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Abstract
Most cells in nature are not actively dividing, yet are able to return to the cell cycle given the appropriate environmental signals. There is now ample evidence that quiescent G0 cells are not shut-down but still metabolically and transcriptionally active. Quiescent cells must maintain a basal transcriptional capacity to maintain transcripts and proteins necessary for survival. This implies a tight control over RNA polymerases: RNA pol II for mRNA transcription during G0, but especially RNA pol I and RNA pol III to maintain an appropriate level of structural RNAs, raising the possibility that specific transcriptional control mechanisms evolved in quiescent cells. In accordance with this, we recently discovered that RNA interference is necessary to control RNA polymerase I transcription during G0. While this mini-review focuses on yeast model organisms (Saccharomyces cerevisiae and Schizosaccharomyces pombe), parallels are drawn to other eukaryotes and mammalian systems, in particular stem cells.
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Affiliation(s)
- Benjamin Roche
- a Cold Spring Harbor Laboratory , Cold Spring Harbor , NY , USA
| | - Benoit Arcangioli
- b Genome Dynamics Unit , UMR 3525 CNRS, Institut Pasteur, 25-28 rue du Docteur Roux , Paris , France
| | - Robert Martienssen
- a Cold Spring Harbor Laboratory , Cold Spring Harbor , NY , USA.,c Howard Hughes Medical Institute-Gordon and Betty Moore Foundation (HHMI-GBM) Investigator , NY , USA
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52
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Brönner C, Salvi L, Zocco M, Ugolini I, Halic M. Accumulation of RNA on chromatin disrupts heterochromatic silencing. Genome Res 2017; 27:1174-1183. [PMID: 28404620 PMCID: PMC5495069 DOI: 10.1101/gr.216986.116] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/11/2017] [Indexed: 12/13/2022]
Abstract
Long noncoding RNAs (lncRNAs) play a conserved role in regulating gene expression, chromatin dynamics, and cell differentiation. They serve as a platform for RNA interference (RNAi)–mediated heterochromatin formation or DNA methylation in many eukaryotic organisms. We found in Schizosaccharomyces pombe that heterochromatin is lost at transcribed regions in the absence of RNA degradation. We show that heterochromatic RNAs are retained on chromatin, form DNA:RNA hybrids, and need to be degraded by the Ccr4-Not complex or RNAi to maintain heterochromatic silencing. The Ccr4-Not complex is localized to chromatin independently of H3K9me and degrades chromatin-associated transcripts, which is required for transcriptional silencing. Overexpression of heterochromatic RNA, but not euchromatic RNA, leads to chromatin localization and loss of silencing of a distant ade6 reporter in wild-type cells. Our results demonstrate that chromatin-bound RNAs disrupt heterochromatin organization and need to be degraded in a process of heterochromatin formation.
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Affiliation(s)
- Cornelia Brönner
- Department of Biochemistry, Gene Center, University of Munich (LMU), 81377 Munich, Germany
| | - Luca Salvi
- Department of Biochemistry, Gene Center, University of Munich (LMU), 81377 Munich, Germany
| | - Manuel Zocco
- Department of Biochemistry, Gene Center, University of Munich (LMU), 81377 Munich, Germany
| | - Ilaria Ugolini
- Department of Biochemistry, Gene Center, University of Munich (LMU), 81377 Munich, Germany
| | - Mario Halic
- Department of Biochemistry, Gene Center, University of Munich (LMU), 81377 Munich, Germany
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53
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Forsburg SL, Shen KF. Centromere Stability: The Replication Connection. Genes (Basel) 2017; 8:genes8010037. [PMID: 28106789 PMCID: PMC5295031 DOI: 10.3390/genes8010037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/10/2017] [Accepted: 01/12/2017] [Indexed: 11/16/2022] Open
Abstract
The fission yeast centromere, which is similar to metazoan centromeres, contains highly repetitive pericentromere sequences that are assembled into heterochromatin. This is required for the recruitment of cohesin and proper chromosome segregation. Surprisingly, the pericentromere replicates early in the S phase. Loss of heterochromatin causes this domain to become very sensitive to replication fork defects, leading to gross chromosome rearrangements. This review examines the interplay between components of DNA replication, heterochromatin assembly, and cohesin dynamics that ensures maintenance of genome stability and proper chromosome segregation.
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Affiliation(s)
- Susan L Forsburg
- Program in Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA.
| | - Kuo-Fang Shen
- Program in Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089-2910, USA.
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54
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Roche B, Arcangioli B, Martienssen RA. RNA interference is essential for cellular quiescence. Science 2016; 354:science.aah5651. [PMID: 27738016 DOI: 10.1126/science.aah5651] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/27/2016] [Indexed: 12/19/2022]
Abstract
Quiescent cells play a predominant role in most organisms. Here we identify RNA interference (RNAi) as a major requirement for quiescence (G0 phase of the cell cycle) in Schizosaccharomyces pombe RNAi mutants lose viability at G0 entry and are unable to maintain long-term quiescence. We identified suppressors of G0 defects in cells lacking Dicer (dcr1Δ), which mapped to genes involved in chromosome segregation, RNA polymerase-associated factors, and heterochromatin formation. We propose a model in which RNAi promotes the release of RNA polymerase in cycling and quiescent cells: (i) RNA polymerase II release mediates heterochromatin formation at centromeres, allowing proper chromosome segregation during mitotic growth and G0 entry, and (ii) RNA polymerase I release prevents heterochromatin formation at ribosomal DNA during quiescence maintenance. Our model may account for the codependency of RNAi and histone H3 lysine 9 methylation throughout eukaryotic evolution.
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Affiliation(s)
- B Roche
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - B Arcangioli
- Dynamics of the Genome Unit, Department of Genomes and Genetics, Institut Pasteur, UMR3525, 25-28 rue du Docteur Roux, Paris 75015, France
| | - R A Martienssen
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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55
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Koo DH, Zhao H, Jiang J. Chromatin-associated transcripts of tandemly repetitive DNA sequences revealed by RNA-FISH. Chromosome Res 2016; 24:467-480. [PMID: 27590598 DOI: 10.1007/s10577-016-9537-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/18/2016] [Accepted: 08/24/2016] [Indexed: 02/05/2023]
Abstract
Tandemly repetitive DNA sequences, also named satellite repeats, are major DNA components of heterochromatin and are often organized as long arrays in the pericentromeric, centromeric, and subtelomeric regions of eukaryotic chromosomes. An increasing amount of evidence indicates that transcripts derived from some satellite repeats play important roles in various biological functions. We used a RNA-fluorescence in situ hybridization (RNA-FISH) technique to investigate the transcription of the four well-characterized satellite repeats of maize (Zea mays), including the 180-bp knob repeat, the telomeric (TTTAGGG)n repeat, the 156-bp centromeric repeat CentC, and a 350-bp subtelomeric repeat. Although few transcripts derived from these four repeats were found in the expressed sequence tag and RNA-seq databases, RNA-FISH consistently detected the transcripts from three of the four repeats on interphase nuclei, suggesting that the transcripts from the three repeats are largely integrated into chromatin. The transcripts from the knob and telomeric repeats were mapped to the related DNA loci. In contrast, the transcripts from the CentC repeats were mainly localized to the nucleolus, although nucleoplasmic CentC transcripts were also detectable. The nucleolus and nuclear RNAs appeared to be important for the nuclear localization for at least one centromeric protein, Mis12. We demonstrate that RNA-FISH is a powerful tool to assess the level of transcription as well as to physically map the nuclear locations of the transcripts derived from satellite repeats.
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Affiliation(s)
- Dal-Hoe Koo
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Hainan Zhao
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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56
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Böhmdorfer G, Wierzbicki AT. Control of Chromatin Structure by Long Noncoding RNA. Trends Cell Biol 2016; 25:623-632. [PMID: 26410408 DOI: 10.1016/j.tcb.2015.07.002] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/22/2015] [Accepted: 07/17/2015] [Indexed: 12/11/2022]
Abstract
Long noncoding RNA (lncRNA) is a pivotal factor regulating various aspects of genome activity. Genome regulation via DNA methylation and post-translational histone modifications is a well-documented function of lncRNA in plants, fungi, and animals. Here, we summarize evidence showing that lncRNA also controls chromatin structure, including nucleosome positioning and chromosome looping. We focus on data from plant experimental systems, discussed in the context of other eukaryotes. We explain the mechanisms of lncRNA-controlled chromatin remodeling and the implications of the functional interplay between noncoding transcription and several different chromatin remodelers. We propose that the unique properties of RNA make it suitable for controlling chromatin modifications and structure.
