA
| | - Wei Li
- Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Katrin F Chua
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Geriatric Research, Education, and Clinical Center, Veterans Affairs, Palo Alto Health Care System, Palo Alto, California, USA
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58
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Tucker JF, Ohle C, Schermann G, Bendrin K, Zhang W, Fischer T, Zhang K. A Novel Epigenetic Silencing Pathway Involving the Highly Conserved 5'-3' Exoribonuclease Dhp1/Rat1/Xrn2 in Schizosaccharomyces pombe. PLoS Genet 2016; 12:e1005873. [PMID: 26889830 PMCID: PMC4758730 DOI: 10.1371/journal.pgen.1005873] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 01/26/2016] [Indexed: 01/09/2023] Open
Abstract
Epigenetic gene silencing plays a critical role in regulating gene expression and contributes to organismal development and cell fate acquisition in eukaryotes. In fission yeast, Schizosaccharomyces pombe, heterochromatin-associated gene silencing is known to be mediated by RNA processing pathways including RNA interference (RNAi) and a 3’-5’ exoribonuclease complex, the exosome. Here, we report a new RNA-processing pathway that contributes to epigenetic gene silencing and assembly of heterochromatin mediated by 5’-3’ exoribonuclease Dhp1/Rat1/Xrn2. Dhp1 mutation causes defective gene silencing both at peri-centromeric regions and at the silent mating type locus. Intriguingly, mutation in either of the two well-characterized Dhp1-interacting proteins, the Din1 pyrophosphohydrolase or the Rhn1 transcription termination factor, does not result in silencing defects at the main heterochromatic regions. We demonstrate that Dhp1 interacts with heterochromatic factors and is essential in the sequential steps of establishing silencing in a manner independent of both RNAi and the exosome. Genomic and genetic analyses suggest that Dhp1 is involved in post-transcriptional silencing of repetitive regions through its RNA processing activity. The results describe the unexpected role of Dhp1/Rat1/Xrn2 in chromatin-based silencing and elucidate how various RNA-processing pathways, acting together or independently, contribute to epigenetic regulation of the eukaryotic genome. Epigenetic mechanisms regulate when, where, and how an organism uses the genetic information stored in its genome. They are essential to many cellular processes, such as the regulation of gene expression, genome organization, and cell-fate determination. They also govern growth, development, and ultimately human health. Heterochromatin constitutes silenced chromatic domains, in which gene silencing occurs through epigenetic mechanisms. RNA processing pathways, such as RNA interference (RNAi) and the exosome, are known to mediate the silencing of genes via degradation of unwanted or aberrant transcripts. In this study, we describe a new RNA processing mechanism in epigenetic silencing using fission yeast, a premier model for studying these processes. With genetic, cell biology, and genomic approaches, we uncovered a previously unrecognized function of Dhp1, a highly conserved 5’-3’ exoribonuclease and ortholog of budding yeast Rat1 and metazoan Xrn2. We show that Dhp1 mediates a novel RNA processing mechanism in epigenetic silencing which occurs independently of both RNAi and the exosome. Our results clarify how multiple RNA processing pathways are involved in the regulation of eukaryotic gene expression and chromatin organization.
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Affiliation(s)
- James Franklin Tucker
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Corina Ohle
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Géza Schermann
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Katja Bendrin
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Wei Zhang
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Tamás Fischer
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Ke Zhang
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
- * E-mail:
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59
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Verrier L, Taglini F, Barrales RR, Webb S, Urano T, Braun S, Bayne EH. Global regulation of heterochromatin spreading by Leo1. Open Biol 2016; 5:rsob.150045. [PMID: 25972440 PMCID: PMC4450266 DOI: 10.1098/rsob.150045] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Heterochromatin plays important roles in eukaryotic genome regulation. However, the repressive nature of heterochromatin combined with its propensity to self-propagate necessitates robust mechanisms to contain heterochromatin within defined boundaries and thus prevent silencing of expressed genes. Here we show that loss of the PAF complex (PAFc) component Leo1 compromises chromatin boundaries, resulting in invasion of heterochromatin into flanking euchromatin domains. Similar effects are seen upon deletion of other PAFc components, but not other factors with related functions in transcription-associated chromatin modification, indicating a specific role for PAFc in heterochromatin regulation. Loss of Leo1 results in reduced levels of H4K16 acetylation at boundary regions, while tethering of the H4K16 acetyltransferase Mst1 to boundary chromatin suppresses heterochromatin spreading in leo1Δ cells, suggesting that Leo1 antagonises heterochromatin spreading by promoting H4K16 acetylation. Our findings reveal a previously undescribed role for PAFc in regulating global heterochromatin distribution.
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Affiliation(s)
- Laure Verrier
- Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | | | - Ramon R Barrales
- Butenandt Institute of Physiological Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Shaun Webb
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Takeshi Urano
- Department of Biochemistry, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Sigurd Braun
- Butenandt Institute of Physiological Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
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60
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Ellahi A, Rine J. Evolution and Functional Trajectory of Sir1 in Gene Silencing. Mol Cell Biol 2016; 36:1164-79. [PMID: 26811328 PMCID: PMC4800792 DOI: 10.1128/mcb.01013-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 12/08/2015] [Accepted: 01/21/2016] [Indexed: 01/28/2023] Open
Abstract
We used the budding yeasts Saccharomyces cerevisiae and Torulaspora delbrueckii to examine the evolution of Sir-based silencing, focusing on Sir1, silencers, the molecular topography of silenced chromatin, and the roles of SIR and RNA interference (RNAi) genes in T. delbrueckii. Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) analysis of Sir proteins in T. delbrueckii revealed a different topography of chromatin at the HML and HMR loci than was observed in S. cerevisiae. S. cerevisiae Sir1, enriched at the silencers of HMLα and HMR A: , was absent from telomeres and did not repress subtelomeric genes. In contrast to S. cerevisiae SIR1's partially dispensable role in silencing, the T. delbrueckii SIR1 paralog KOS3 was essential for silencing. KOS3 was also found at telomeres with T. delbrueckii Sir2 (Td-Sir2) and Td-Sir4 and repressed subtelomeric genes. Silencer mapping in T. delbrueckii revealed single silencers at HML and HMR, bound by Td-Kos3, Td-Sir2, and Td-Sir4. The KOS3 gene mapped near HMR, and its expression was regulated by Sir-based silencing, providing feedback regulation of a silencing protein by silencing. In contrast to the prominent role of Sir proteins in silencing, T. delbrueckii RNAi genes AGO1 and DCR1 did not function in heterochromatin formation. These results highlighted the shifting role of silencing genes and the diverse chromatin architectures underlying heterochromatin.
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Affiliation(s)
- Aisha Ellahi
- Department of Molecular and Cell Biology and California Institute of Quantitative Biology, University of California Berkeley, Berkeley, California, USA
| | - Jasper Rine
- Department of Molecular and Cell Biology and California Institute of Quantitative Biology, University of California Berkeley, Berkeley, California, USA
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61
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Suzuki S, Kato H, Suzuki Y, Chikashige Y, Hiraoka Y, Kimura H, Nagao K, Obuse C, Takahata S, Murakami Y. Histone H3K36 trimethylation is essential for multiple silencing mechanisms in fission yeast. Nucleic Acids Res 2016; 44:4147-62. [PMID: 26792892 PMCID: PMC4872076 DOI: 10.1093/nar/gkw008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 12/30/2015] [Indexed: 01/09/2023] Open
Abstract
In budding yeast, Set2 catalyzes di- and trimethylation of H3K36 (H3K36me2 and H3K36me3) via an interaction between its Set2–Rpb1 interaction (SRI) domain and C-terminal repeats of RNA polymerase II (Pol2) phosphorylated at Ser2 and Ser5 (CTD-S2,5-P). H3K36me2 is sufficient for recruitment of the Rpd3S histone deacetylase complex to repress cryptic transcription from transcribed regions. In fission yeast, Set2 is also responsible for H3K36 methylation, which represses a subset of RNAs including heterochromatic and subtelomeric RNAs, at least in part via recruitment of Clr6 complex II, a homolog of Rpd3S. Here, we show that CTD-S2P-dependent interaction of fission yeast Set2 with Pol2 via the SRI domain is required for formation of H3K36me3, but not H3K36me2. H3K36me3 silenced heterochromatic and subtelomeric transcripts mainly through post-transcriptional and transcriptional mechanisms, respectively, whereas H3K36me2 was not enough for silencing. Clr6 complex II appeared not to be responsible for heterochromatic silencing by H3K36me3. Our results demonstrate that H3K36 methylation has multiple outputs in fission yeast; these findings provide insights into the distinct roles of H3K36 methylation in metazoans, which have different enzymes for synthesis of H3K36me1/2 and H3K36me3.
