1,535
Views
68
CrossRef citations to date
0
Altmetric
Research Paper

Distinct RNA degradation pathways and 3' extensions of yeast non-coding RNA species

Pages 145-154 | Received 04 Apr 2011, Accepted 05 May 2011, Published online: 01 May 2011

References

  • Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell 2009; 136:629 - 641
  • Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007; 447:799 - 816
  • Liu F, Marquardt S, Lister C, Swiezewski S, Dean C. Targeted 3′ processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing. Science 2010; 327:94 - 97
  • Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009; 458:223 - 227
  • Grewal SI. RNAi-dependent formation of heterochromatin and its diverse functions. Curr Opin Genet Dev 2010; 20:134 - 141
  • Drinnenberg IA, Weinberg DE, Xie KT, Mower JP, Wolfe KH, Fink GR, et al. RNAi in budding yeast. Science 2009; 326:544 - 550
  • Camblong J, Iglesias N, Fickentscher C, Dieppois G, Stutz F. Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell 2007; 131:706 - 717
  • Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007; 129:1311 - 1323
  • Houseley J, Rubbi L, Grunstein M, Tollervey D, Vogelauer M. A ncRNA modulates histone modification and mRNA induction in the yeast GAL gene cluster. Mol Cell 2008; 32:685 - 695
  • Hongay CF, Grisafi PL, Galitski T, Fink GR. Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell 2006; 127:735 - 745
  • Martens JA, Laprade L, Winston F. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 2004; 429:571 - 574
  • Uhler JP, Hertel C, Svejstrup JQ. A role for noncoding transcription in activation of the yeast PHO5 gene. Proc Natl Acad Sci USA 2007; 104:8011 - 8016
  • Mattick JS. The genetic signatures of noncoding RNAs. PLoS Genet 2009; 5:1000459
  • Xu Z, Wei W, Gagneur J, Perocchi F, Clauder-Munster S, Camblong J, et al. Bidirectional promoters generate pervasive transcription in yeast. Nature 2009; 457:1033 - 1037
  • Vasiljeva L, Buratowski S. Nrd1 interacts with the nuclear exosome for 3′ processing of RNA polymerase II transcripts. Mol Cell 2006; 21:239 - 248
  • Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME, Boulay J, et al. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 2005; 121:725 - 737
  • 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 - 323
  • Arigo JT, Eyler DE, Carroll KL, Corden JL. Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3. Mol Cell 2006; 23:841 - 851
  • Thiebaut M, Kisseleva-Romanova E, Rougemaille M, Boulay J, Libri D. Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the nrd1-nab3 pathway in genome surveillance. Mol Cell 2006; 23:853 - 864
  • Preker P, Nielsen J, Kammler S, Lykke-Andersen S, Christensen MS, Mapendano CK, et al. RNA exosome depletion reveals transcription upstream of active human promoters. Science 2008; 322:1851 - 1854
  • Chekanova JA, Gregory BD, Reverdatto SV, Chen H, Kumar R, Hooker T, et al. Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell 2007; 131:1340 - 1353
  • Steinmetz EJ, Brow DA. Repression of gene expression by an exogenous sequence element acting in concert with a heterogeneous nuclear ribonucleoprotein-like protein, Nrd1, and the putative helicase Sen1. Mol Cell Biol 1996; 16:6993 - 7003
  • Thompson DM, Parker R. Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae. Mol Cell Biol 2007; 27:92 - 101
  • Berretta J, Pinskaya M, Morillon A. A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae. Genes Dev 2008; 22:615 - 626
  • Xu Z, Wei W, Gagneur J, Clauder-Munster S, Smolik M, Huber W, et al. Antisense expression increases gene expression variability and locus interdependency. Mol Syst Biol 2011; 7:468
  • Camblong J, Beyrouthy N, Guffanti E, Schlaepfer G, Steinmetz LM, Stutz F. Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae. Genes Dev 2009; 23:1534 - 1545
  • Whitehouse I, Rando OJ, Delrow J, Tsukiyama T. Chromatin remodelling at promoters suppresses antisense transcription. Nature 2007; 450:1031 - 1035
