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Coy S, Vasiljeva L. The exosome and heterochromatin : multilevel regulation of gene silencing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 702:105-21. [PMID: 21713681 DOI: 10.1007/978-1-4419-7841-7_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Heterochromatic silencing is important for repressing gene expression, protecting cells against viral invasion, maintaining DNA integrity and for proper chromosome segregation. Recently, it has become apparent that expression of eukaryotic genomesis far more complex than had previously been anticipated. Strikingly, it has emerged that most of the genome is transcribed including intergenic regions and heterochromatin, calling for us to re-address the question of how gene silencing is regulated and re-evaluate the concept ofheterochromatic regions of the genome being transcriptionally inactive. Although heterochromatic silencing can be regulated at the transcriptional level, RNA degrading activities supplied either by the exosome complex or RNAi also significantly contribute to this process. The exosome also regulates noncoding RNAs (ncRNAs) involved in the establishment of heterochromatin, further underscoring its role as the major cellular machinery involved in RNA processing and turn-over. This multilevel control of the transcriptome may be utilized to ensure greater accuracy of gene expression and allow distinction between functional transcripts and background noise. In this chapter, we will discuss the regulation of gene silencing across species, with special emphasis on the exosome's contribution to the process. We will also discuss the links between transcriptional and posttranscriptional mechanisms for gene silencing and their impact on the regulation of eukaryotic transcriptomes.
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Affiliation(s)
- Sarah Coy
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
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52
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Pancaldi V, Schubert F, Bähler J. Meta-analysis of genome regulation and expression variability across hundreds of environmental and genetic perturbations in fission yeast. ACTA ACUST UNITED AC 2010; 6:543-52. [DOI: 10.1039/b913876p] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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53
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Butler JS, Mitchell P. Rrp6, Rrp47 and Cofactors of the Nuclear Exosome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 702:91-104. [DOI: 10.1007/978-1-4419-7841-7_8] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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54
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Splicing factor Spf30 assists exosome-mediated gene silencing in fission yeast. Mol Cell Biol 2009; 30:1145-57. [PMID: 20028739 DOI: 10.1128/mcb.01317-09] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Heterochromatin assembly in fission yeast relies on the processing of cognate noncoding RNAs by both the RNA interference and the exosome degradation pathways. Recent evidence indicates that splicing factors facilitate the cotranscriptional processing of centromeric transcripts into small interfering RNAs (siRNAs). In contrast, how the exosome contributes to heterochromatin assembly and whether it also relies upon splicing factors were unknown. We provide here evidence that fission yeast Spf30 is a splicing factor involved in the exosome pathway of heterochromatin silencing. Spf30 and Dis3, the main exosome RNase, colocalize at centromeric heterochromatin and euchromatic genes. At the centromeres, Dis3 helps recruiting Spf30, whose deficiency phenocopies the dis3-54 mutant: heterochromatin is impaired, as evidenced by reduced silencing and the accumulation of polyadenylated centromeric transcripts, but the production of siRNAs appears to be unaffected. Consistent with a direct role, Spf30 binds centromeric transcripts and locates at the centromeres in an RNA-dependent manner. We propose that Spf30, bound to nascent centromeric transcripts, perhaps with other splicing factors, assists their processing by the exosome. Splicing factor intercession may thus be a common feature of gene silencing pathways.