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Affiliation(s)
- Shota Suzuki
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Hiroaki Kato
- Department of Biochemistry, Shimane University School of Medicine, Izumo 693-8501, Japan PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi 332-0012, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Yuji Chikashige
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Hiroshi Kimura
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Koji Nagao
- Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Chikashi Obuse
- Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Shinya Takahata
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yota Murakami
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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62
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Ni JZ, Kalinava N, Chen E, Huang A, Trinh T, Gu SG. A transgenerational role of the germline nuclear RNAi pathway in repressing heat stress-induced transcriptional activation in C. elegans. Epigenetics Chromatin 2016; 9:3. [PMID: 26779286 PMCID: PMC4714518 DOI: 10.1186/s13072-016-0052-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/05/2016] [Indexed: 02/07/2023] Open
Abstract
Background Environmental stress-induced transgenerational epigenetic effects have been observed in various model organisms and human. The capacity and mechanism of such phenomena are poorly understood. In C. elegans, siRNA mediates transgenerational gene
silencing through the germline nuclear RNAi pathway. This pathway is also required to maintain the germline immortality when C. elegans is under heat stress. However, the underlying molecular mechanism is unknown. In this study, we investigated the impact of heat stress on chromatin, transcription, and siRNAs at the whole-genome level, and whether any of the heat-induced effects is transgenerationally heritable in either the wild-type or the germline nuclear RNAi mutant animals. Results We performed 12-generation temperature-shift experiments using the wild-type C. elegans and a mutant strain that lacks the germline-specific nuclear Argonaute protein HRDE-1/WAGO-9. By examining the mRNA, small RNA, RNA polymerase II, and H3K9 trimethylation profiles at the whole-genome level, we revealed an epigenetic role of HRDE-1 in repressing heat stress-induced transcriptional activation of over 280 genes. Many of these genes are in or near LTR (long-terminal repeat) retrotransposons. Strikingly, for some of these genes, the heat stress-induced transcriptional activation in the hrde-1 mutant intensifies in the late generations under the heat stress and is heritable for at least two generations after the mutant animals are shifted back to lower temperature. hrde-1 mutation also leads to siRNA expression changes of many genes. This effect on siRNA is dependent on both the temperature and generation. Conclusions Our study demonstrated that a large number of the endogenous targets of the germline nuclear RNAi pathway in C. elegans are sensitive to heat-induced transcriptional activation. This effect at certain genomic loci including LTR retrotransposons is transgenerational. Germline nuclear RNAi antagonizes this temperature effect at the transcriptional level and therefore may play a key role in heat stress response in C. elegans. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0052-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julie Zhouli Ni
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Natallia Kalinava
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Esteban Chen
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Alex Huang
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Thi Trinh
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Sam Guoping Gu
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA ; Nelson Labs A125, 604 Allison Road, Piscataway, NJ 08854 USA
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Barrales RR, Forn M, Georgescu PR, Sarkadi Z, Braun S. Control of heterochromatin localization and silencing by the nuclear membrane protein Lem2. Genes Dev 2016; 30:133-48. [PMID: 26744419 PMCID: PMC4719305 DOI: 10.1101/gad.271288.115] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/07/2015] [Indexed: 01/08/2023]
Abstract
Transcriptionally silent chromatin localizes to the nuclear periphery, which provides a special microenvironment for gene repression. A variety of nuclear membrane proteins interact with repressed chromatin, yet the functional role of these interactions remains poorly understood. Here, we show that, in Schizosaccharomyces pombe, the nuclear membrane protein Lem2 associates with chromatin and mediates silencing and heterochromatin localization. Unexpectedly, we found that these functions can be separated and assigned to different structural domains within Lem2, excluding a simple tethering mechanism. Chromatin association and tethering of centromeres to the periphery are mediated by the N-terminal LEM (LAP2-Emerin-MAN1) domain of Lem2, whereas telomere anchoring and heterochromatin silencing require exclusively its conserved C-terminal MSC (MAN1-Src1 C-terminal) domain. Particularly, silencing by Lem2 is epistatic with the Snf2/HDAC (histone deacetylase) repressor complex SHREC at telomeres, while its necessity can be bypassed by deleting Epe1, a JmjC protein with anti-silencing activity. Furthermore, we found that loss of Lem2 reduces heterochromatin association of SHREC, which is accompanied by increased binding of Epe1. This reveals a critical function of Lem2 in coordinating these antagonistic factors at heterochromatin. The distinct silencing and localization functions mediated by Lem2 suggest that these conserved LEM-containing proteins go beyond simple tethering to play active roles in perinuclear silencing.
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Affiliation(s)
- Ramón Ramos Barrales
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-University of Munich, 82152 Martinsried, Germany
| | - Marta Forn
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-University of Munich, 82152 Martinsried, Germany
| | - Paula Raluca Georgescu
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-University of Munich, 82152 Martinsried, Germany
| | - Zsuzsa Sarkadi
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-University of Munich, 82152 Martinsried, Germany
| | - Sigurd Braun
- Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-University of Munich, 82152 Martinsried, Germany; International Max Planck Research School for Molecular and Cellular Life Sciences, 82152 Martinsried, Germany
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A diffusion model for the coordination of DNA replication in Schizosaccharomyces pombe. Sci Rep 2016; 6:18757. [PMID: 26729303 PMCID: PMC4700429 DOI: 10.1038/srep18757] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/25/2015] [Indexed: 01/28/2023] Open
Abstract
The locations of proteins and epigenetic marks on the chromosomal DNA sequence are believed to demarcate the eukaryotic genome into distinct structural and functional domains that contribute to gene regulation and genome organization. However, how these proteins and epigenetic marks are organized in three dimensions remains unknown. Recent advances in proximity-ligation methodologies and high resolution microscopy have begun to expand our understanding of these spatial relationships. Here we use polymer models to examine the spatial organization of epigenetic marks, euchromatin and heterochromatin, and origins of replication within the Schizosaccharomyces pombe genome. These models incorporate data from microscopy and proximity-ligation experiments that inform on the positions of certain elements and contacts within and between chromosomes. Our results show a striking degree of compartmentalization of epigenetic and genomic features and lead to the proposal of a diffusion based mechanism, centred on the spindle pole body, for the coordination of DNA replication in S. pombe.
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Bayne EH, Bijos DA, White SA, de Lima Alves F, Rappsilber J, Allshire RC. A systematic genetic screen identifies new factors influencing centromeric heterochromatin integrity in fission yeast. Genome Biol 2015; 15:481. [PMID: 25274039 PMCID: PMC4210515 DOI: 10.1186/s13059-014-0481-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Indexed: 12/20/2022] Open
Abstract
Background Heterochromatin plays important roles in the regulation and stability of eukaryotic genomes. Both heterochromatin components and pathways that promote heterochromatin assembly, including RNA interference, RNAi, are broadly conserved between the fission yeast Schizosaccharomyces pombe and humans. As a result, fission yeast has emerged as an important model system for dissecting mechanisms governing heterochromatin integrity. Thus far, over 50 proteins have been found to contribute to heterochromatin assembly at fission yeast centromeres. However, previous studies have not been exhaustive, and it is therefore likely that further factors remain to be identified. Results To gain a more complete understanding of heterochromatin assembly pathways, we have performed a systematic genetic screen for factors required for centromeric heterochromatin integrity. In addition to known RNAi and chromatin modification components, we identified several proteins with previously undescribed roles in heterochromatin regulation. These included both known and newly characterised splicing-associated proteins, which are required for proper processing of centromeric transcripts by the RNAi pathway, and COP9 signalosome components Csn1 and Csn2, whose role in heterochromatin assembly can be explained at least in part by a role in the Ddb1-dependent degradation of the heterochromatin regulator Epe1. Conclusions This work has revealed new factors involved in RNAi-directed heterochromatin assembly in fission yeast. Our findings support and extend previous observations that implicate components of the splicing machinery as a platform for RNAi, and demonstrate a novel role for the COP9 signalosome in heterochromatin regulation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0481-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth H Bayne
- Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, UK.