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Affiliation(s)
- Gudrun Böhmdorfer
- University of Michigan, Department of Molecular, Cellular, and Developmental Biology, Ann Arbor, MI 48109, USA
| | - Andrzej T Wierzbicki
- University of Michigan, Department of Molecular, Cellular, and Developmental Biology, Ann Arbor, MI 48109, USA.
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57
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Yang J, Li F. Are all repeats created equal? Understanding DNA repeats at an individual level. Curr Genet 2016; 63:57-63. [PMID: 27260214 DOI: 10.1007/s00294-016-0619-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 01/24/2023]
Abstract
Repetitive DNA sequences, comprising up to 50 % of the genome in all eukaryotes, play important roles in a wide range of cellular functions, such as transcriptional regulation, genome stability, and cellular differentiation. However, due to technical difficulties in differentiating their sequences, DNA repeats remain one of the most mysterious parts of eukaryotic genomes. Key questions, such as how repetitive entities behave at individual level and how the internal architecture of these repeats is organized, are still poorly understood. Recent advances from our group reveal unexpected position-dependent variation within tandem DNA repeats in fission yeast. Despite sharing identical DNA sequences, the peri-centromeric repeats are organized into diverse epigenetic states and chromatin structures. We demonstrate that this position-dependent variation requires key heterochromatin factors and condensin. Our works further suggest that the peri-centromeric repeats are organized into distinct higher order structures that ensure a proper positioning of CENP-A, the centromere-specific histone H3 variant, to centromeres. These most recent developments offer insights into the mechanisms underlying the position effect within tandem DNA arrays, and have broad implications in the field of epigenetics and chromatin biology.
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Affiliation(s)
- Jinpu Yang
- Department of Biology, New York University, New York, NY, 10003, USA
| | - Fei Li
- Department of Biology, New York University, New York, NY, 10003, USA. .,1009 Silver Center, 100 Washington Square East, New York, NY, 10003-6688, USA.
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58
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Zhang H, Wang P, Hou H, Wen H, Zhou H, Gao F, Wu J, Qiu Z, Li L. Histone Modification Is Involved in Okadaic Acid (OA) Induced DNA Damage Response and G2-M Transition Arrest in Maize. PLoS One 2016; 11:e0155852. [PMID: 27196101 PMCID: PMC4873197 DOI: 10.1371/journal.pone.0155852] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 05/05/2016] [Indexed: 12/28/2022] Open
Abstract
Histone modifications are involved in regulation of chromatin structure. To investigate the relationship between chromatin modification and cell cycle regulation during plant cell proliferation, Okadaic acid (OA), a specific inhibitor of serine/threonine protein phosphatase, was applied in this study. The results showed that OA caused the cell cycle arrest at preprophase, leading to seedling growth inhibition. Western blotting assay revealed that the spatial distribution of phosphorylation of Ser10 histone H3 tails (H3S10ph) signals was altered under OA treatment. Reactive oxygen species (ROS) was found to be at higher levels and TdT-mediated dUTP nick end labeling (TUNEL) assay displayed DNA breaks happened at the chromatin after treatment with OA, companied with an increase in the acetylation of histone H4 at lysine 5 (H4K5ac) level. From these observations, we speculated that the alteration of the spatial distribution of H3S10ph and the level of H4K5ac was involved in the procedure that OA induced DNA breaks and G2-M arrested by the accumulation of ROS, and that the histone H3S10ph and H4K5ac might facilitate DNA repair by their association with the chromatin decondensation.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Pu Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Haoli Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Huan Wen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hong Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fei Gao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jinping Wu
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Hongshan District, Wuhan City, Hubei Province, China
| | - Zhengming Qiu
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Hongshan District, Wuhan City, Hubei Province, China
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail:
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59
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Wang J, Jia ST, Jia S. New Insights into the Regulation of Heterochromatin. Trends Genet 2016; 32:284-294. [PMID: 27005444 DOI: 10.1016/j.tig.2016.02.005] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 02/22/2016] [Accepted: 02/29/2016] [Indexed: 10/22/2022]
Abstract
All living organisms are constantly exposed to stresses from internal biological processes and surrounding environments, which induce many adaptive changes in cellular physiology and gene expression programs. Unexpectedly, constitutive heterochromatin, which is generally associated with the stable maintenance of gene silencing, is also dynamically regulated in response to stimuli. In this review we discuss the mechanism of constitutive heterochromatin assembly, its dynamic nature, and its responses to environmental changes.
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Affiliation(s)
- Jiyong Wang
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Sharon T Jia
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, NY, USA.
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60
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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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61
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He H, Zhang S, Wang D, Hochwagen A, Li F. Condensin Promotes Position Effects within Tandem DNA Repeats via the RITS Complex. Cell Rep 2016; 14:1018-1024. [PMID: 26832414 DOI: 10.1016/j.celrep.2016.01.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 10/30/2015] [Accepted: 12/29/2015] [Indexed: 11/28/2022] Open
Abstract
Tandem repetitive DNA is highly abundant in eukaryotic genomes and contributes to transcription control and genome stability. However, how the individual sequences within tandem repeats behave remains largely unknown. Here we develop a collection of fission yeast strains with a reporter gene inserted at different units in a tandem repeat array. We show that, contrary to what is usually assumed, transcriptional silencing and replication timing among the individual repeats differ significantly. RNAi-mediated H3K9 methylation is essential for the silencing position effect. A short hairpin RNA of ura4(+) induces silencing in trans within the tandem array in a position-dependent manner. Importantly, the position effect depends on the condensin subunit, cut3(+). Cut3 promotes the position effect via interaction with the RNA-induced transcriptional silencing (RITS) complex. This study reveals variations in silencing within tandem DNA repeats and provides mechanistic insights into how DNA repeats at the individual level are regulated.
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Affiliation(s)
- Haijin He
- Department of Biology, New York University, New York, NY 10003-6688, USA
| | - Shu Zhang
- Department of Biology, New York University, New York, NY 10003-6688, USA
| | - Danni Wang
- Department of Biology, New York University, New York, NY 10003-6688, USA
| | - Andreas Hochwagen
- Department of Biology, New York University, New York, NY 10003-6688, USA
| | - Fei Li
- Department of Biology, New York University, New York, NY 10003-6688, USA.
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62
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Maurer-Alcalá XX, Katz LA. An epigenetic toolkit allows for diverse genome architectures in eukaryotes. Curr Opin Genet Dev 2015; 35:93-9. [PMID: 26649755 DOI: 10.1016/j.gde.2015.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 10/21/2015] [Accepted: 10/22/2015] [Indexed: 02/04/2023]
Abstract
Genome architecture varies considerably among eukaryotes in terms of both size and structure (e.g. distribution of sequences within the genome, elimination of DNA during formation of somatic nuclei). The diversity in eukaryotic genome architectures and the dynamic processes are only possible due to the well-developed epigenetic toolkit, which probably existed in the Last Eukaryotic Common Ancestor (LECA). This toolkit may have arisen as a means of navigating the genomic conflict that arose from the expansion of transposable elements within the ancestral eukaryotic genome. This toolkit has been coopted to support the dynamic nature of genomes in lineages across the eukaryotic tree of life. Here we highlight how the changes in genome architecture in diverse eukaryotes are regulated by epigenetic processes, such as DNA elimination, genome rearrangements, and adaptive changes to genome architecture. The ability to epigenetically modify and regulate genomes has contributed greatly to the diversity of eukaryotes observed today.
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Affiliation(s)
- Xyrus X Maurer-Alcalá
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA; Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA 01063, USA; Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA.