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55
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Callahan KP, Butler JS. TRAMP complex enhances RNA degradation by the nuclear exosome component Rrp6. J Biol Chem 2009; 285:3540-3547. [PMID: 19955569 DOI: 10.1074/jbc.m109.058396] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RNA-processing exosome contains ribonucleases that degrade aberrant RNAs in archael and eukaryotic cells. In Saccharomyces cerevisiae, the nuclear/nucleolar 3'-5' exoribonuclease Rrp6 distinguishes the nuclear exosome from the cytoplasmic exosome. In vivo, the TRAMP complex enhances the ability of the nuclear exosome to destroy some aberrant RNAs. Previous reports showed that purified TRAMP enhanced RNA degradation by the nuclear exosome in vitro. However, the exoribonucleolytic component(s) of the nuclear exosome enhanced by TRAMP remain unidentified. We show that TRAMP does not significantly enhance RNA degradation by purified exosomes lacking Rrp6 in vitro, suggesting that TRAMP activation experiments with nuclear exosome preparations reflect, in part, effects on the activity of Rrp6. Consistent with this, we show that incubation of purified TRAMP with recombinant Rrp6 results in a 10-fold enhancement of the rate of RNA degradation. This increased activity results from enhancement of the hydrolytic activity of Rrp6 because TRAMP cannot enhance the activity of an Rrp6 mutant lacking a key amino acid side chain in its active site. We observed no ATP or polyadenylation dependence for the enhancement of Rrp6 activity by TRAMP, suggesting that neither the poly(A) polymerase activity of Trf4 nor the helicase activity of Mtr4 plays a role in the enhancement. These findings identify TRAMP as an exosome-independent enhancer of Rrp6 activity.
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Affiliation(s)
- Kevin P Callahan
- From the Departments of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642
| | - J Scott Butler
- From the Departments of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642; Departments of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642; the Center for RNA Biology: From Genome to Medicine, University of Rochester Medical Center, Rochester, New York 14642.
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56
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Silent chromatin at the middle and ends: lessons from yeasts. EMBO J 2009; 28:2149-61. [PMID: 19629038 PMCID: PMC2722250 DOI: 10.1038/emboj.2009.185] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Accepted: 06/15/2009] [Indexed: 11/09/2022] Open
Abstract
Eukaryotic centromeres and telomeres are specialized chromosomal regions that share one common characteristic: their underlying DNA sequences are assembled into heritably repressed chromatin. Silent chromatin in budding and fission yeast is composed of fundamentally divergent proteins tat assemble very different chromatin structures. However, the ultimate behaviour of silent chromatin and the pathways that assemble it seem strikingly similar among Saccharomyces cerevisiae (S. cerevisiae), Schizosaccharomyces pombe (S. pombe) and other eukaryotes. Thus, studies in both yeasts have been instrumental in dissecting the mechanisms that establish and maintain silent chromatin in eukaryotes, contributing substantially to our understanding of epigenetic processes. In this review, we discuss current models for the generation of heterochromatic domains at centromeres and telomeres in the two yeast species.
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57
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The fission yeast HIRA histone chaperone is required for promoter silencing and the suppression of cryptic antisense transcripts. Mol Cell Biol 2009; 29:5158-67. [PMID: 19620282 DOI: 10.1128/mcb.00698-09] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The assembly of nucleosomes by histone chaperones is an important component of transcriptional regulation. Here, we have assessed the global roles of the HIRA histone chaperone in Schizosaccharomyces pombe. Microarray analysis indicates that inactivation of the HIRA complex results in increased expression of at least 4% of fission yeast genes. HIRA-regulated genes overlap with those which are normally repressed in vegetatively growing cells, such as targets of the Clr6 histone deacetylase and silenced genes located in subtelomeric regions. HIRA is also required for silencing of all 13 intact copies of the Tf2 long terminal repeat (LTR) retrotransposon. However, the role of HIRA is not restricted to bona fide promoters, because HIRA also suppresses noncoding transcripts from solo LTR elements and spurious antisense transcripts from cryptic promoters associated with transcribed regions. Furthermore, the HIRA complex is essential in the absence of the quality control provided by nuclear exosome-mediated degradation of illegitimate transcripts. This suggests that HIRA restricts genomic accessibility, and consistent with this, the chromosomes of cells lacking HIRA are more susceptible to genotoxic agents that cause double-strand breaks. Thus, the HIRA histone chaperone is required to maintain the protective functions of chromatin.