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Yamashita A, Shichino Y, Yamamoto M. The long non-coding RNA world in yeasts. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:147-54. [PMID: 26265144 DOI: 10.1016/j.bbagrm.2015.08.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/29/2015] [Accepted: 08/06/2015] [Indexed: 12/26/2022]
Abstract
In recent years, it has become evident that eukaryotic genomes are pervasively transcribed and produce numerous non-coding transcripts, including long non-coding RNAs (lncRNAs). Although research of such genomic enigmas is in the early stages, a growing number of lncRNAs have been characterized and found to be principal actors in a variety of biological processes rather than merely representing transcriptional noise. Here, we review recent findings on lncRNAs in yeast systems. We especially focus on lncRNA-mediated cellular regulations to respond to environmental changes in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Akira Yamashita
- Laboratory of Cell Responses, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.
| | - Yuichi Shichino
- Laboratory of Cell Responses, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Masayuki Yamamoto
- Laboratory of Cell Responses, National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
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67
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Pilu R. Paramutation phenomena in plants. Semin Cell Dev Biol 2015; 44:2-10. [DOI: 10.1016/j.semcdb.2015.08.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 08/26/2015] [Indexed: 02/05/2023]
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68
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González-Buendía E, Escamilla-Del-Arenal M, Pérez-Molina R, Tena JJ, Guerrero G, Suaste-Olmos F, Ayala-Ortega E, Gómez-Skarmeta JL, Recillas-Targa F. A novel chromatin insulator regulates the chicken folate receptor gene from the influence of nearby constitutive heterochromatin and the β-globin locus. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:955-65. [DOI: 10.1016/j.bbagrm.2015.05.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/22/2015] [Accepted: 05/25/2015] [Indexed: 11/17/2022]
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Rando OJ, Simmons RA. I'm eating for two: parental dietary effects on offspring metabolism. Cell 2015; 161:93-105. [PMID: 25815988 PMCID: PMC4465102 DOI: 10.1016/j.cell.2015.02.021] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/22/2015] [Accepted: 02/06/2015] [Indexed: 12/18/2022]
Abstract
It has long been understood that the pathogenesis of complex diseases such as diabetes includes both genetic and environmental components. More recently, it has become clear that not only does an individual's environment influence their own metabolism, but in some cases, the environment experienced by their parents may also contribute to their risk of metabolic disease. Here, we review the evidence that parental diet influences metabolic phenotype in offspring in mammals and provide a current survey of our mechanistic understanding of these effects.
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Affiliation(s)
- Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Rebecca A Simmons
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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Marinov GK, Wang J, Handler D, Wold BJ, Weng Z, Hannon GJ, Aravin AA, Zamore PD, Brennecke J, Toth KF. Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified. Dev Cell 2015; 32:765-71. [PMID: 25805138 PMCID: PMC4494788 DOI: 10.1016/j.devcel.2015.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 12/18/2014] [Accepted: 01/14/2015] [Indexed: 11/27/2022]
Abstract
Huang et al. (2013) recently reported that chromatin immunoprecipitation sequencing (ChIP-seq) reveals the genome-wide sites of occupancy by Piwi, a piRNA-guided Argonaute protein central to transposon silencing in Drosophila. Their study also reported that loss of Piwi causes widespread rewiring of transcriptional patterns, as evidenced by changes in RNA polymerase II occupancy across the genome. Here we reanalyze their data and report that the underlying deep-sequencing dataset does not support the authors' genome-wide conclusions.
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Affiliation(s)
- Georgi K Marinov
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jie Wang
- Department of Biochemistry, University at Buffalo, Buffalo, NY 14214, USA
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences IMBA, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Barbara J Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Gregory J Hannon
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Alexei A Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Phillip D Zamore
- Howard Hughes Medical Institute, RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences IMBA, Vienna Biocenter (VBC), 1030 Vienna, Austria.
| | - Katalin Fejes Toth
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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Ni JZ, Chen E, Gu SG. Complex coding of endogenous siRNA, transcriptional silencing and H3K9 methylation on native targets of germline nuclear RNAi in C. elegans. BMC Genomics 2014; 15:1157. [PMID: 25534009 PMCID: PMC4367959 DOI: 10.1186/1471-2164-15-1157] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 12/10/2014] [Indexed: 11/14/2022] Open
Abstract
Background Small RNA-guided transcriptional silencing (nuclear RNAi) is fundamental to genome integrity and epigenetic inheritance. Despite recent progress in identifying the capability and genetic requirements for nuclear RNAi in Caenorhabditis elegans, the natural targets and cellular functions of nuclear RNAi remain elusive. Methods To resolve this gap, we coordinately examined the genome-wide profiles of transcription, histone H3 lysine 9 methylation (H3K9me) and endogenous siRNAs of a germline nuclear Argonaute (hrde-1/wago-9) mutant and identified regions on which transcription activity is markedly increased and/or H3K9me level is markedly decreased relative to wild type animals. Results Our data revealed a distinct set of native targets of germline nuclear RNAi, with the H3K9me response exhibiting both overlapping and non-overlapping distribution with the transcriptional silencing response. Interestingly LTR retrotransposons, but not DNA transposons, are highly enriched in the targets of germline nuclear RNAi. The genomic distribution of the native targets is highly constrained, with >99% of the identified targets present in five autosomes but not in the sex chromosome. By contrast, HRDE-1-associated small RNAs correspond to all chromosomes. In addition, we found that the piRNA pathway is not required for germline nuclear RNAi activity on native targets. Conclusion Germline nuclear RNAi in C. elegans is required to silence retrotransposons but not DNA transposon. Transcriptional silencing and H3K9me can occur independently of each other on the native targets of nuclear RNAi in C. elegans. Our results rule out a simple model in which nuclear Argonaute protein-associated-small RNAs are sufficient to trigger germline nuclear RNAi responses. In addition, the piRNA pathway and germline nuclear RNAi are specialized to target different types of foreign genetic elements for genome surveillance in C. elegans. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1157) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Sam Guoping Gu
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Nelson Labs A125, 604 Allison Road, Piscataway, NJ 08854, USA.
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Panspecies small-molecule disruptors of heterochromatin-mediated transcriptional gene silencing. Mol Cell Biol 2014; 35:662-74. [PMID: 25487573 PMCID: PMC4301722 DOI: 10.1128/mcb.01102-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Heterochromatin underpins gene repression, genome integrity, and chromosome segregation. In the fission yeast Schizosaccharomyces pombe, conserved protein complexes effect heterochromatin formation via RNA interference-mediated recruitment of a histone H3 lysine 9 methyltransferase to cognate chromatin regions. To identify small molecules that inhibit heterochromatin formation, we performed an in vivo screen for loss of silencing of a dominant selectable kanMX reporter gene embedded within fission yeast centromeric heterochromatin. Two structurally unrelated compounds, HMS-I1 and HMS-I2, alleviated kanMX silencing and decreased repressive H3K9 methylation levels at the transgene. The decrease in methylation caused by HMS-I1 and HMS-I2 was observed at all loci regulated by histone methylation, including centromeric repeats, telomeric regions, and the mating-type locus, consistent with inhibition of the histone deacetylases (HDACs) Clr3 and/or Sir2. Chemical-genetic epistasis and expression profiles revealed that both compounds affect the activity of the Clr3-containing Snf2/HDAC repressor complex (SHREC). In vitro HDAC assays revealed that HMS-I1 and HMS-I2 inhibit Clr3 HDAC activity. HMS-I1 also alleviated transgene reporter silencing by heterochromatin in Arabidopsis and a mouse cell line, suggesting a conserved mechanism of action. HMS-I1 and HMS-I2 bear no resemblance to known inhibitors of chromatin-based activities and thus represent novel chemical probes for heterochromatin formation and function.