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63
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Rondinelli B, Rosano D, Antonini E, Frenquelli M, Montanini L, Huang D, Segalla S, Yoshihara K, Amin SB, Lazarevic D, The BT, Verhaak RGW, Futreal PA, Di Croce L, Chin L, Cittaro D, Tonon G. Histone demethylase JARID1C inactivation triggers genomic instability in sporadic renal cancer. J Clin Invest 2015; 125:4625-37. [PMID: 26551685 DOI: 10.1172/jci81040] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 10/08/2015] [Indexed: 12/16/2022] Open
Abstract
Mutations in genes encoding chromatin-remodeling proteins are often identified in a variety of cancers. For example, the histone demethylase JARID1C is frequently inactivated in patients with clear cell renal cell carcinoma (ccRCC); however, it is largely unknown how JARID1C dysfunction promotes cancer. Here, we determined that JARID1C binds broadly to chromatin domains characterized by the trimethylation of lysine 9 (H3K9me3), which is a histone mark enriched in heterochromatin. Moreover, we found that JARID1C localizes on heterochromatin, is required for heterochromatin replication, and forms a complex with established players of heterochromatin assembly, including SUV39H1 and HP1α, as well as with proteins not previously associated with heterochromatin assembly, such as the cullin 4 (CUL4) complex adaptor protein DDB1. Transcription on heterochromatin is tightly suppressed to safeguard the genome, and in ccRCC cells, JARID1C inactivation led to the unrestrained expression of heterochromatic noncoding RNAs (ncRNAs) that in turn triggered genomic instability. Moreover, ccRCC patients harboring JARID1C mutations exhibited aberrant ncRNA expression and increased genomic rearrangements compared with ccRCC patients with tumors endowed with other genetic lesions. Together, these data suggest that inactivation of JARID1C in renal cancer leads to heterochromatin disruption, genomic rearrangement, and aggressive ccRCCs. Moreover, our results shed light on a mechanism that underlies genomic instability in sporadic cancers.
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64
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Abstract
Plant genomes encode various small RNAs that function in distinct, yet overlapping, genetic and epigenetic silencing pathways. However, the abundance and diversity of small-RNA classes varies among plant species, suggesting coevolution between environmental adaptations and gene-silencing mechanisms. Biogenesis of small RNAs in plants is well understood, but we are just beginning to uncover their intricate regulation and activity. Here, we discuss the biogenesis of plant small RNAs, such as microRNAs, secondary siRNAs and heterochromatic siRNAs, and their diverse cellular and developmental functions, including in reproductive transitions, genomic imprinting and paramutation. We also discuss the diversification of small-RNA-directed silencing pathways through the expansion of RNA-dependent RNA polymerases, DICER proteins and ARGONAUTE proteins.
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65
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Linking replication stress with heterochromatin formation. Chromosoma 2015; 125:523-33. [PMID: 26511280 PMCID: PMC4901112 DOI: 10.1007/s00412-015-0545-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 09/27/2015] [Accepted: 09/30/2015] [Indexed: 11/23/2022]
Abstract
The eukaryotic genome can be roughly divided into euchromatin and heterochromatin domains that are structurally and functionally distinct. Heterochromatin is characterized by its high compaction that impedes DNA transactions such as gene transcription, replication, or recombination. Beyond its role in regulating DNA accessibility, heterochromatin plays essential roles in nuclear architecture, chromosome segregation, and genome stability. The formation of heterochromatin involves special histone modifications and the recruitment and spreading of silencing complexes that impact the higher-order structures of chromatin; however, its molecular nature varies between different chromosomal regions and between species. Although heterochromatin has been extensively characterized, its formation and maintenance throughout the cell cycle are not yet fully understood. The biggest challenge for the faithful transmission of chromatin domains is the destabilization of chromatin structures followed by their reassembly on a novel DNA template during genomic replication. This destabilizing event also provides a window of opportunity for the de novo establishment of heterochromatin. In recent years, it has become clear that different types of obstacles such as tight protein-DNA complexes, highly transcribed genes, and secondary DNA structures could impede the normal progression of the replisome and thus have the potential to endanger the integrity of the genome. Multiple studies carried out in different model organisms have demonstrated the capacity of such replisome impediments to favor the formation of heterochromatin. Our review summarizes these reports and discusses the potential role of replication stress in the formation and maintenance of heterochromatin and the role that silencing proteins could play at sites where the integrity of the genome is compromised.
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66
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Stunnenberg R, Kulasegaran-Shylini R, Keller C, Kirschmann MA, Gelman L, Bühler M. H3K9 methylation extends across natural boundaries of heterochromatin in the absence of an HP1 protein. EMBO J 2015; 34:2789-803. [PMID: 26438724 PMCID: PMC4682641 DOI: 10.15252/embj.201591320] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 09/03/2015] [Indexed: 12/13/2022] Open
Abstract
Proteins of the conserved HP1 family are elementary components of heterochromatin and are generally assumed to play a central role in the creation of a rigid, densely packed heterochromatic network that is inaccessible to the transcription machinery. Here, we demonstrate that the fission yeast HP1 protein Swi6 exists as a single highly dynamic population that rapidly exchanges in cis and in trans between different heterochromatic regions. Binding to methylated H3K9 or to heterochromatic RNA decelerates Swi6 mobility. We further show that Swi6 is largely dispensable to the maintenance of heterochromatin domains. In the absence of Swi6, H3K9 methylation levels are maintained by a mechanism that depends on polymeric self‐association properties of Tas3, a subunit of the RNA‐induced transcriptional silencing complex. Our results disclose a surprising role for Swi6 dimerization in demarcating constitutive heterochromatin from neighboring euchromatin. Thus, rather than promoting maintenance and spreading of heterochromatin, Swi6 appears to limit these processes and appropriately confine heterochromatin.
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Affiliation(s)
- Rieka Stunnenberg
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland University of Basel, Basel, Switzerland
| | | | - Claudia Keller
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland University of Basel, Basel, Switzerland
| | | | - Laurent Gelman
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland University of Basel, Basel, Switzerland
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Husso T, Turunen MP, Parker N, Ylä-Herttuala S. Epigenetherapy, a new concept. Biomol Concepts 2015; 2:127-34. [PMID: 25962024 DOI: 10.1515/bmc.2011.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 02/26/2011] [Indexed: 11/15/2022] Open
Abstract
Small RNAs have been shown to regulate gene transcription by interacting with the promoter region and modifying the histone code. The exact mechanism of function is still unclear but the feasibility to activate or repress endogenous gene expression with small RNA molecules has already been demonstrated in vitro and in vivo. In traditional gene therapy non-mutated or otherwise useful genes are inserted into patient's cells to treat a disease. In epigenetherapy the action of small RNAs is utilized by delivering only the small RNAs to patient's cells where they then regulate gene expression by epigenetic mechanisms. This method could be widely useful not only for basic research but also for clinical applications of small RNAs.
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Mojardín L, Botet J, Moreno S, Salas M. Chromosome segregation and organization are targets of 5'-Fluorouracil in eukaryotic cells. Cell Cycle 2015; 14:206-18. [PMID: 25483073 DOI: 10.4161/15384101.2014.974425] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The antimetabolite 5'-Fluorouracil (5FU) is an analog of uracil commonly employed as a chemotherapeutic agent in the treatment of a range of cancers including colorectal tumors. To assess the cellular effects of 5FU, we performed a genome-wide screening of the haploid deletion library of the eukaryotic model Schizosaccharomyces pombe. Our analysis validated previously characterized drug targets including RNA metabolism, but it also revealed unexpected mechanisms of action associated with chromosome segregation and organization (post-translational histone modification, histone exchange, heterochromatin). Further analysis showed that 5FU affects the heterochromatin structure (decreased levels of histone H3 lysine 9 methylation) and silencing (down-regulation of heterochromatic dg/dh transcripts). To our knowledge, this is the first time that defects in heterochromatin have been correlated with increased cytotoxicity to an anticancer drug. Moreover, the segregation of chromosomes, a process that requires an intact heterochromatin at centromeres, was impaired after drug exposure. These defects could be related to the induction of genes involved in chromatid cohesion and kinetochore assembly. Interestingly, we also observed that thiabendazole, a microtubule-destabilizing agent, synergistically enhanced the cytotoxic effects of 5FU. These findings point to new targets and drug combinations that could potentiate the effectiveness of 5FU-based treatments.