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58
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Paolo SS, Vanacova S, Schenk L, Scherrer T, Blank D, Keller W, Gerber AP. Distinct roles of non-canonical poly(A) polymerases in RNA metabolism. PLoS Genet 2009; 5:e1000555. [PMID: 19593367 PMCID: PMC2700272 DOI: 10.1371/journal.pgen.1000555] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 06/09/2009] [Indexed: 11/19/2022] Open
Abstract
Trf4p and Trf5p are non-canonical poly(A) polymerases and are part of the heteromeric protein complexes TRAMP4 and TRAMP5 that promote the degradation of aberrant and short-lived RNA substrates by interacting with the nuclear exosome. To assess the level of functional redundancy between the paralogous Trf4 and Trf5 proteins and to investigate the role of the Trf4-dependent polyadenylation in vivo, we used DNA microarrays to compare gene expression of the wild-type yeast strain of S. cerevisiae with either that of trf4Δ or trf5Δ mutant strains or the trf4Δ mutant expressing the polyadenylation-defective Trf4(DADA) protein. We found little overlap between the sets of transcripts with altered expression in the trf4Δ or the trf5Δ mutants, suggesting that Trf4p and Trf5p target distinct groups of RNAs for degradation. Surprisingly, most RNAs the expression of which was altered by the trf4 deletion were restored to wild-type levels by overexpression of TRF4(DADA), showing that the polyadenylation activity of Trf4p is dispensable in vivo. Apart from previously reported Trf4p and Trf5p target RNAs, this analysis along with in vivo cross-linking and RNA immunopurification-chip experiments revealed that both the TRAMP4 and the TRAMP5 complexes stimulate the degradation of spliced-out introns via a mechanism that is independent of the polyadenylation activity of Trf4p. In addition, we show that disruption of trf4 causes severe shortening of telomeres suggesting that TRF4 functions in the maintenance of telomere length. Finally, our study demonstrates that TRF4, the exosome, and TRF5 participate in antisense RNA–mediated regulation of genes involved in phosphate metabolism. In conclusion, our results suggest that paralogous TRAMP complexes have distinct RNA selectivities with functional implications in RNA surveillance as well as other RNA–related processes. This indicates widespread and integrative functions of TRAMP complexes for the coordination of different gene expression regulatory processes. The discovery that most regions of the genome are actively transcribed into non-coding RNAs has dramatically increased interest in their function and regulation. Recent data from us and others have shed light on the molecular machinery that promotes the decay of such transcripts. In the yeast S. cerevisiae, Trf4p and Trf5p are alternative subunits of the so-called TRAMP complex, which degrades aberrant and short-lived RNAs. They add short poly(A) tails to their substrate RNAs that function as landing pads for exonucleases mediating RNA decay. Although alternate compositions of TRAMP complexes exist, the RNA substrate specificities and the processes controlled by them have not been determined. Applying a genome-wide approach, we describe overlapping yet distinct functional implications of different TRAMP complexes, and we demonstrate strong connections between RNA quality control and other RNA–related processes such as telomer length maintenance. Moreover, our study shows that the degradation of specific target RNAs is not strictly dependent on the polyadenylation activity of Trf proteins in vivo. These results suggest novel and integrative functions of TRAMP complexes for RNA regulation.