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Zhang X, Li H, Burnett JC, Rossi JJ. The role of antisense long noncoding RNA in small RNA-triggered gene activation. RNA (NEW YORK, N.Y.) 2014; 20:1916-28. [PMID: 25344398 PMCID: PMC4238356 DOI: 10.1261/rna.043968.113] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) are known to regulate neighboring protein-coding genes by directing chromatin remodeling complexes, imprinting, and X-chromosome inactivation. In this study, we explore the function of lncRNAs in small RNA-triggered transcriptional gene activation (TGA), a process in which microRNAs (miRNAs) or small interfering RNAs (siRNAs) associated with Argonaute (Ago) proteins induce chromatin remodeling and gene activation at promoters with sequence complementarity. We designed a model system with different lncRNA and chromatin environments to elucidate the molecular mechanisms required for mammalian TGA. Using RNA-fluorescence in situ hybridization (FISH) and rapid amplification of cDNA ends (RACE)-PCR, we demonstrated that small RNA-triggered TGA occurs at sites where antisense lncRNAs are transcribed through the reporter gene and promoter. Small RNA-induced TGA coincided with the enrichment of Ago2 at the promoter region, but Ago2-mediated cleavage of antisense lncRNAs was not observed. Moreover, we examined the allele-specific effects of lncRNAs through a Cre-induced inversion of a poly(A) sequence that was designed to block the transcription of antisense lncRNAs through the reporter gene region in an inducible and reversible manner. Termination of nascent antisense lncRNAs abrogated gene activation triggered by small RNAs, and only allele-specific cis-acting antisense lncRNAs, but not trans-acting lncRNAs, were capable of rescuing TGA. Hence, this model revealed that antisense lncRNAs can mediate TGA in cis and not in trans, serving as a molecular scaffold for a small RNA-Ago2 complex and chromatin remodeling.
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Affiliation(s)
- Xizhe Zhang
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute at the City of Hope, Duarte, California 91010, USA
| | - Haitang Li
- Department of Molecular and Cellular Biology, Beckman Research Institute at the City of Hope, Duarte, California 91010, USA
| | - John C Burnett
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute at the City of Hope, Duarte, California 91010, USA Department of Molecular and Cellular Biology, Beckman Research Institute at the City of Hope, Duarte, California 91010, USA
| | - John J Rossi
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute at the City of Hope, Duarte, California 91010, USA Department of Molecular and Cellular Biology, Beckman Research Institute at the City of Hope, Duarte, California 91010, USA
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McCue AD, Panda K, Nuthikattu S, Choudury SG, Thomas EN, Slotkin RK. ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation. EMBO J 2014; 34:20-35. [PMID: 25388951 DOI: 10.15252/embj.201489499] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Transposable elements (TEs) generate mutations and chromosomal instability when active. To repress TE activity, eukaryotic cells evolved mechanisms to both degrade TE mRNAs into small interfering RNAs (siRNAs) and modify TE chromatin to epigenetically inhibit transcription. Since the populations of small RNAs that participate in TE post-transcriptional regulation differ from those that establish RNA-directed DNA methylation (RdDM), the mechanism through which transcriptionally active TEs transition from post-transcriptional RNAi regulation to chromatin level control has remained unclear. We have identified the molecular mechanism of a plant pathway that functions to direct DNA methylation to transcriptionally active TEs. We demonstrated that 21-22 nucleotide (nt) siRNA degradation products from the RNAi of TE mRNAs are directly incorporated into the ARGONAUTE 6 (AGO6) protein and direct AGO6 to TE chromatin to guide its function in RdDM. We find that this pathway functions in reproductive precursor cells to primarily target long centromeric high-copy transcriptionally active TEs for RdDM prior to gametogenesis. This study provides a direct mechanism that bridges the gap between the post-transcriptional regulation of TEs and the establishment of TE epigenetic silencing.
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Affiliation(s)
- Andrea D McCue
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Kaushik Panda
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | | | - Sarah G Choudury
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - Erica N Thomas
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
| | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
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Mikheyeva IV, Grady PJR, Tamburini FB, Lorenz DR, Cam HP. Multifaceted genome control by Set1 Dependent and Independent of H3K4 methylation and the Set1C/COMPASS complex. PLoS Genet 2014; 10:e1004740. [PMID: 25356590 PMCID: PMC4214589 DOI: 10.1371/journal.pgen.1004740] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 09/08/2014] [Indexed: 12/21/2022] Open
Abstract
Histone modifiers are critical regulators of chromatin-based processes in eukaryotes. The histone methyltransferase Set1, a component of the Set1C/COMPASS complex, catalyzes the methylation at lysine 4 of histone H3 (H3K4me), a hallmark of euchromatin. Here, we show that the fission yeast Schizosaccharomyces pombe Set1 utilizes distinct domain modules to regulate disparate classes of repetitive elements associated with euchromatin and heterochromatin via H3K4me-dependent and -independent pathways. Set1 employs its RNA-binding RRM2 and catalytic SET domains to repress Tf2 retrotransposons and pericentromeric repeats while relying on its H3K4me function to maintain transcriptional repression at the silent mating type (mat) locus and subtelomeric regions. These repressive functions of Set1 correlate with the requirement of Set1C components to maintain repression at the mat locus and subtelomeres while dispensing Set1C in repressing Tf2s and pericentromeric repeats. We show that the contributions of several Set1C subunits to the states of H3K4me diverge considerably from those of Saccharomyces cerevisiae orthologs. Moreover, unlike S. cerevisiae, the regulation of Set1 protein level is not coupled to the status of H3K4me or histone H2B ubiquitination by the HULC complex. Intriguingly, we uncover a genome organization role for Set1C and H3K4me in mediating the clustering of Tf2s into Tf bodies by antagonizing the acetyltransferase Mst1-mediated H3K4 acetylation. Our study provides unexpected insights into the regulatory intricacies of a highly conserved chromatin-modifying complex with diverse roles in genome control. Methylation of histone H3 at lysine 4 (H3K4me) is a well-documented mark associated with euchromatin. In this study, we investigate the contributions of the histone methyltransferase Set1 (KMT2) and its associated Set1C/COMPASS complex in the fission yeast Schizosaccharomyces pombe to histone H3 lysine 4 methylation (H3K4me), transcriptional repression, and genome organization. We show that Set1 exhibits multiple modes of transcriptional repression at different types of repetitive elements, requiring distinct domains of Set1 and other Set1C subunits. Despite high conservation of subunits between the S. pombe and S. cerevisiae Set1C complexes, there are considerable differences in contributions to H3K4me by several individual subunits. Furthermore, unlike a recent report in S. cerevisiae, the abundance of Set1 proteins in S. pombe is generally not coupled to either the status of H3K4 methylation or H2B ubiquitination, further highlighting critical differences in Set1 regulation between the two yeast species. We describe a role for the Set1C complex in the nuclear organization of dispersed retrotransposons into Tf bodies. Set1C maintains Tf body integrity by employing H3K4me to antagonize the activities of the H3K4 acetyltransferase Mst1. Collectively, our findings dramatically expand the regulatory landscape controlled by the Set1C complex, an important and highly conserved chromatin-modifying complex with diverse roles in genome control and development.
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Affiliation(s)
- Irina V. Mikheyeva
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Patrick J. R. Grady
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Fiona B. Tamburini
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - David R. Lorenz
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Hugh P. Cam
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
- * E-mail:
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Meglicki M, Teperek-Tkacz M, Borsuk E. Appearance and heterochromatin localization of HP1α in early mouse embryos depends on cytoplasmic clock and H3S10 phosphorylation. Cell Cycle 2014; 11:2189-205. [DOI: 10.4161/cc.20705] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Marquardt S, Hazelbaker DZ, Buratowski S. Distinct RNA degradation pathways and 3' extensions of yeast non-coding RNA species. Transcription 2014; 2:145-154. [PMID: 21826286 DOI: 10.4161/trns.2.3.16298] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 05/04/2011] [Accepted: 05/05/2011] [Indexed: 01/02/2023] Open
Abstract
Non-coding transcripts originating from bidirectional promoters have been reported in a wide range of organisms. In yeast, these divergent transcripts can be subdivided into two classes. Some are designated Cryptic Unstable Transcripts (CUTs) because they are terminated by the Nrd1-Nab3-Sen1 pathway and then rapidly degraded by the nuclear exosome. This is the same processing pathway used by yeast snoRNAs. Whereas CUTs are only easily observed in cells lacking the Rrp6 or Rrp47 subunits of the nuclear exosome, Stable Uncharacterized Transcripts (SUTs) are present even in wild-type cells. Here we show that SUTs are partially susceptible to the nuclear exosome, but are primarily degraded by cytoplasmic 5' to 3' degradation and nonsense-mediated decay (NMD). Therefore, SUTs may be processed similarly to mRNAs. Surprisingly, both CUTs and SUTs were found to produce 3' extended species that were also subject to cytoplasmic degradation. The functions, if any, of these extended CUTs and SUTs are unknown, but their discovery suggests that yeasts generate transcripts reminiscent of long non-coding RNAs found in higher eukaryotes.