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Key Words
- 5FU, 5′-Fluorouracil, 5FU
- 5′-Fluorouracil
- Anticancer drug
- CENP-A, centromere-associated protein A
- CLRC, Clr4 methyltransferase complex
- ChIP, chromatin immunoprecipitation
- FUTP, fluorouridine triphosphate
- FdUMP, fluorodeoxyuridine monophosphate
- FdUTP, fluorodeoxyuridine triphosphate
- G1 phase, gap 1 phase of cell cycle
- GO, Gene Ontology
- H3K9me, H3 lysine 9 methylation
- HAT, histone acetyltransferase
- HDAC, histone deacetylase
- HMT, histone methyltransferase
- HP1, heterochromatin protein 1
- HULC, histone H2B ubiquitin ligase complex
- MNAse, micrococcal nuclease
- RDRC, RNA-directed RNA polymerase complex
- RITS, RNA-induced transcriptional silencing
- RNAi, interference RNA
- S phase, synthesis phase of cell cycle
- Schizosaccharomyces pombe
- TBZ, thiabendazole
- centromere
- chromosome organization
- chromosome segregation
- cnt, central core
- dsRNA, double-stranded RNA
- heterochromatin
- histone modification
- imr, innermost repeats
- siRNA, small interfering RNA
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Affiliation(s)
- Laura Mojardín
- a Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Centro de Biología Molecular "Severo Ochoa" (CSIC-Universidad Autónoma) ; Cantoblanco , Madrid , Spain
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69
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Abstract
SUMMARY The involvement of RNA interference (RNAi) in heterochromatin formation has become clear largely through studies in the fission yeast Schizosaccharomyces pombe and plants like Arabidopsis thaliana. This article discusses how heterochromatic small interfering RNAs are produced and how the RNAi machinery participates in the formation and function of heterochromatin.
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Affiliation(s)
| | - Danesh Moazed
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115-5730
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70
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Allshire RC, Ekwall K. Epigenetic Regulation of Chromatin States in Schizosaccharomyces pombe. Cold Spring Harb Perspect Biol 2015; 7:a018770. [PMID: 26134317 DOI: 10.1101/cshperspect.a018770] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This article discusses the advances made in epigenetic research using the model organism fission yeast Schizosaccharomyces pombe. S. pombe has been used for epigenetic research since the discovery of position effect variegation (PEV). This is a phenomenon in which a transgene inserted within heterochromatin is variably expressed, but can be stably inherited in subsequent cell generations. PEV occurs at centromeres, telomeres, ribosomal DNA (rDNA) loci, and mating-type regions of S. pombe chromosomes. Heterochromatin assembly in these regions requires enzymes that modify histones and the RNA interference (RNAi) machinery. One of the key histone-modifying enzymes is the lysine methyltransferase Clr4, which methylates histone H3 on lysine 9 (H3K9), a classic hallmark of heterochromatin. The kinetochore is assembled on specialized chromatin in which histone H3 is replaced by the variant CENP-A. Studies in fission yeast have contributed to our understanding of the establishment and maintenance of CENP-A chromatin and the epigenetic activation and inactivation of centromeres.
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Affiliation(s)
- Robin C Allshire
- Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, United Kingdom
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Center for Biosciences, NOVUM, S-141 83, Huddinge, Sweden
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71
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Audergon PNCB, Catania S, Kagansky A, Tong P, Shukla M, Pidoux AL, Allshire RC. Epigenetics. Restricted epigenetic inheritance of H3K9 methylation. Science 2015; 348:132-5. [PMID: 25838386 PMCID: PMC4397586 DOI: 10.1126/science.1260638] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Posttranslational histone modifications are believed to allow the epigenetic transmission of distinct chromatin states, independently of associated DNA sequences. Histone H3 lysine 9 (H3K9) methylation is essential for heterochromatin formation; however, a demonstration of its epigenetic heritability is lacking. Fission yeast has a single H3K9 methyltransferase, Clr4, that directs all H3K9 methylation and heterochromatin. Using releasable tethered Clr4 reveals that an active process rapidly erases H3K9 methylation from tethering sites in wild-type cells. However, inactivation of the putative histone demethylase Epe1 allows H3K9 methylation and silent chromatin maintenance at the tethering site through many mitotic divisions, and transgenerationally through meiosis, after release of tethered Clr4. Thus, H3K9 methylation is a heritable epigenetic mark whose transmission is usually countered by its active removal, which prevents the unauthorized inheritance of heterochromatin.
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Affiliation(s)
- Pauline N C B Audergon
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Sandra Catania
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Alexander Kagansky
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Pin Tong
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Manu Shukla
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Alison L Pidoux
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK
| | - Robin C Allshire
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK.
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72
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Dicer and Hsp104 function in a negative feedback loop to confer robustness to environmental stress. Cell Rep 2014; 10:47-61. [PMID: 25543137 DOI: 10.1016/j.celrep.2014.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 11/06/2014] [Accepted: 12/02/2014] [Indexed: 11/22/2022] Open
Abstract
Epigenetic mechanisms can be influenced by environmental cues and thus evoke phenotypic variation. This plasticity can be advantageous for adaptation but also detrimental if not tightly controlled. Although having attracted considerable interest, it remains largely unknown if and how environmental cues such as temperature trigger epigenetic alterations. Using fission yeast, we demonstrate that environmentally induced discontinuous phenotypic variation is buffered by a negative feedback loop that involves the RNase Dicer and the protein disaggregase Hsp104. In the absence of Hsp104, Dicer accumulates in cytoplasmic inclusions and heterochromatin becomes unstable at elevated temperatures, an epigenetic state inherited for many cell divisions after the heat stress. Loss of Dicer leads to toxic aggregation of an exogenous prionogenic protein. Our results highlight the importance of feedback regulation in building epigenetic memory and uncover Hsp104 and Dicer as homeostatic controllers that buffer environmentally induced stochastic epigenetic variation and toxic aggregation of prionogenic proteins.
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73
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Choi Y, Mango SE. Hunting for Darwin's gemmules and Lamarck's fluid: Transgenerational signaling and histone methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1440-53. [DOI: 10.1016/j.bbagrm.2014.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 05/07/2014] [Accepted: 05/13/2014] [Indexed: 01/22/2023]
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74
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Wang J, Lawry ST, Cohen AL, Jia S. Chromosome boundary elements and regulation of heterochromatin spreading. Cell Mol Life Sci 2014; 71:4841-52. [PMID: 25192661 PMCID: PMC4234687 DOI: 10.1007/s00018-014-1725-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 08/27/2014] [Accepted: 08/29/2014] [Indexed: 11/29/2022]
Abstract
Chromatin is generally classified as euchromatin or heterochromatin, each with distinct histone modifications, compaction levels, and gene expression patterns. Although the proper formation of heterochromatin is essential for maintaining genome integrity and regulating gene expression, heterochromatin can also spread into neighboring regions in a sequence-independent manner, leading to the inactivation of genes. Because the distance of heterochromatin spreading is stochastic, the formation of boundaries, which block the spreading of heterochromatin, is critical for maintaining stable gene expression patterns. Here we review the current understanding of the mechanisms underlying heterochromatin spreading and boundary formation.
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Affiliation(s)
- Jiyong Wang
- Department of Biological Sciences, Columbia University, New York, NY, USA
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75
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Grand RS, Pichugina T, Gehlen LR, Jones MB, Tsai P, Allison JR, Martienssen R, O'Sullivan JM. Chromosome conformation maps in fission yeast reveal cell cycle dependent sub nuclear structure. Nucleic Acids Res 2014; 42:12585-99. [PMID: 25342201 PMCID: PMC4227791 DOI: 10.1093/nar/gku965] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Successful progression through the cell cycle requires spatial and temporal regulation of gene transcript levels and the number, positions and condensation levels of chromosomes. Here we present a high resolution survey of genome interactions in Schizosaccharomyces pombe using synchronized cells to investigate cell cycle dependent changes in genome organization and transcription. Cell cycle dependent interactions were captured between and within S. pombe chromosomes. Known features of genome organization (e.g. the clustering of telomeres and retrotransposon long terminal repeats (LTRs)) were observed throughout the cell cycle. There were clear correlations between transcript levels and chromosomal interactions between genes, consistent with a role for interactions in transcriptional regulation at specific stages of the cell cycle. In silico reconstructions of the chromosome organization within the S. pombe nuclei were made by polymer modeling. These models suggest that groups of genes with high and low, or differentially regulated transcript levels have preferred positions within the S. pombe nucleus. We conclude that the S. pombe nucleus is spatially divided into functional sub-nuclear domains that correlate with gene activity. The observation that chromosomal interactions are maintained even when chromosomes are fully condensed in M phase implicates genome organization in epigenetic inheritance and bookmarking.