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Affiliation(s)
- Salvatore San Paolo
- Department of Cell Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Stepanka Vanacova
- National Center for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Luca Schenk
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Tanja Scherrer
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Diana Blank
- Department of Cell Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Walter Keller
- Department of Cell Biology, Biozentrum, University of Basel, Basel, Switzerland
- * E-mail: (WK); (APG)
| | - André P. Gerber
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
- * E-mail: (WK); (APG)
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59
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Belostotsky D. Exosome complex and pervasive transcription in eukaryotic genomes. Curr Opin Cell Biol 2009; 21:352-8. [DOI: 10.1016/j.ceb.2009.04.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Revised: 04/19/2009] [Accepted: 04/20/2009] [Indexed: 12/27/2022]
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60
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Schmid M, Küchler B, Eckmann CR. Two conserved regulatory cytoplasmic poly(A) polymerases, GLD-4 and GLD-2, regulate meiotic progression in C. elegans. Genes Dev 2009; 23:824-36. [PMID: 19339688 DOI: 10.1101/gad.494009] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Translational regulation is heavily employed during developmental processes to control the timely accumulation of proteins independently of gene transcription. In particular, mRNA poly(A) tail metabolism in the cytoplasm is a key determinant for balancing an mRNA's translational output and its decay rate. Noncanonical poly(A) polymerases (PAPs), such as germline development defective-2 (GLD-2), can mediate poly(A) tail extension. Little is known about the regulation and functional complexity of cytoplasmic PAPs. Here we report the discovery of Caenorhabditis elegans GLD-4, a cytoplasmic PAP present in P granules that is orthologous to Trf4/5p from budding yeast. GLD-4 enzymatic activity is enhanced by its interaction with GLS-1, a protein associated with the RNA-binding protein GLD-3. GLD-4 is predominantly expressed in germ cells, and its activity is essential for early meiotic progression of male and female gametes in the absence of GLD-2. For commitment into female meiosis, both PAPs converge on at least one common target mRNA-i.e., gld-1 mRNA-and, as a consequence, counteract the repressive action of two PUF proteins and the putative deadenylase CCR-4. Together our findings suggest that two different cytoplasmic PAPs stabilize and translationally activate several meiotic mRNAs to provide a strong fail-safe mechanism for early meiotic progression.
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Affiliation(s)
- Mark Schmid
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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61
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McPheeters DS, Cremona N, Sunder S, Chen HM, Averbeck N, Leatherwood J, Wise JA. A complex gene regulatory mechanism that operates at the nexus of multiple RNA processing decisions. Nat Struct Mol Biol 2009; 16:255-64. [PMID: 19198588 PMCID: PMC2776722 DOI: 10.1038/nsmb.1556] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Accepted: 01/07/2009] [Indexed: 11/30/2022]
Abstract
Expression of crs1 pre-mRNA, encoding a meiotic cyclin, is blocked in actively growing fission yeast cells by a multifaceted mechanism. The most striking feature is that crs1 transcripts are continuously synthesized in vegetative cells, but are targeted for degradation rather than splicing and polyadenylation. Turnover of crs1 RNA requires the exosome, similar to previously described nuclear surveillance and silencing mechanisms, but does not involve a non-canonical poly(A) polymerase. Instead, crs1 transcripts are targeted for destruction by a factor previously implicated in turnover of meiotic RNAs in growing cells. Like exosome mutants, mmi1 mutants splice and polyadenylate vegetative crs1 transcripts. Two regulatory elements are located at the 3′ end of the crs1 gene, consistent with the increased accumulation of spliced RNA in polyadenylation factor mutants. This highly integrated regulatory strategy may ensure a rapid response to adverse conditions, thereby guaranteeing survival.
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Affiliation(s)
- David S McPheeters
- Center for RNA Molecular Biology and Department of Molecular Biology & Microbiology, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106-4960, USA
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62
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Lepère G, Nowacki M, Serrano V, Gout JF, Guglielmi G, Duharcourt S, Meyer E. Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia. Nucleic Acids Res 2008; 37:903-15. [PMID: 19103667 PMCID: PMC2647294 DOI: 10.1093/nar/gkn1018] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Distinct small RNA pathways are involved in the two types of homology-dependent effects described in Paramecium tetraurelia, as shown by a functional analysis of Dicer and Dicer-like genes and by the sequencing of small RNAs. The siRNAs that mediate post-transcriptional gene silencing when cells are fed with double-stranded RNA (dsRNA) were found to comprise two subclasses. DCR1-dependent cleavage of the inducing dsRNA generates approximately 23-nt primary siRNAs from both strands, while a different subclass of approximately 24-nt RNAs, characterized by a short untemplated poly-A tail, is strictly antisense to the targeted mRNA, suggestive of secondary siRNAs that depend on an RNA-dependent RNA polymerase. An entirely distinct pathway is responsible for homology-dependent regulation of developmental genome rearrangements after sexual reproduction. During early meiosis, the DCL2 and DCL3 genes are required for the production of a highly complex population of approximately 25-nt scnRNAs from all types of germline sequences, including both strands of exons, introns, intergenic regions, transposons and Internal Eliminated Sequences. A prominent 5'-UNG signature, and a minor fraction showing the complementary signature at positions 21-23, indicate that scnRNAs are cleaved from dsRNA precursors as duplexes with 2-nt 3' overhangs at both ends, followed by preferential stabilization of the 5'-UNG strand.