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Affiliation(s)
- Sebastian Marquardt
- Department of Biological Chemistry and Molecular Pharmacology; Harvard Medical School; Boston, MA USA
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78
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Castel SE, Ren J, Bhattacharjee S, Chang AY, Sánchez M, Valbuena A, Antequera F, Martienssen RA. Dicer promotes transcription termination at sites of replication stress to maintain genome stability. Cell 2014; 159:572-83. [PMID: 25417108 DOI: 10.1016/j.cell.2014.09.031] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/29/2014] [Accepted: 09/17/2014] [Indexed: 12/12/2022]
Abstract
Nuclear RNAi is an important regulator of transcription and epigenetic modification, but the underlying mechanisms remain elusive. Using a genome-wide approach in the fission yeast S. pombe, we have found that Dcr1, but not other components of the canonical RNAi pathway, promotes the release of Pol II from the 3? end of highly transcribed genes, and, surprisingly, from antisense transcription of rRNA and tRNA genes, which are normally transcribed by Pol I and Pol III. These Dcr1-terminated loci correspond to sites of replication stress and DNA damage, likely resulting from transcription-replication collisions. At the rDNA loci, release of Pol II facilitates DNA replication and prevents homologous recombination, which would otherwise lead to loss of rDNA repeats especially during meiosis. Our results reveal a novel role for Dcr1-mediated transcription termination in genome maintenance and may account for widespread regulation of genome stability by nuclear RNAi in higher eukaryotes.
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Affiliation(s)
- Stephane E Castel
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jie Ren
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sonali Bhattacharjee
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - An-Yun Chang
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY 11794, USA
| | - Mar Sánchez
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca 37007, Spain
| | - Alberto Valbuena
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca 37007, Spain
| | - Francisco Antequera
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca 37007, Spain
| | - Robert A Martienssen
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY 11794, USA.
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79
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Le Thomas A, Stuwe E, Li S, Du J, Marinov G, Rozhkov N, Chen YCA, Luo Y, Sachidanandam R, Toth KF, Patel D, Aravin AA. Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing. Genes Dev 2014; 28:1667-80. [PMID: 25085419 PMCID: PMC4117942 DOI: 10.1101/gad.245514.114] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
piRNAs guide the repression of diverse transposable elements in metazoan germ cells. Le Thomas et al. show that piRNA biogenesis in Drosophila germ cells depends on the inheritance of homologous piRNAs from the previous generation. Transgenerationally inherited piRNAs trigger piRNA biogenesis in the progeny by two different mechanisms. First, inherited piRNAs guide post-transcriptional processing of precursors into mature piRNAs. Second, inherited piRNAs direct the modification of the chromatin state of cluster sequences. This study provides key insights into the transgenerational mechanism that specifies piRNA biogenesis in the germline. Small noncoding RNAs that associate with Piwi proteins, called piRNAs, serve as guides for repression of diverse transposable elements in germ cells of metazoa. In Drosophila, the genomic regions that give rise to piRNAs, the so-called piRNA clusters, are transcribed to generate long precursor molecules that are processed into mature piRNAs. How genomic regions that give rise to piRNA precursor transcripts are differentiated from the rest of the genome and how these transcripts are specifically channeled into the piRNA biogenesis pathway are not known. We found that transgenerationally inherited piRNAs provide the critical trigger for piRNA production from homologous genomic regions in the next generation by two different mechanisms. First, inherited piRNAs enhance processing of homologous transcripts into mature piRNAs by initiating the ping-pong cycle in the cytoplasm. Second, inherited piRNAs induce installment of the histone 3 Lys9 trimethylation (H3K9me3) mark on genomic piRNA cluster sequences. The heterochromatin protein 1 (HP1) homolog Rhino binds to the H3K9me3 mark through its chromodomain and is enriched over piRNA clusters. Rhino recruits the piRNA biogenesis factor Cutoff to piRNA clusters and is required for efficient transcription of piRNA precursors. We propose that transgenerationally inherited piRNAs act as an epigenetic memory for identification of substrates for piRNA biogenesis on two levels: by inducing a permissive chromatin environment for piRNA precursor synthesis and by enhancing processing of these precursors.
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Affiliation(s)
- Adrien Le Thomas
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA; Ecole Doctorale Complexité du Vivant, Université Pierre et Marie Curie, 75005 Paris, France
| | - Evelyn Stuwe
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA; Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Sisi Li
- Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
| | - Jiamu Du
- Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA;
| | - Georgi Marinov
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Nikolay Rozhkov
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Yung-Chia Ariel Chen
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Yicheng Luo
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Ravi Sachidanandam
- Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York 10029, USA
| | - Katalin Fejes Toth
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Dinshaw Patel
- Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
| | - Alexei A Aravin
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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80
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Abstract
Centromeres are specialized domains of heterochromatin that provide the foundation for the kinetochore. Centromeric heterochromatin is characterized by specific histone modifications, a centromere-specific histone H3 variant (CENP-A), and the enrichment of cohesin, condensin, and topoisomerase II. Centromere DNA varies orders of magnitude in size from 125 bp (budding yeast) to several megabases (human). In metaphase, sister kinetochores on the surface of replicated chromosomes face away from each other, where they establish microtubule attachment and bi-orientation. Despite the disparity in centromere size, the distance between separated sister kinetochores is remarkably conserved (approximately 1 μm) throughout phylogeny. The centromere functions as a molecular spring that resists microtubule-based extensional forces in mitosis. This review explores the physical properties of DNA in order to understand how the molecular spring is built and how it contributes to the fidelity of chromosome segregation.
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Affiliation(s)
- Kerry S Bloom
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3280;
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81
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Abstract
Eukaryotic chromatin is remodelled by the evolutionarily conserved Snf2 family of enzymes in an ATP-dependent manner. Several Snf2 enzymes are part of CRCs (chromatin remodelling complexes). In the present review we focus our attention on the functions of Snf2 enzymes and CRCs in fission yeast. We discuss their molecular mechanisms and roles and in regulating gene expression, DNA recombination, euchromatin and heterochromatin structure.
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82
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Simmons MJ, Thorp MW, Buschette JT, Becker JR. Transposon regulation in Drosophila: piRNA-producing P elements facilitate repression of hybrid dysgenesis by a P element that encodes a repressor polypeptide. Mol Genet Genomics 2014; 290:127-40. [DOI: 10.1007/s00438-014-0902-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 08/19/2014] [Indexed: 10/24/2022]
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83
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Zhang Z, Wang J, Schultz N, Zhang F, Parhad SS, Tu S, Vreven T, Zamore PD, Weng Z, Theurkauf WE. The HP1 homolog rhino anchors a nuclear complex that suppresses piRNA precursor splicing. Cell 2014; 157:1353-1363. [PMID: 24906152 DOI: 10.1016/j.cell.2014.04.030] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 01/15/2014] [Accepted: 04/09/2014] [Indexed: 01/25/2023]
Abstract
piRNAs guide an adaptive genome defense system that silences transposons during germline development. The Drosophila HP1 homolog Rhino is required for germline piRNA production. We show that Rhino binds specifically to the heterochromatic clusters that produce piRNA precursors, and that binding directly correlates with piRNA production. Rhino colocalizes to germline nuclear foci with Rai1/DXO-related protein Cuff and the DEAD box protein UAP56, which are also required for germline piRNA production. RNA sequencing indicates that most cluster transcripts are not spliced and that rhino, cuff, and uap56 mutations increase expression of spliced cluster transcripts over 100-fold. LacI::Rhino fusion protein binding suppresses splicing of a reporter transgene and is sufficient to trigger piRNA production from a trans combination of sense and antisense reporters. We therefore propose that Rhino anchors a nuclear complex that suppresses cluster transcript splicing and speculate that stalled splicing differentiates piRNA precursors from mRNAs.