  • Zofall M, Fischer T, Zhang K, Zhou M, Cui B, Veenstra TD, et al. Histone H2A.Z cooperates with RNAi and heterochromatin factors to suppress antisense RNAs. Nature 2009; 461:419 - 422
  • Neil H, Malabat C, d'Aubenton-Carafa Y, Xu Z, Steinmetz LM, Jacquier A. Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 2009; 457:1038 - 1042
  • Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, et al. Divergent transcription from active promoters. Science 2008; 322:1849 - 1851
  • Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 2008; 322:1845 - 1848
  • Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007; 316:1484 - 1488
  • Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, et al. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 2005; 123:593 - 605
  • Keogh MC, Buratowski S. Using chromatin immunoprecipitation to map cotranscriptional mRNA processing in Saccharomyces cerevisiae. Methods Mol Biol 2004; 257:1 - 16
  • Geisberg JV, Struhl K. Analysis of protein co-occupancy by quantitative sequential chromatin immunoprecipitation. Curr Protoc Mol Biol 2005; 21:8
  • Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc 2008; 3:1101 - 1108
  • Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001; 25:402 - 408
  • Conrad NK, Wilson SM, Steinmetz EJ, Patturajan M, Brow DA, Swanson MS, et al. A yeast heterogeneous nuclear ribonucleoprotein complex associated with RNA polymerase II. Genetics 2000; 154:557 - 571
  • Houseley J, Tollervey D. The many pathways of RNA degradation. Cell 2009; 136:763 - 776
  • Vasiljeva L, Kim M, Mutschler H, Buratowski S, Meinhart A. The Nrd1-Nab3-Sen1 termination complex interacts with the Ser5-phosphorylated RNA polymerase II C-terminal domain. Nat Struct Mol Biol 2008; 15:795 - 804
  • Gudipati RK, Villa T, Boulay J, Libri D. Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice. Nat Struct Mol Biol 2008; 15:786 - 794
  • Carroll KL, Pradhan DA, Granek JA, Clarke ND, Corden JL. Identification of cis elements directing termination of yeast nonpolyadenylated snoRNA transcripts. Mol Cell Biol 2004; 24:6241 - 6252
  • Houseley J, Tollervey D. The nuclear RNA surveillance machinery: the link between ncRNAs and genome structure in budding yeast?. Biochim Biophys Acta 2008; 1779:239 - 246
  • Koziol MJ, Rinn JL. RNA traffic control of chromatin complexes. Curr Opin Genet Dev 2010; 20:142 - 148
  • Minvielle-Sebastia L, Preker PJ, Keller W. RNA14 and RNA15 proteins as components of a yeast pre-mRNA 3′-end processing factor. Science 1994; 266:1702 - 1705
  • Seila AC, Core LJ, Lis JT, Sharp PA. Divergent transcription: a new feature of active promoters. Cell Cycle 2009; 8:2557 - 2564
  • Steinmetz EJ, Warren CL, Kuehner JN, Panbehi B, Ansari AZ, Brow DA. Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase. Mol Cell 2006; 24:735 - 746
  • Rondon AG, Mischo HE, Kawauchi J, Proudfoot NJ. Fail-safe transcriptional termination for protein-coding genes in S. cerevisiae. Mol Cell 2009; 36:88 - 98
  • Kondo T, Plaza S, Zanet J, Benrabah E, Valenti P, Hashimoto Y, et al. Small peptides switch the transcriptional activity of Shavenbaby during Drosophila embryogenesis. Science 2010; 329:336 - 339
  • Twede VD, Miljanich G, Olivera BM, Bulaj G. Neuroprotective and cardioprotective conopeptides: an emerging class of drug leads. Curr Opin Drug Discov Devel 2009; 12:231 - 239
  • Hainer SJ, Pruneski JA, Mitchell RD, Monteverde RM, Martens JA. Intergenic transcription causes repression by directing nucleosome assembly. Genes Dev 2011; 25:29 - 40
  • Berretta J, Morillon A. Pervasive transcription constitutes a new level of eukaryotic genome regulation. EMBO Rep 2009; 10:973 - 982
  • Chow J, Heard E. X inactivation and the complexities of silencing a sex chromosome. Curr Opin Cell Biol 2009; 21:359 - 366
  • Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472:120 - 124
  • Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D, et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010; 142:409 - 419
  • Arigo JT, Carroll KL, Ames JM, Corden JL. Regulation of yeast NRD1 expression by premature transcription termination. Mol Cell 2006; 21:641 - 651