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Affiliation(s)
- Gersende Lepère
- Ecole Normale Supérieure, Laboratoire de Génétique Moléculaire, CNRS, UMR8541, 46 rue d'Ulm, 75005 Paris, France
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63
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Bühler M. RNA turnover and chromatin-dependent gene silencing. Chromosoma 2008; 118:141-51. [DOI: 10.1007/s00412-008-0195-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2008] [Revised: 10/31/2008] [Accepted: 11/03/2008] [Indexed: 12/31/2022]
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64
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Thon G. Competing to destroy: a fight between two RNA-degradation systems. Nat Struct Mol Biol 2008; 15:1001-2. [DOI: 10.1038/nsmb1008-1001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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65
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Schmid M, Jensen TH. The exosome: a multipurpose RNA-decay machine. Trends Biochem Sci 2008; 33:501-10. [PMID: 18786828 DOI: 10.1016/j.tibs.2008.07.003] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 07/03/2008] [Accepted: 07/07/2008] [Indexed: 10/21/2022]
Abstract
The diversity of RNAs in the cell continues to amaze. In addition to the 'classic' species of mRNA, tRNA, rRNA, snRNA and snoRNA, it is now clear that the majority of genomic information is transcribed into RNA molecules. The resulting complexity of the transcriptome poses a serious challenge to cells because they must manage numerous RNA-processing reactions, yet, at the same time, eradicate surplus and aberrant material without destroying functional RNA. The 3'-->5' exonucleolytic RNA exosome is emerging as a major facilitator of such events. Recent structural and functional data regarding this fascinating complex and its many co-factors illuminate its diverse biochemical properties and indicate mechanisms by which RNAs are targeted for either processing or degradation.
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Affiliation(s)
- Manfred Schmid
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology, University of Aarhus, C.F. Møllers Alle, Bldg. 130, 8000 Aarhus C., Denmark
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66
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Bühler M, Spies N, Bartel DP, Moazed D. TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway. Nat Struct Mol Biol 2008; 15:1015-23. [PMID: 18776903 PMCID: PMC3240669 DOI: 10.1038/nsmb.1481] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Accepted: 07/24/2008] [Indexed: 12/27/2022]
Abstract
In the fission yeast Schizosaccharomyces pombe, the RNA interference (RNAi) machinery is required to generate small interfering RNAs (siRNAs) that mediate heterochromatic gene silencing. Efficient silencing also requires the TRAMP complex, which contains the noncanonical Cid14 poly(A) polymerase and targets aberrant RNAs for degradation. Here we use high-throughput sequencing to analyze Argonaute-associated small RNAs (sRNAs) in both the presence and absence of Cid14. Most sRNAs in fission yeast start with a 5′ uracil, and we argue these are loaded most efficiently into Argonaute. In wild-type cells most sRNAs match to repeated regions of the genome, whereas in cid14Δ cells the sRNA profile changes to include major new classes of sRNAs originating from ribosomal RNAs and a tRNA. Thus, Cid14 prevents certain abundant RNAs from becoming substrates for the RNAi machinery, thereby freeing the RNAi machinery to act on its proper targets.