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Affiliation(s)
- Zhao Zhang
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester MA 01605, USA
| | - Jie Wang
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester MA 01605, USA
| | - Nadine Schultz
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Fan Zhang
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Swapnil S Parhad
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA
| | - Shikui Tu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester MA 01605, USA
| | - Thom Vreven
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester MA 01605, USA
| | - Phillip D Zamore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester MA 01605, USA; Howard Hughes Medical Institute
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester MA 01605, USA.
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA.
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84
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Thapa S, Procunier W, Henry W, Chhetri S. Heterochromatin and sibling species of Simulium praelargum s.l. (Diptera: Simuliidae). Genome 2014; 57:223-32. [PMID: 25005610 DOI: 10.1139/gen-2014-0025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cytological descriptions are given for two sympatric sibling species, Simulium praelargum IIIL-st and Simulium praelargum IIIL-1.2, from Darjeeling, West Bengal, India. Sibling IIIL-1.2 differs from IIIL-st by a two step fixed included inversion (IIIL-1.2) found on the long arm of chromosome III. Both siblings possess heterochromatinized IIIS polytene chromosome ends, while IIIL-1.2 is unique within the Simuliidae in that it exhibits a very large enhanced chromocentre that persists in normal somatic tissue, contrary to other chromocentre-containing taxa. In IIIL-1.2, the chromocentre occurs as a positively allocyclic heteropycnotic body in normal mitotic interphase cells of neuroblast ganglia, oogonia, and spermatogonia. In mitotic metaphase chromosomes, the chromocentre forms large pronounced primary (centromere) constrictions and appears to be associated with nonhomologous pairing. Initial cytological studies on taxa within the feuerborni group have revealed heterochromatic chromosomal polymorphisms. Progressive fixation of these polymorphisms in different taxa within the group opens up the possibility of using comparative molecular or genomic approaches to begin to define the functional and structural aspects of the epigenome and to further characterize mitosis and meiosis in S. praelargum IIIL-1.2.
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Affiliation(s)
- Sachin Thapa
- a P.G. Department of Zoology, Darjeeling Government College, Darjeeling 734101, West Bengal, India
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85
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Aravind L, Burroughs AM, Zhang D, Iyer LM. Protein and DNA modifications: evolutionary imprints of bacterial biochemical diversification and geochemistry on the provenance of eukaryotic epigenetics. Cold Spring Harb Perspect Biol 2014; 6:a016063. [PMID: 24984775 DOI: 10.1101/cshperspect.a016063] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Epigenetic information, which plays a major role in eukaryotic biology, is transmitted by covalent modifications of nuclear proteins (e.g., histones) and DNA, along with poorly understood processes involving cytoplasmic/secreted proteins and RNAs. The origin of eukaryotes was accompanied by emergence of a highly developed biochemical apparatus for encoding, resetting, and reading covalent epigenetic marks in proteins such as histones and tubulins. The provenance of this apparatus remained unclear until recently. Developments in comparative genomics show that key components of eukaryotic epigenetics emerged as part of the extensive biochemical innovation of secondary metabolism and intergenomic/interorganismal conflict systems in prokaryotes, particularly bacteria. These supplied not only enzymatic components for encoding and removing epigenetic modifications, but also readers of some of these marks. Diversification of these prokaryotic systems and subsequently eukaryotic epigenetics appear to have been considerably influenced by the great oxygenation event in the Earth's history.
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Affiliation(s)
- L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Dapeng Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
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86
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Mohn F, Sienski G, Handler D, Brennecke J. The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila. Cell 2014; 157:1364-1379. [DOI: 10.1016/j.cell.2014.04.031] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 03/10/2014] [Accepted: 04/11/2014] [Indexed: 01/25/2023]
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87
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White E, Schlackow M, Kamieniarz-Gdula K, Proudfoot NJ, Gullerova M. Human nuclear Dicer restricts the deleterious accumulation of endogenous double-stranded RNA. Nat Struct Mol Biol 2014; 21:552-9. [PMID: 24814348 PMCID: PMC4129937 DOI: 10.1038/nsmb.2827] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 04/11/2014] [Indexed: 12/12/2022]
Abstract
Dicer is a central enzymatic player in RNA-interference pathways that acts to regulate gene expression in nearly all eukaryotes. Although the cytoplasmic function of Dicer is well documented in mammals, its nuclear function remains obscure. Here we show that Dicer is present in both the nucleus and cytoplasm, and its nuclear levels are tightly regulated. Dicer interacts with RNA polymerase II (Pol II) at actively transcribed gene loci. Loss of Dicer causes the appearance of endogenous double-stranded RNA (dsRNA), which in turn leads to induction of the interferon-response pathway and consequent cell death. Our results suggest that Pol II-associated Dicer restricts endogenous dsRNA formation from overlapping noncoding-RNA transcription units. Failure to do so has catastrophic effects on cell function.
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Affiliation(s)
- Eleanor White
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | | | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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88
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Mann JR. Epigenetics and memigenetics. Cell Mol Life Sci 2014; 71:1117-22. [PMID: 24445814 PMCID: PMC11113772 DOI: 10.1007/s00018-014-1560-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 12/20/2013] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
The field of epigenetics is expanding rapidly, yet there is persistent uncertainty in the definition of the term. The word was coined in the mid-twentieth century as a descriptor of how intrinsic, yet largely unknown, forces act with genes to channel progenitor cells along pathways of differentiation. Near the end of the twentieth century, epigenetics was defined more specifically as the study of changes in gene activity states. In some definitions, only those activity states that are inherited across cell division were considered. Other definitions were broader, also including activity states that are transient, or occurring in non-dividing cells. The greatest point of disagreement in these current definitions, is if the term should concern only inherited activity states. To alleviate this disparity, an alternative term, 'memigenetics', could be used in place of epigenetics to describe inherited chromatin activity states. The advantage of this term is that it is self-defining, and would serve to emphasize the important concept of cell memory. It would also free the term epigenetics to be used in a broader sense in accord with the meaning of the prefix 'epi', that is, as a descriptor of what is 'over' DNA at any point in time.
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Affiliation(s)
- Jeffrey R Mann
- Theme of Genetics, Murdoch Childrens Research Institute, The Royal Children's Hospital, Flemington Road, Parkville, 3052, VIC, Australia,
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89
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Global effects of the CSR-1 RNA interference pathway on the transcriptional landscape. Nat Struct Mol Biol 2014; 21:358-65. [PMID: 24681887 PMCID: PMC4068146 DOI: 10.1038/nsmb.2801] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 03/02/2014] [Indexed: 12/20/2022]
Abstract
Argonaute proteins and their small RNA cofactors short interfering RNAs are known to inhibit gene expression at the transcriptional and post-transcriptional levels. In Caenorhabditis elegans, the Argonaute CSR-1 binds thousands of endogenous siRNAs (endo-siRNAs) that are antisense to germline transcripts. However, its role in gene expression regulation remains controversial. Here we used genome-wide profiling of nascent RNA transcripts and found that the CSR-1 RNA interference pathway promoted sense-oriented RNA polymerase II transcription. Moreover, a loss of CSR-1 function resulted in global increase in antisense transcription and ectopic transcription of silent chromatin domains, which led to reduced chromatin incorporation of centromere-specific histone H3. On the basis of these findings, we propose that the CSR-1 pathway helps maintain the directionality of active transcription, thereby propagating the distinction between transcriptionally active and silent genomic regions.
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90
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Huang CF, Zhu JK. RNA Splicing Factors and RNA-Directed DNA Methylation. BIOLOGY 2014; 3:243-54. [PMID: 24833507 PMCID: PMC4085605 DOI: 10.3390/biology3020243] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 03/18/2014] [Accepted: 03/20/2014] [Indexed: 11/16/2022]
Abstract
RNA-directed histone and/or DNA modification is a conserved mechanism for the establishment of epigenetic marks from yeasts and plants to mammals. The heterochromation formation in yeast is mediated by RNAi-directed silencing mechanism, while the establishment of DNA methylation in plants is through the RNA-directed DNA methylation (RdDM) pathway. Recently, splicing factors are reported to be involved in both RNAi-directed heterochromatin formation in yeast and the RdDM pathway in plants. In yeast, splicing factors may provide a platform for facilitating the siRNA generation through an interaction with RDRC and thereby affect the heterochromatin formation, whereas in plants, various splicing factors seem to act at different steps in the RdDM pathway.
