Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions

BMC Biology

Volumn 5, Issue , 2007, Pages

  Steigele, Stephan ^a,b   Huber, Wolfgang ^c   Stocsits, Claudia ^b   Stadler, Peter F ^b,d,e   Nieselt, Kay ^a  

^a UNIVERSITY OF TÜBINGEN   (Germany)

^b UNIVERSITY OF LEIPZIG   (Germany)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^d UNIVERSITY OF VIENNA   (Austria)

^e SANTA FE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL RNA; UNTRANSLATED RNA;

ARTICLE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENE FUNCTION; GENE LOCUS; GENETIC CODE; GENETIC CONSERVATION; GENOME; NUCLEOTIDE SEQUENCE; POSTTRANSCRIPTIONAL GENE SILENCING; PREDICTION; PROMOTER REGION; RNA SEQUENCE; RNA STRUCTURE; SACCHAROMYCES; SACCHAROMYCES BAYANUS; SACCHAROMYCES CASTELLI; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES KLUYVERI; SACCHAROMYCES KUDRIAVZEII; SACCHAROMYCES MIKATAE; SACCHAROMYCES PARADOXUS; UNTRANSLATED REGION; BIOLOGY; COMPARATIVE STUDY; CONFORMATION; GENETICS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SPECIES DIFFERENCE;

EUKARYOTA;

BASE SEQUENCE; COMPUTATIONAL BIOLOGY; GENOME, FUNGAL; NUCLEIC ACID CONFORMATION; RNA, FUNGAL; RNA, UNTRANSLATED; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; SPECIES SPECIFICITY;

EID: 34547135988     PISSN: None     EISSN: 17417007     Source Type: Journal    
DOI: 10.1186/1741-7007-5-25     Document Type: Article

References (66)