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Affiliation(s)
- Ralph S Grand
- Liggins institute, University of Auckland, Grafton Auckland 1032, NZ Institute of Natural and Mathematical Sciences, Massey University, Albany, Auckland 0745, NZ
| | - Tatyana Pichugina
- Liggins institute, University of Auckland, Grafton Auckland 1032, NZ
| | - Lutz R Gehlen
- Institute of Natural and Mathematical Sciences, Massey University, Albany, Auckland 0745, NZ
| | - M Beatrix Jones
- Institute of Natural and Mathematical Sciences, Massey University, Albany, Auckland 0745, NZ
| | - Peter Tsai
- School of Biological Sciences, University of Auckland, Auckland 1023, NZ
| | - Jane R Allison
- Institute of Natural and Mathematical Sciences, Massey University, Albany, Auckland 0745, NZ
| | - Robert Martienssen
- HHMI-GBMF, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York, NY 11724, USA
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76
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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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77
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Ghosh S, Kakumani PK, Kumar A, Malhotra P, Mukherjee SK, Bhatnagar RK. Genome wide screening of RNAi factors of Sf21 cells reveal several novel pathway associated proteins. BMC Genomics 2014; 15:775. [PMID: 25199785 PMCID: PMC4247154 DOI: 10.1186/1471-2164-15-775] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 08/29/2014] [Indexed: 12/18/2022] Open
Abstract
Background RNA interference (RNAi) leads to sequence specific knock-down of gene expression and has emerged as an important tool to analyse gene functions, pathway analysis and gene therapy. Although RNAi is a conserved cellular process involving common elements and factors, species-specific differences have been observed among different eukaryotes. Identification of components for RNAi pathway is pursued intensively and successful genome-wide screens have been performed for components of RNAi pathways in various organisms. Functional comparative genomics analysis offers evolutionary insight that forms basis of discoveries of novel RNAi-factors within related organisms. Keeping in view the academic and commercial utility of insect derived cell-line from Spodoptera frugiperda, we pursued the identification and functional analysis of components of RNAi-machinery of Sf21 cell-line using genome-wide application. Results The genome and transcriptome of Sf21 was assembled and annotated. In silico application of comparative genome analysis among insects allowed us to identify several RNAi factors in Sf21 line. The candidate RNAi factors from assembled genome were validated by knockdown analysis of candidate factors using the siRNA screens on the Sf21-gfp reporter cell-line. Forty two (42) potential factors were identified using the cell based assay. These include core RNAi elements including Dicer-2, Argonaute-1, Drosha, Aubergine and auxiliary modules like chromatin factors, RNA helicases, RNA processing module, signalling allied proteins and others. Phylogenetic analyses and domain architecture revealed that Spodoptera frugiperda homologs retained identity with Lepidoptera (Bombyx mori) or Coleoptera (Tribolium castaneum) sustaining an evolutionary conserved scaffold in post-transcriptional gene silencing paradigm within insects. Conclusion The database of RNAi-factors generated by whole genome association survey offers comprehensive outlook about conservation as well as specific differences of the proteins of RNAi machinery. Understanding the interior involved in different phases of gene silencing also offers impending tool for RNAi-based applications. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-775) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Pawan Malhotra
- Insect Resistance Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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78
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Abstract
Replication stress is a significant contributor to genome instability. Recent studies suggest that the centromere is particularly susceptible to replication stress and prone to rearrangements and genome damage, as well as chromosome loss. This effect is enhanced by loss of heterochromatin. The resulting changes in genetic organization, including chromosome loss, increased mutation and loss of heterozygosity, are important contributors to malignant growth.
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79
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Prontera P, Donti E. Hypothesis: gonadal temperature influences sex-specific imprinting. Front Genet 2014; 5:294. [PMID: 25202325 PMCID: PMC4142806 DOI: 10.3389/fgene.2014.00294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/07/2014] [Indexed: 11/29/2022] Open
Abstract
Various explanations have been advanced for the evolution of genomic imprinting, the most popular of these being the parental conflict hypothesis. However, while this theory may explain why there has been selection for imprinting certain genes, it does not explain how the maternal and paternal genomes can be distinguished from each other. Here, we hypothesize that the temperature at which male and female gonads are physiologically exposed could be, at least for some loci, the primary factor leading to the different imprinting between the sexes.
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Affiliation(s)
- Paolo Prontera
- Medical Genetics Unit, Department of Surgical and Biomedical Sciences, University of Perugia Perugia, Italy
| | - Emilio Donti
- Medical Genetics Unit, Department of Surgical and Biomedical Sciences, University of Perugia Perugia, Italy
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80
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Wheeler BS. Small RNAs, big impact: small RNA pathways in transposon control and their effect on the host stress response. Chromosome Res 2014; 21:587-600. [PMID: 24254230 DOI: 10.1007/s10577-013-9394-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Transposons are mobile genetic elements that are a major constituent of most genomes. Organisms regulate transposable element expression, transposition, and insertion site preference, mitigating the genome instability caused by uncontrolled transposition. A recent burst of research has demonstrated the critical role of small non-coding RNAs in regulating transposition in fungi, plants, and animals. While mechanistically distinct, these pathways work through a conserved paradigm. The presence of a transposon is communicated by the presence of its RNA or by its integration into specific genomic loci. These signals are then translated into small non-coding RNAs that guide epigenetic modifications and gene silencing back to the transposon. In addition to being regulated by the host, transposable elements are themselves capable of influencing host gene expression. Transposon expression is responsive to environmental signals, and many transposons are activated by various cellular stresses. TEs can confer local gene regulation by acting as enhancers and can also confer global gene regulation through their non-coding RNAs. Thus, transposable elements can act as stress-responsive regulators that control host gene expression in cis and trans.
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Affiliation(s)
- Bayly S Wheeler
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, 94720, USA,
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81
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Joh RI, Palmieri CM, Hill IT, Motamedi M. Regulation of histone methylation by noncoding RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1385-94. [PMID: 24954181 DOI: 10.1016/j.bbagrm.2014.06.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/30/2014] [Accepted: 06/09/2014] [Indexed: 12/19/2022]
Abstract
Cells can adapt to their environment and develop distinct identities by rewiring their transcriptional networks to regulate the output of key biological pathways without concomitant mutations to the underlying genes. These alterations, called epigenetic changes, persist stably through mitotic or, in some instances, meiotic cell divisions. In eukaryotes, heritable changes to chromatin structure are a prominent, but not exclusive, mechanism by which epigenetic changes are mediated. These changes are initiated by sequence-specific events, which trigger a cascade of molecular interactions resulting in feedback mechanisms, alterations in chromatin structure, histone posttranslational modifications (PTMs), and ultimately establishment of distinct transcriptional states. In recent years, advances in next generation sequencing have led to the discovery of several novel classes of noncoding RNAs (ncRNAs). In addition to their well-established cytoplasmic roles in posttranscriptional regulation of gene expression, ncRNAs have emerged as key regulators of epigenetic changes via chromatin-dependent mechanisms in organisms ranging from yeast to man. They function by affecting chromatin structure, histone PTMs, and the recruitment of transcriptional activating or repressing complexes. Among histone PTMs, lysine methylation serves as the binding substrate for the recruitment of key protein complexes involved in the regulation of genome architecture, stability, and gene expression. In this review, we will outline the known mechanisms by which ncRNAs of different origins regulate histone methylation, and in doing so contribute to a variety of genome regulatory functions in eukaryotes.