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Affiliation(s)
- Chao-Feng Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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91
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Pitchiaya S, Heinicke LA, Custer TC, Walter NG. Single molecule fluorescence approaches shed light on intracellular RNAs. Chem Rev 2014; 114:3224-65. [PMID: 24417544 PMCID: PMC3968247 DOI: 10.1021/cr400496q] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sethuramasundaram Pitchiaya
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Laurie A. Heinicke
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thomas C. Custer
- Program in Chemical Biology, University of Michigan,
Ann Arbor, MI 48109-1055, USA
| | - Nils G. Walter
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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92
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Abstract
Small regulatory RNAs (sRNAs) that act by base-pairing were first discovered in so-called accessory DNA elements—plasmids, phages, and transposons—where they control replication, maintenance, and transposition. Since 2001, a huge body of work has been performed to predict and identify sRNAs in a multitude of bacterial genomes. The majority of chromosome-encoded sRNAs have been investigated in E. coli and other Gram-negative bacteria. However, during the past five years an increasing number of sRNAs were found in Gram-positive bacteria. Here, we outline our current knowledge on chromosome-encoded sRNAs from low-GC Gram-positive species that act by base-pairing, i.e., an antisense mechanism. We will focus on sRNAs with known targets and defined regulatory mechanisms with special emphasis on Bacillus subtilis.
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Affiliation(s)
- Sabine Brantl
- Friedrich-Schiller-Universität Jena; Biologisch-Pharmazeutische Fakultät; AG Bakteriengenetik; Philosophenweg 12; Jena, Germany
| | - Reinhold Brückner
- Mikrobiologie; TU Kaiserslautern; Paul-Ehrlich-Str. 23; D-67663 Kaiserslautern, Germany
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93
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Saito K. The epigenetic regulation of transposable elements by PIWI-interacting RNAs in Drosophila. Genes Genet Syst 2014; 88:9-17. [PMID: 23676706 DOI: 10.1266/ggs.88.9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A mechanism is required to repress the expression and transposition of transposable elements (TEs) to ensure the stable inheritance of genomic information. Accumulating evidence indicates that small non-coding RNAs are important regulators of TEs. Among small non-coding RNAs, PIWI-interacting RNAs (piRNAs) serve as guide molecules for recognizing and silencing numerous TEs and work in collaboration with PIWI subfamily proteins in gonadal cells. Disruption of the piRNA pathway correlates with loss of proper genomic organization, gene expression control and fertility. Moreover, recent studies on the molecular mechanisms of piRNA biogenesis and on piRNA function have shown that piRNAs act as maternally inherited genic elements, transferring information about repressed TEs to progeny. These findings enable a molecular explanation of mysterious epigenetic phenomena, such as hybrid dysgenesis and TE adaptation with age. Here, I review our current knowledge of piRNAs derived from biochemical and genetic studies and discuss how small RNAs are utilized to maintain genome organization and to provide non-DNA genetic information. I mainly focus on Drosophila but also discuss comparisons with other species.
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Affiliation(s)
- Kuniaki Saito
- Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi,Shinjuku-ku, Tokyo 160-8582, Japan.
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94
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Vogt A, Mochizuki K. A domesticated PiggyBac transposase interacts with heterochromatin and catalyzes reproducible DNA elimination in Tetrahymena. PLoS Genet 2013; 9:e1004032. [PMID: 24348275 PMCID: PMC3861120 DOI: 10.1371/journal.pgen.1004032] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 10/31/2013] [Indexed: 12/20/2022] Open
Abstract
The somatic genome of the ciliated protist Tetrahymena undergoes DNA elimination of defined sequences called internal eliminated sequences (IESs), which account for ~30% of the germline genome. During DNA elimination, IES regions are heterochromatinized and assembled into heterochromatin bodies in the developing somatic nucleus. The domesticated piggyBac transposase Tpb2p is essential for the formation of heterochromatin bodies and DNA elimination. In this study, we demonstrate that the activities of Tpb2p involved in forming heterochromatin bodies and executing DNA elimination are genetically separable. The cysteine-rich domain of Tpb2p, which interacts with the heterochromatin-specific histone modifications, is necessary for both heterochromatin body formation and DNA elimination, whereas the endonuclease activity of Tpb2p is only necessary for DNA elimination. Furthermore, we demonstrate that the endonuclease activity of Tpb2p in vitro and the endonuclease activity that executes DNA elimination in vivo have similar substrate sequence preferences. These results strongly indicate that Tpb2p is the endonuclease that directly catalyzes the excision of IESs and that the boundaries of IESs are at least partially determined by the combination of Tpb2p-heterochromatin interaction and relaxed sequence preference of the endonuclease activity of Tpb2p.
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Affiliation(s)
- Alexander Vogt
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) Vienna, Austria
| | - Kazufumi Mochizuki
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) Vienna, Austria
- * E-mail:
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95
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Tanaka TU, Clayton L, Natsume T. Three wise centromere functions: see no error, hear no break, speak no delay. EMBO Rep 2013; 14:1073-83. [PMID: 24232185 PMCID: PMC3849490 DOI: 10.1038/embor.2013.181] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 10/18/2013] [Indexed: 12/17/2022] Open
Abstract
The main function of the centromere is to promote kinetochore assembly for spindle microtubule attachment. Two additional functions of the centromere, however, are becoming increasingly clear: facilitation of robust sister-chromatid cohesion at pericentromeres and advancement of replication of centromeric regions. The combination of these three centromere functions ensures correct chromosome segregation during mitosis. Here, we review the mechanisms of the kinetochore-microtubule interaction, focusing on sister-kinetochore bi-orientation (or chromosome bi-orientation). We also discuss the biological importance of robust pericentromeric cohesion and early centromere replication, as well as the mechanisms orchestrating these two functions at the microtubule attachment site.
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Affiliation(s)
- Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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96
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Dönertas D, Sienski G, Brennecke J. Drosophila Gtsf1 is an essential component of the Piwi-mediated transcriptional silencing complex. Genes Dev 2013; 27:1693-705. [PMID: 23913922 DOI: 10.1101/gad.221150.113] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The PIWI-interacting RNA (piRNA) pathway is a small RNA silencing system that keeps selfish genetic elements such as transposons under control in animal gonads. Several lines of evidence indicate that nuclear PIWI family proteins guide transcriptional silencing of their targets, yet the composition of the underlying silencing complex is unknown. Here we demonstrate that the double CHHC zinc finger protein gametocyte-specific factor 1 (Gtsf1) is an essential factor for Piwi-mediated transcriptional repression in Drosophila. Cells lacking Gtsf1 contain nuclear Piwi loaded with piRNAs, yet Piwi's silencing capacity is ablated. Gtsf1 interacts directly with a small subpool of nuclear Piwi, and loss of Gtsf1 phenocopies loss of Piwi in terms of deregulation of transposons, loss of H3K9 trimethylation (H3K9me3) marks at euchromatic transposon insertions, and deregulation of genes in proximity to repressed transposons. We propose that only a small fraction of nuclear Piwi is actively engaged in target silencing and that Gtsf1 is an essential component of the underlying Piwi-centered silencing complex.
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Affiliation(s)
- Derya Dönertas
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences IMBA, 1030 Vienna, Austria
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97
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Catania S, Allshire RC. Anarchic centromeres: deciphering order from apparent chaos. Curr Opin Cell Biol 2013; 26:41-50. [PMID: 24529245 PMCID: PMC3978670 DOI: 10.1016/j.ceb.2013.09.004] [Citation(s) in RCA: 21] [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: 08/21/2013] [Revised: 09/20/2013] [Accepted: 09/24/2013] [Indexed: 12/16/2022]
Abstract
Specialised chromatin in which canonical histone H3 is replaced by CENP-A, an H3 related protein, is a signature of active centromeres and provides the foundation for kinetochore assembly. The location of centromeres is not fixed since centromeres can be inactivated and new centromeres can arise at novel locations independently of specific DNA sequence elements. Therefore, the establishment and maintenance of CENP-A chromatin and kinetochores provide an exquisite example of genuine epigenetic regulation. The composition of CENP-A nucleosomes is contentious but several studies suggest that, like regular H3 particles, they are octamers. Recent analyses have provided insight into how CENP-A is recognised and propagated, identified roles for post-translational modifications and dissected how CENP-A recruits other centromere proteins to mediate kinetochore assembly.