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Affiliation(s)
- Marc Bühler
- Department of Cell Biology, 240 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115 USA
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67
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Abstract
The Saccharomyces cerevisiae poly(A) polymerases Trf4 and Trf5 are involved in an RNA quality control mechanism, where polyadenylated RNAs are degraded by the nuclear exosome. Although Trf4/5 homologue genes are distributed throughout multicellular organisms, their biological roles remain to be elucidated. We isolated here the two homologues of Trf4/5 in Drosophila melanogaster, named DmTRF4-1 and DmTRF4-2, and investigated their biological function. DmTRF4-1 displayed poly(A) polymerase activity in vitro, whereas DmTRF4-2 did not. Gene knockdown of DmTRF4-1 by RNA interference is lethal in flies, as is the case for the trf4 trf5 double mutants. In contrast, disruption of DmTRF4-2 results in viable flies. Cellular localization analysis suggested that DmTRF4-1 localizes in the nucleolus. Abnormal polyadenylation of snRNAs was observed in transgenic flies overexpressing DmTRF4-1 and was slightly increased by the suppression of DmRrp6, the 3'-5' exonuclease of the nuclear exosome. These results suggest that DmTRF4-1 and DmRrp6 are involved in the polyadenylation-mediated degradation of snRNAs in vivo.
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68
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A yeast exosome cofactor, Mpp6, functions in RNA surveillance and in the degradation of noncoding RNA transcripts. Mol Cell Biol 2008; 28:5446-57. [PMID: 18591258 PMCID: PMC2519741 DOI: 10.1128/mcb.00463-08] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A genome-wide screen for synthetic lethal (SL) interactions with loss of the nuclear exosome cofactors Rrp47/Lrp1 or Air1 identified 3'-->5' exonucleases, the THO complex required for mRNP assembly, and Ynr024w (Mpp6). SL interactions with mpp6Delta were confirmed for rrp47Delta and nuclear exosome component Rrp6. The results of bioinformatic analyses revealed homology between Mpp6 and a human exosome cofactor, underlining the high conservation of the RNA surveillance system. Mpp6 is an RNA binding protein that physically associates with the exosome and was localized throughout the nucleus. The results of functional analyses demonstrated roles for Mpp6 in the surveillance of both pre-rRNA and pre-mRNAs and in the degradation of "cryptic" noncoding RNAs (ncRNAs) derived from intergenic regions and the ribosomal DNA spacer heterochromatin. Strikingly, these ncRNAs are also targeted by other exosome cofactors, including Rrp47, the TRAMP complex (which includes Air1), and the Nrd1/Nab3 complex, and are degraded by both Rrp6 and the core exosome. Heterochromatic transcripts and other ncRNAs are characterized by very rapid degradation, and we predict that functional redundancy is an important feature of ncRNA metabolism.
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69
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Vasiljeva L, Kim M, Terzi N, Soares LM, Buratowski S. Transcription termination and RNA degradation contribute to silencing of RNA polymerase II transcription within heterochromatin. Mol Cell 2008; 29:313-23. [PMID: 18280237 DOI: 10.1016/j.molcel.2008.01.011] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Revised: 12/12/2007] [Accepted: 01/30/2008] [Indexed: 01/19/2023]
Abstract
Within the heterochromatin of budding yeast, RNA polymerase II (RNAPII) transcription is repressed by the Sir2 deacetylase. Although heterochromatic silencing is generally thought to be due to limited accessibility of the underlying DNA, there are several reports of RNAPII and basal transcription factors within silenced regions. Analysis of the rDNA array revealed cryptic RNAPII transcription within the "nontranscribed" spacer region. These transcripts are terminated by the Nrd1/Sen1 complex and degraded by the exosome. Mutations in this pathway lead to decreased silencing and dramatic chromatin changes in the rDNA locus. Interestingly, Nrd1 mutants also show higher levels of rDNA recombination, suggesting that the cryptic RNAPII transcription might have a physiological role in regulating rDNA copy number. The Nrd1/Sen1/exosome pathway also contributes to silencing at telomeric loci. These results suggest that silencing of heterochromatic genes in Saccharomyces cerevisiae occurs at both transcriptional and posttranscriptional levels.
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Affiliation(s)
- Lidia Vasiljeva
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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70
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Houseley J, Tollervey D. The nuclear RNA surveillance machinery: The link between ncRNAs and genome structure in budding yeast? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1779:239-46. [DOI: 10.1016/j.bbagrm.2007.12.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Revised: 12/18/2007] [Accepted: 12/20/2007] [Indexed: 11/26/2022]
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