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Affiliation(s)
- Richard I Joh
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School,149 13th Street, Charlestown, MA 02129, USA
| | - Christina M Palmieri
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School,149 13th Street, Charlestown, MA 02129, USA
| | - Ian T Hill
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School,149 13th Street, Charlestown, MA 02129, USA; PhD Program in Biological and Biomedical Sciences, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Mo Motamedi
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School,149 13th Street, Charlestown, MA 02129, USA.
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82
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Maiolica A, de Medina-Redondo M, Schoof EM, Chaikuad A, Villa F, Gatti M, Jeganathan S, Lou HJ, Novy K, Hauri S, Toprak UH, Herzog F, Meraldi P, Penengo L, Turk BE, Knapp S, Linding R, Aebersold R. Modulation of the chromatin phosphoproteome by the Haspin protein kinase. Mol Cell Proteomics 2014; 13:1724-40. [PMID: 24732914 DOI: 10.1074/mcp.m113.034819] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Recent discoveries have highlighted the importance of Haspin kinase activity for the correct positioning of the kinase Aurora B at the centromere. Haspin phosphorylates Thr(3) of the histone H3 (H3), which provides a signal for Aurora B to localize to the centromere of mitotic chromosomes. To date, histone H3 is the only confirmed Haspin substrate. We used a combination of biochemical, pharmacological, and mass spectrometric approaches to study the consequences of Haspin inhibition in mitotic cells. We quantified 3964 phosphorylation sites on chromatin-associated proteins and identified a Haspin protein-protein interaction network. We determined the Haspin consensus motif and the co-crystal structure of the kinase with the histone H3 tail. The structure revealed a unique bent substrate binding mode positioning the histone H3 residues Arg(2) and Lys(4) adjacent to the Haspin phosphorylated threonine into acidic binding pockets. This unique conformation of the kinase-substrate complex explains the reported modulation of Haspin activity by methylation of Lys(4) of the histone H3. In addition, the identification of the structural basis of substrate recognition and the amino acid sequence preferences of Haspin aided the identification of novel candidate Haspin substrates. In particular, we validated the phosphorylation of Ser(137) of the histone variant macroH2A as a target of Haspin kinase activity. MacroH2A Ser(137) resides in a basic stretch of about 40 amino acids that is required to stabilize extranucleosomal DNA, suggesting that phosphorylation of Ser(137) might regulate the interactions of macroH2A and DNA. Overall, our data suggest that Haspin activity affects the phosphorylation state of proteins involved in gene expression regulation and splicing.
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Affiliation(s)
- Alessio Maiolica
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Maria de Medina-Redondo
- §Department of Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Erwin M Schoof
- ¶Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Lyngby, Denmark
| | - Apirat Chaikuad
- ‖Oxford University, Nuffield Department of Clinical Medicine, Target Discovery Institute (TDI) and Structural Genomics Consortium (SGC), Oxford OX3 7FZ, United Kingdom
| | - Fabrizio Villa
- **Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Marco Gatti
- ‡‡Department of Pharmaceutical Sciences, University of Piemonte Orientale "A. Avogadro" Novara, Italy
| | - Siva Jeganathan
- §§Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Hua Jane Lou
- ¶¶Yale University School of Medicine, Department of Pharmacology, New Haven, Connecticut 06520, USA
| | - Karel Novy
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Simon Hauri
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Umut H Toprak
- §Department of Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Franz Herzog
- ‖‖Gene Center Munich Ludwig-Maximilians-Universität München, Munich, Germany
| | - Patrick Meraldi
- §Department of Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Lorenza Penengo
- ‡‡Department of Pharmaceutical Sciences, University of Piemonte Orientale "A. Avogadro" Novara, Italy
| | - Benjamin E Turk
- ¶¶Yale University School of Medicine, Department of Pharmacology, New Haven, Connecticut 06520, USA
| | - Stefan Knapp
- ‖Oxford University, Nuffield Department of Clinical Medicine, Target Discovery Institute (TDI) and Structural Genomics Consortium (SGC), Oxford OX3 7FZ, United Kingdom
| | - Rune Linding
- ¶Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Lyngby, Denmark
| | - Ruedi Aebersold
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland
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83
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DNA replication components as regulators of epigenetic inheritance--lesson from fission yeast centromere. Protein Cell 2014; 5:411-9. [PMID: 24691906 PMCID: PMC4026425 DOI: 10.1007/s13238-014-0049-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 02/24/2014] [Indexed: 01/30/2023] Open
Abstract
Genetic information stored in DNA is accurately copied and transferred to subsequent generations through DNA replication. This process is accomplished through the concerted actions of highly conserved DNA replication components. Epigenetic information stored in the form of histone modifications and DNA methylation, constitutes a second layer of regulatory information important for many cellular processes, such as gene expression regulation, chromatin organization, and genome stability. During DNA replication, epigenetic information must also be faithfully transmitted to subsequent generations. How this monumental task is achieved remains poorly understood. In this review, we will discuss recent advances on the role of DNA replication components in the inheritance of epigenetic marks, with a particular focus on epigenetic regulation in fission yeast. Based on these findings, we propose that specific DNA replication components function as key regulators in the replication of epigenetic information across the genome.
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84
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Smialowska A, Djupedal I, Wang J, Kylsten P, Swoboda P, Ekwall K. RNAi mediates post-transcriptional repression of gene expression in fission yeast Schizosaccharomyces pombe. Biochem Biophys Res Commun 2014; 444:254-9. [PMID: 24462781 DOI: 10.1016/j.bbrc.2014.01.057] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 01/15/2014] [Indexed: 11/25/2022]
Abstract
RNA interference (RNAi) is a gene silencing mechanism conserved from fungi to mammals. Small interfering RNAs are products and mediators of the RNAi pathway and act as specificity factors in recruiting effector complexes. The Schizosaccharomyces pombe genome encodes one of each of the core RNAi proteins, Dicer, Argonaute and RNA-dependent RNA polymerase (dcr1, ago1, rdp1). Even though the function of RNAi in heterochromatin assembly in S. pombe is established, its role in controlling gene expression is elusive. Here, we report the identification of small RNAs mapped anti-sense to protein coding genes in fission yeast. We demonstrate that these genes are up-regulated at the protein level in RNAi mutants, while their mRNA levels are not significantly changed. We show that the repression by RNAi is not a result of heterochromatin formation. Thus, we conclude that RNAi is involved in post-transcriptional gene silencing in S. pombe.
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Affiliation(s)
- Agata Smialowska
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institute, Huddinge 141-83, Sweden; School of Life Sciences, Södertörn Högskola, Huddinge 141-89, Sweden.
| | - Ingela Djupedal
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institute, Huddinge 141-83, Sweden
| | - Jingwen Wang
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institute, Huddinge 141-83, Sweden
| | - Per Kylsten
- School of Life Sciences, Södertörn Högskola, Huddinge 141-89, Sweden
| | - Peter Swoboda
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institute, Huddinge 141-83, Sweden
| | - Karl Ekwall
- Center for Biosciences, Department of Biosciences and Nutrition, Karolinska Institute, Huddinge 141-83, Sweden; School of Life Sciences, Södertörn Högskola, Huddinge 141-89, Sweden.
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85
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Abstract
RNA transcripts that do not code for proteins have been long known to lie at the heart of many biological processes, such as splicing and translation. Yet their full potential has only been appreciated recently and non-coding RNAs (ncRNAs) are now attracting increasing attention. Pioneering work in yeast and plant systems has revealed that non-coding RNAs can have a major influence on the deposition of histone and DNA modifications. This can introduce heritable variation into gene expression and, thus, be the basis of epigenetic phenomena. Mechanistically, such processes have been studied extensively in the fission yeast Schizosaccharomyces pombe, providing an important conceptual framework for possible modes of action of ncRNAs also in other organisms. In this review, we highlight mechanistic insights into chromatin-associated ncRNA activities gained from work with fission yeast, and we draw parallels to studies in other eukaryotes that indicate evolutionary conservation.