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Affiliation(s)
- Sandra Catania
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, 6.34 Swann Building, Mayfield Road, Edinburgh EH9 3JR, Scotland, UK
| | - Robin C Allshire
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, 6.34 Swann Building, Mayfield Road, Edinburgh EH9 3JR, Scotland, UK.
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98
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Huang CF, Miki D, Tang K, Zhou HR, Zheng Z, Chen W, Ma ZY, Yang L, Zhang H, Liu R, He XJ, Zhu JK. A Pre-mRNA-splicing factor is required for RNA-directed DNA methylation in Arabidopsis. PLoS Genet 2013; 9:e1003779. [PMID: 24068953 PMCID: PMC3772050 DOI: 10.1371/journal.pgen.1003779] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 07/25/2013] [Indexed: 12/16/2022] Open
Abstract
Cytosine DNA methylation is a stable epigenetic mark that is frequently associated with the silencing of genes and transposable elements (TEs). In Arabidopsis, the establishment of DNA methylation is through the RNA-directed DNA methylation (RdDM) pathway. Here, we report the identification and characterization of RDM16, a new factor in the RdDM pathway. Mutation of RDM16 reduced the DNA methylation levels and partially released the silencing of a reporter gene as well as some endogenous genomic loci in the DNA demethylase ros1-1 mutant background. The rdm16 mutant had morphological defects and was hypersensitive to salt stress and abscisic acid (ABA). Map-based cloning and complementation test led to the identification of RDM16, which encodes a pre-mRNA-splicing factor 3, a component of the U4/U6 snRNP. RNA-seq analysis showed that 308 intron retention events occurred in rdm16, confirming that RDM16 is involved in pre-mRNA splicing in planta. RNA-seq and mRNA expression analysis also revealed that the RDM16 mutation did not affect the pre-mRNA splicing of known RdDM genes, suggesting that RDM16 might be directly involved in RdDM. Small RNA expression analysis on loci showing RDM16-dependent DNA methylation suggested that unlike the previously reported putative splicing factor mutants, rdm16 did not affect small RNA levels; instead, the rdm16 mutation caused a decrease in the levels of Pol V transcripts. ChIP assays revealed that RDM16 was enriched at some Pol V target loci. Our results suggest that RDM16 regulates DNA methylation through influencing Pol V transcript levels. Finally, our genome-wide DNA methylation analysis indicated that RDM16 regulates the overall methylation of TEs and gene-surrounding regions, and preferentially targets Pol IV-dependent DNA methylation loci and the ROS1 target loci. Our work thus contributes to the understanding of RdDM and its interactions with active DNA demethylation. Both plants and animals utilize cytosine DNA methylation as an important epigenetic mark to suppress transposable elements (TEs), repeat sequences and genes, which is crucial for the genome integrity and development. In plants, de novo DNA methylation can be mediated by the RNA-directed DNA methylation (RdDM) pathway. Plants have also evolved a pathway for active DNA demethylation that is initiated by the ROS1 subfamily of 5-methylcytosine DNA glycosylases, to counteract the RdDM pathway to prevent undesirable silencing. In this study, we identified RDM16, a new factor in the RdDM pathway. We show that RDM16 is a pre-mRNA splicing factor and its function in the regulation of DNA methylation and gene silencing is not through influencing siRNA levels or the expression or splicing of genes encoding known RdDM components, but likely through affecting Pol V transcripts. We also show that RDM16 preferentially affects ROS1 target loci. Together, our findings contribute to the understanding of RdDM and its interactions with ROS1-mediated DNA demethylation.
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Affiliation(s)
- Chao-Feng Huang
- Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, China
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kai Tang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
| | - Hao-Ran Zhou
- National Institute of Biological Sciences, Beijing, China
| | - Zhimin Zheng
- Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wei Chen
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
| | - Ze-Yang Ma
- National Institute of Biological Sciences, Beijing, China
| | - Lan Yang
- Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Renyi Liu
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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99
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Nakamura T, Pluskal T, Nakaseko Y, Yanagida M. Impaired coenzyme A synthesis in fission yeast causes defective mitosis, quiescence-exit failure, histone hypoacetylation and fragile DNA. Open Biol 2013; 2:120117. [PMID: 23091701 PMCID: PMC3472395 DOI: 10.1098/rsob.120117] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 08/22/2012] [Indexed: 12/02/2022] Open
Abstract
Biosynthesis of coenzyme A (CoA) requires a five-step process using pantothenate and cysteine in the fission yeast Schizosaccharomyces pombe. CoA contains a thiol (SH) group, which reacts with carboxylic acid to form thioesters, giving rise to acyl-activated CoAs such as acetyl-CoA. Acetyl-CoA is essential for energy metabolism and protein acetylation, and, in higher eukaryotes, for the production of neurotransmitters. We isolated a novel S. pombe temperature-sensitive strain ppc1-537 mutated in the catalytic region of phosphopantothenoylcysteine synthetase (designated Ppc1), which is essential for CoA synthesis. The mutant becomes auxotrophic to pantothenate at permissive temperature, displaying greatly decreased levels of CoA, acetyl-CoA and histone acetylation. Moreover, ppc1-537 mutant cells failed to restore proliferation from quiescence. Ppc1 is thus the product of a super-housekeeping gene. The ppc1-537 mutant showed combined synthetic lethal defects with five of six histone deacetylase mutants, whereas sir2 deletion exceptionally rescued the ppc1-537 phenotype. In synchronous cultures, ppc1-537 cells can proceed to the S phase, but lose viability during mitosis failing in sister centromere/kinetochore segregation and nuclear division. Additionally, double-strand break repair is defective in the ppc1-537 mutant, producing fragile broken DNA, probably owing to diminished histone acetylation. The CoA-supported metabolism thus controls the state of chromosome DNA.
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Affiliation(s)
- Takahiro Nakamura
- Okinawa Institute of Science and Technology Graduate University, Tancha 1919-1, Onna, Okinawa 904-0495, Japan
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100
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Dou K, Huang CF, Ma ZY, Zhang CJ, Zhou JX, Huang HW, Cai T, Tang K, Zhu JK, He XJ. The PRP6-like splicing factor STA1 is involved in RNA-directed DNA methylation by facilitating the production of Pol V-dependent scaffold RNAs. Nucleic Acids Res 2013; 41:8489-502. [PMID: 23877244 PMCID: PMC3794598 DOI: 10.1093/nar/gkt639] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
DNA methylation is a conserved epigenetic marker in plants and animals. In Arabidopsis, DNA methylation can be established through an RNA-directed DNA methylation (RdDM) pathway. By screening for suppressors of ros1, we identified STA1, a PRP6-like splicing factor, as a new RdDM regulator. Whole-genome bisulfite sequencing suggested that STA1 and the RdDM pathway share a large number of common targets in the Arabidopsis genome. Small RNA deep sequencing demonstrated that STA1 is predominantly involved in the accumulation of the siRNAs that depend on both Pol IV and Pol V. Moreover, the sta1 mutation partially reduces the levels of Pol V-dependent RNA transcripts. Immunolocalization assay indicated that STA1 signals are exclusively present in the Cajal body and overlap with AGO4 in most nuclei. STA1 signals are also partially overlap with NRPE1. Localization of STA1 to AGO4 and NRPE1 signals is probably related to the function of STA1 in the RdDM pathway. Based on these results, we propose that STA1 acts downstream of siRNA biogenesis and facilitates the production of Pol V-dependent RNA transcripts in the RdDM pathway.
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Affiliation(s)
- Kun Dou
- National Institute of Biological Sciences, Beijing 102206, China, College of Life Science, Beijing Normal University, Beijing 100875, China, Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China and Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
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