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Affiliation(s)
- Claudia Keller
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
- University of Basel, Petersplatz 10, 4003 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
- University of Basel, Petersplatz 10, 4003 Basel, Switzerland
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86
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Dantzer F, Santoro R. The expanding role of PARPs in the establishment and maintenance of heterochromatin. FEBS J 2013; 280:3508-18. [DOI: 10.1111/febs.12368] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 04/26/2013] [Accepted: 05/24/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Françoise Dantzer
- UMR7242; Centre National de la Recherche Scientifique Université de Strasbourg; Laboratoire d'Excellence Medalis; Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg; Ecole Supérieure de Biotechnologie de Strasbourg; Illkirch France
| | - Raffaella Santoro
- Institute of Veterinary Biochemistry and Molecular Biology; University of Zürich; Zürich Switzerland
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87
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Le AH, Mastro TL, Forsburg SL. The C-terminus of S. pombe DDK subunit Dfp1 is required for meiosis-specific transcription and cohesin cleavage. Biol Open 2013; 2:728-38. [PMID: 23862021 PMCID: PMC3711041 DOI: 10.1242/bio.20135173] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 05/14/2013] [Indexed: 11/24/2022] Open
Abstract
The DDK complex is a conserved kinase complex, consisting of a catalytic subunit, Hsk1 (Cdc7), and its regulatory subunit Dfp1 (Dbf4). This kinase is essential for DNA replication. In this work, we show that dfp1-r35, which truncates the Dfp1 C-terminus zinc finger, causes severe meiotic defects, including reduced spore viability, reduced formation of programmed double strand breaks, altered expression of meiotic genes, and disrupted chromosome segregation. There is a high frequency of dyad formation. Mutants are also defective in the phosphorylation and degradation of the meiotic cohesion, Rec8, resulting in a failure to proceed through the MII division. These defects are more pronounced in a haploid meiosis model than in a normal diploid meiosis. Thus, several critical meiotic functions are linked specifically to the C-terminus of Dfp1, which may target specific substrates for phosphorylation by Hsk1.
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Affiliation(s)
- Anh-Huy Le
- Program in Molecular and Computational Biology, University of Southern California , Los Angeles, CA 90089-2910 , USA
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88
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Li PC, Green MD, Forsburg SL. Mutations disrupting histone methylation have different effects on replication timing in S. pombe centromere. PLoS One 2013; 8:e61464. [PMID: 23658693 PMCID: PMC3641051 DOI: 10.1371/journal.pone.0061464] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 03/11/2013] [Indexed: 11/19/2022] Open
Abstract
The fission yeast pericentromere comprises repetitive sequence elements packaged into heterchromatin marked by histone H3K9 methylation and Swi6 binding. Transient disruption of Swi6 during S phase allows a period of RNA synthesis which programs the RNAi machinery to maintain histone methylation. However, Swi6 is also required for early replication timing. We show that not only Swi6 but also the chromodomain protein Chp1 are delocalized during S phase. Different from loss of swi6, mutations that disrupt histone methylation in the centromere, chp1Δ and clr4Δ, undergo early DNA replication. However, timing is modestly delayed in RNAi mutants dcr1Δ or rdp1Δ, while hrr1Δ mutants resemble swi6Δ in their replication delay. Finally, we show that recruitment of RNA polymerase II in the centromere occurs independently of replication. These different effects indicate that replication timing is not simply linked to histone methylation.
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Affiliation(s)
- Pao-Chen Li
- Molecular & Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
| | - Marc D. Green
- Molecular & Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
| | - Susan L. Forsburg
- Molecular & Computational Biology Program, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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89
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Structural analysis of Stc1 provides insights into the coupling of RNAi and chromatin modification. Proc Natl Acad Sci U S A 2013; 110:E1879-88. [PMID: 23613586 DOI: 10.1073/pnas.1212155110] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Noncoding RNAs can modulate gene expression by directing modifications to histones that alter chromatin structure. In fission yeast, siRNAs produced via the RNAi pathway direct modifications associated with heterochromatin formation. siRNAs associate with the RNAi effector protein Argonaute 1 (Ago1), targeting the Ago1-containing RNA-induced transcriptional silencing (RITS) complex to homologous nascent transcripts. This promotes recruitment of the Clr4 complex (CLRC), which mediates methylation of histone H3 on lysine 9 (H3K9me) in cognate chromatin. A key question is how the RNAi and chromatin modification machineries are connected. Stc1 is a small protein recently shown to associate with both Ago1 and CLRC and to play a pivotal role in mediating the RNAi-dependent recruitment of CLRC to chromatin. To understand its mode of action, we have performed a detailed structural and functional analysis of the Stc1 protein. Our analyses reveal that the conserved N-terminal region of Stc1 represents an unusual tandem zinc finger domain, with similarities to common LIM domains but distinguished by a lack of preferred relative orientation of the two zinc fingers. We demonstrate that this tandem zinc finger domain is involved in binding Ago1, whereas the nonconserved C-terminal region mediates association with CLRC. These findings elucidate the molecular basis for the coupling of RNAi to chromatin modification in fission yeast.
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90
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Distinct roles for Sir2 and RNAi in centromeric heterochromatin nucleation, spreading and maintenance. EMBO J 2013; 32:1250-64. [PMID: 23572080 PMCID: PMC3642681 DOI: 10.1038/emboj.2013.72] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 03/08/2013] [Indexed: 11/08/2022] Open
Abstract
Epigenetically regulated heterochromatin domains govern essential cellular activities. A key feature of heterochromatin domains is the presence of hypoacetylated nucleosomes, which are methylated on lysine 9 of histone H3 (H3K9me). Here, we investigate the requirements for establishment, spreading and maintenance of heterochromatin using fission yeast centromeres as a paradigm. We show that establishment of heterochromatin on centromeric repeats is initiated at modular 'nucleation sites' by RNA interference (RNAi), ensuring the mitotic stability of centromere-bearing minichromosomes. We demonstrate that the histone deacetylases Sir2 and Clr3 and the chromodomain protein Swi6(HP1) are required for H3K9me spreading from nucleation sites, thus allowing formation of extended heterochromatin domains. We discovered that RNAi and Sir2 along with Swi6(HP1) operate in two independent pathways to maintain heterochromatin. Finally, we demonstrate that tethering of Sir2 is pivotal to the maintenance of heterochromatin at an ectopic locus in the absence of RNAi. These analyses reveal that Sir2, together with RNAi, are sufficient to ensure heterochromatin integrity and provide evidence for sequential establishment, spreading and maintenance steps in the assembly of centromeric heterochromatin.
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91
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Castel SE, Martienssen RA. RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat Rev Genet 2013; 14:100-12. [PMID: 23329111 DOI: 10.1038/nrg3355] [Citation(s) in RCA: 679] [Impact Index Per Article: 61.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A growing number of functions are emerging for RNA interference (RNAi) in the nucleus, in addition to well-characterized roles in post-transcriptional gene silencing in the cytoplasm. Epigenetic modifications directed by small RNAs have been shown to cause transcriptional repression in plants, fungi and animals. Additionally, increasing evidence indicates that RNAi regulates transcription through interaction with transcriptional machinery. Nuclear small RNAs include small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) and are implicated in nuclear processes such as transposon regulation, heterochromatin formation, developmental gene regulation and genome stability.
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Affiliation(s)
- Stephane E Castel
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York 11724, USA
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92
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Li PC, Petreaca RC, Jensen A, Yuan JP, Green MD, Forsburg SL. Replication fork stability is essential for the maintenance of centromere integrity in the absence of heterochromatin. Cell Rep 2013; 3:638-45. [PMID: 23478021 DOI: 10.1016/j.celrep.2013.02.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 01/06/2013] [Accepted: 02/05/2013] [Indexed: 12/18/2022] Open
Abstract
The centromere of many eukaryotes contains highly repetitive sequences marked by methylation of histone H3K9 by Clr4(KMT1). This recruits multiple heterochromatin proteins, including Swi6 and Chp1, to form a rigid centromere and ensure accurate chromosome segregation. In the absence of heterochromatin, cells show an increased rate of recombination in the centromere, as well as chromosome loss. These defects are severely aggravated by loss of replication fork stability. Thus, heterochromatin proteins and replication fork protection mechanisms work in concert to prevent abnormal recombination, preserve centromere integrity, and ensure faithful chromosome segregation.
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Affiliation(s)
- Pao-Chen Li
- Molecular & Computational Biology Program, University of Southern California, Los Angeles, CA 90089-2910, USA
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93
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Mehić B. Something about genetics in psychiatry. Bosn J Basic Med Sci 2013; 12:211-2. [PMID: 23330218 DOI: 10.17305/bjbms.2012.2439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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94
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Fadloun A, Eid A, Torres-Padilla ME. Mechanisms and dynamics of heterochromatin formation during mammalian development: closed paths and open questions. Curr Top Dev Biol 2013; 104:1-45. [PMID: 23587237 DOI: 10.1016/b978-0-12-416027-9.00001-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Early embryonic development in mammals is characterized by major changes in the components of the chromatin and its remodeling. The embryonic chromatin and the nuclear organization in the mouse preimplantation embryo display particular features that are dramatically different from somatic cells. These include the highly specific organization of the pericentromeric heterochromatin within the nucleus and the suggested lack of conventional heterochromatin. We postulate that the plasticity of the cells in the early embryo relies on the distinctive heterochromatin features that prevail during early embryogenesis. Here, we review some of these features and discuss recent findings on the mechanisms driving heterochromatin formation after fertilization, in particular, the emerging role of RNA as a regulator of heterochromatic loci also in mammals. Finally, we believe that there are at least three major avenues that should be addressed in the coming years: (i) Is heterochromatin a driving force in development? (ii) Does it have a role in lineage allocation? (iii) How can heterochromatin "regulate" epigenetic reprogramming?
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Affiliation(s)
- Anas Fadloun
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM U964, Université de Strasbourg, Illkirch, France
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95
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Cell cycle-dependent deposition of CENP-A requires the Dos1/2-Cdc20 complex. Proc Natl Acad Sci U S A 2012; 110:606-11. [PMID: 23267073 DOI: 10.1073/pnas.1214874110] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Centromeric histone CENP-A, a variant of canonical histone H3, plays a central role in proper chromosome segregation. Loading of CENP-A at centromeres is cell cycle-regulated: parental CENP-A is deposited at centromeres during S phase, whereas newly synthesized CENP-A is deposited during later stages of the cell cycle. The mechanisms involved in deposition of CENP-A at centromeres during S phase remain poorly understood. In fission yeast, loading of CENP-A during S phase is regulated by the GATA-type factor, Ams2. Here we show that the Dos1/2-Cdc20 complex, previously characterized as a silencing complex essential for inheritance of H3K9 methylation during S phase, is also required for localization of CENP-A(cnp1) at centromeres at this stage. Disruption of Dos1 (also known as Raf1/Clr8/Cmc1), Dos2 (also known as Raf2/Clr7/Cmc2), or Cdc20, a DNA polymerase epsilon subunit, results in dissociation of CENP-A from centromeres and mislocalization of the protein to noncentromeric sites. All three mutants display spindle disorganization and mitotic defects. Inactivation of Dos1 or Cdc20 also results in accumulation of noncoding RNA transcripts from centromeric cores, a feature common to mutants affecting kinetochore integrity. We further find that Dos1 physically associates with Ams2 and is required for the association of Ams2 with centromeric cores during S phase. Finally, we show that Dos2 associates with centromeric cores during S phase and that its recruitment to centromeric cores depends on Cdc20. This study identifies a physical link between DNA replication and CENP-A assembly machinery and provides mechanistic insight into how CENP-A is faithfully inherited during S phase.
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96
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Wang F, Higgins JMG. Histone modifications and mitosis: countermarks, landmarks, and bookmarks. Trends Cell Biol 2012; 23:175-84. [PMID: 23246430 DOI: 10.1016/j.tcb.2012.11.005] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 11/12/2012] [Accepted: 11/13/2012] [Indexed: 11/30/2022]
Abstract
The roles of post-translational histone modifications in regulating transcription and DNA damage have been widely studied and discussed. Although mitotic histone marks, particularly phosphorylation, were discovered four decades ago, their roles in mitosis have been outlined only in the past few years. Here we aim to provide an integrated view of how histone modifications act as 'countermarks', 'landmarks', and 'bookmarks' to displace, recruit, and 'remember' the location of regulatory proteins during and shortly after mitosis. These capabilities allow histone marks to help downregulate interphase functions such as transcription during mitosis, to facilitate chromatin events required to accomplish chromosome segregation, and to contribute to the maintenance of epigenetic states through mitosis.
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Affiliation(s)
- Fangwei Wang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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97
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Shu H, Wildhaber T, Siretskiy A, Gruissem W, Hennig L. Distinct modes of DNA accessibility in plant chromatin. Nat Commun 2012; 3:1281. [DOI: 10.1038/ncomms2259] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 11/05/2012] [Indexed: 01/06/2023] Open
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98
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Alper BJ, Lowe BR, Partridge JF. Centromeric heterochromatin assembly in fission yeast--balancing transcription, RNA interference and chromatin modification. Chromosome Res 2012; 20:521-34. [PMID: 22733402 DOI: 10.1007/s10577-012-9288-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Distinct regions of the eukaryotic genome are packaged into different types of chromatin, with euchromatin representing gene rich, transcriptionally active regions and heterochromatin more condensed and gene poor. The assembly and maintenance of heterochromatin is important for many aspects of genome control, including silencing of gene transcription, suppression of recombination, and to ensure proper chromosome segregation. The precise mechanisms underlying heterochromatin establishment and maintenance are still unclear, but much progress has been made towards understanding this process during the last few years, particularly from studies performed in fission yeast. In this review, we hope to provide a conceptual model of centromeric heterochromatin in fission yeast that integrates our current understanding of the competing forces of transcription, replication, and RNA decay that influence its assembly and propagation.
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Affiliation(s)
- Benjamin J Alper
- Department of Biochemistry, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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99
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Thorsen M, Hansen H, Venturi M, Holmberg S, Thon G. Mediator regulates non-coding RNA transcription at fission yeast centromeres. Epigenetics Chromatin 2012; 5:19. [PMID: 23171760 PMCID: PMC3541127 DOI: 10.1186/1756-8935-5-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Accepted: 11/01/2012] [Indexed: 12/04/2022] Open
Abstract
Background In fission yeast, centromeric heterochromatin is necessary for the fidelity of chromosome segregation. Propagation of heterochromatin in dividing cells requires RNA interference (RNAi) and transcription of centromeric repeats by RNA polymerase II during the S phase of the cell cycle. Results We found that the Med8-Med18-Med20 submodule of the Mediator complex is required for the transcriptional regulation of native centromeric dh and dg repeats and for the silencing of reporter genes inserted in centromeric heterochromatin. Mutations in the Med8-Med18-Med20 submodule did not alter Mediator occupancy at centromeres; however, they led to an increased recruitment of RNA polymerase II to centromeres and reduced levels of centromeric H3K9 methylation accounting for the centromeric desilencing. Further, we observed that Med18 and Med20 were required for efficient processing of dh transcripts into siRNA. Consistent with defects in centromeric heterochromatin, cells lacking Med18 or Med20 displayed elevated rates of mitotic chromosome loss. Conclusions Our data demonstrate a role for the Med8-Med18-Med20 Mediator submodule in the regulation of non-coding RNA transcription at Schizosaccharomyces pombe centromeres. In wild-type cells this submodule limits RNA polymerase II access to the heterochromatic DNA of the centromeres. Additionally, the submodule may act as an assembly platform for the RNAi machinery or regulate the activity of the RNAi pathway. Consequently, Med8-Med18-Med20 is required for silencing of centromeres and proper mitotic chromosome segregation.
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Affiliation(s)
- Michael Thorsen
- Department of Biology, University of Copenhagen, BioCenter, Ole Maaløes vej 5, 2200, Copenhagen, N, Denmark.
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100
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Abstract
There is growing evidence to support the notion that small RNAs derived from noncoding RNAs (ncRNAs) are mobile carriers of epigenetic information in diverse eukaryotic systems. However, challenges remain in defining what messages are being sent and how. In the August 1, 2012, issue of Genes & Development, Schoeberl and colleagues (pp. 1729-1742) reported a detailed analysis of the turnover of small RNAs during the sexual reproduction of the ciliated protozoan Tetrahymena. The results revealed surprisingly complicated roles played by small RNAs in shaping the communication between the germline and the soma.
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Affiliation(s)
- Shan Gao
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
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