1. Galagan JE Calvo SE Borkovich KA Selker EU Read ND Jaffe D FitzHugh W Ma LJ Smirnov S Purcell S The genome sequence of the filamentous fungus Neurospora crassa Nature 2003 422 859-868 10.1038/nature01554 12712197
2. Goffeau A Barrell BG Bussey H Davis RW Dujon B Feldmann H Galibert F Hoheisel JD Jacq C Johnston M Life with 6000 genes Science 1996 274 563-567 10.1126/science.274.5287.546
3. Steigele S Nieselt K Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes Nucleic Acids Res 2005 33 5034-5044 1201330 16147987 10.1093/nar/gki804
4. Havilio M Levanon EY Lerman G Kupiec M Eisenberg E Evidence for abundant transcription of non-coding regions in the Saccharomyces cerevisiae genome BMC Genomics 2005 6 93 1181813 15960846 10.1186/1471-2164-6-93
5. Inagaki S Numata K Kondo T Tomita M Yasuda K Kanai A Kageyama Y Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila Genes Cells 2005 10 1163-1173 10.1111/ j.1365-2443.2005.00910.x 16324153
6. Berteaux N Lottin S Monté D Pinte S Quatannens B Coll J Hondermarck H Curgy JJ Dugimont T Adriaenssens E H19 mRNA-like noncoding RNA promotes breast cancer cell proliferation through positive control by E2F1 J Biol Chem 2005 280 29625-29636 10.1074/jbc.M504033200 15985428
7. Samanta MP Tongprasit W Sethi H Chin CS Stolc V Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway Proc Natl Acad Sci USA 2006 103 4192-4197 1389707 16537507 10.1073/pnas.0507669103
8. Davis CA Ares M Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae Proc Natl Acad Sci USA 2006 103 3262-3267 1413877 16484372 10.1073/pnas.0507783103
9. David L Huber W Granovskaia M Toedling J Palm CJ Bofkin L Jones T Davis RW Steinmetz LM A high-resolution map of transcription in the yeast genome Proc Natl Acad Sci USA 2006 103 5320-5325 1414796 16569694 10.1073/pnas.0601091103
10. McCutcheon JP Eddy SR Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics Nucleic Acids Res 2003 31 4119-4128 165953 12853629 10.1093/nar/gkg438
11. Pesole G Mignone F Gissi C Grillo G Licciulli F Liuni S Structural and functional features of eukaryotic mRNA untranslated regions Gene 2001 276 73-81 10.1016/S0378-1119(01)00674-6 11591473
12. Washietl S Hofacker IL Stadler PF Fast and reliable prediction of noncoding RNAs Proc Natl Acad Sci USA 2005 102 2454-2459 548974 15665081 10.1073/pnas.0409169102
13. Katz L Burge CB Widespread selection for local RNA secondary structure in coding regions of bacterial genes Genome Res 2003 13 2042-2051 403678 12952875 10.1101/gr.1257503
14. Meyer IM Miklós I Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs Nucleic Acids Res 2005 33 6338-6348 1278941 16275783 10.1093/ nar/gki923
15. Pedersen JS Bejerano G Siepel A Rosenbloom K Lindblad-Toh K Lander ES Kent J Miller W Haussler D Identification and classification of conserved RNA secondary structures in the human genome PLoS Comput Biol 2006 2 e33 1440920 16628248 10.1371/journal.pcbi.0020033
16. Harris MA Clark J Ireland A Lomax J Ashburner M Foulger R Eilbeck K Lewis S Marshall B Mungall C The Gene Ontology (GO) database and informatics resource Nucleic Acids Res 2004 32 D258-D261 308770 14681407 10.1093/nar/gkh066
17. Hurowitz EH Brown PO Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae Genome Biol 2003 5 R2 395734 14709174 10.1186/ gb-2003-5-1-r2
18. Harbison CT Gordon DB Lee TI Rinaldi NJ Macisaac KD Danford TW Hannett NM Tagne JB Reynolds DB Yoo J Transcriptional regulatory code of a eukaryotic genome Nature 2004 431 99-104 10.1038/nature02800 15343339
19. Altschul S Gish W Miller W Myers E Lipman D Basic local alignment search tool J Mol Biol 1990 215 403-10 2231712
20. Liu C Bai B Skogerbaz G Cai L Deng W Zhang Y Bu D Zhao Y Chen R NONCODE: an integrated knowledge database of non-coding RNAs Nucleic Acids Res 2005 33 D112-D115 539995 15608158 10.1093/nar/gki041
21. Schattner P Decatur WA Davis CA Ares M Fournier MJ Lowe TM Genome-wide searching for pseudouridylation guide snoRNAs: Analysis of the Saccharomyces cerevisiae genome Nucleic Acids Res 2004 32 4281-4296 514388 15306656 10.1093/nar/gkh768
22. Griffiths-Jones S Bateman A Marshall M Khanna A Eddy SR Rfam: An RNA family database Nucleic Acids Res 2003 31 439-441 165453 12520045 10.1093/nar/gkg006
23. Infernal: Inference of RNA alignments http://infernal.janelia.org/
24. Lowe TM Eddy SR A computational screen for methylation guide snoRNAs in yeast Science 1999 283 1168-1171 10.1126/science.283.5405.1168 10024243
25. Qu LH Henras A Lu YJ Zhou H Zhou WX Zhu YQ Zhao J Henry Y Caizergues-Ferrer M Bachellerie JP Seven novel methylation guide small nucleolar RNAs are processed from a common polycistronic transcript by Rat1p and RNase III in yeast Mol Cell Biol 1999 19 1144-1158 116044 9891049
26. Samarsky DA Balakin AG Fournier MJ Characterization of three new snRNAs from Saccharomyces cerevisiae: SnR34, snR35 and snR36 Nucleic Acids Res 1995 23 2548-2554 307065 7630735 10.1093/nar/23.13.2548
27. Rice P Longden I Bleasby A EMBOSS: The European Molecular Biology Open Software Suite Trends Genet 2000 16 276-7 10.1016/S0168-9525(00)02024-2 10827456
28. Velculescu VE Zhang L Vogelstein B Kinzler KW Serial analysis of gene expression Science 1995 270 484-487 10.1126/science.270.5235.484 7570003
29. Rivas E Klein RJ Jones TA Eddy SR Computational identification of noncoding RNAs in E. coli by comparative genomics Curr Biol 2001 11 1369-1373 10.1016/S0960-9822(01)00401-8 11553332
30. Rivas E Eddy SR Noncoding RNA gene detection using comparative sequence analysis BMC Bioinformatics 2001 2 8 64605 11801179 10.1186/1471-2105-2-8
31. Dayton ET Konings DA Powell DM Shapiro BA Butini L Maizel JV Dayton AI Extensive sequence-specific information throughout the CAR/RRE, the target sequence of the human immunodeficiency virus type 1 Rev protein J Virol 1992 66 1139-1151 240818 1731093
32. Goodfellow IG Kerrigan D Evans DJ Structure and function analysis of the poliovirus cis-acting replication element (CRE) RNA 2003 9 124-137 1370376 12554882 10.1261/rna.2950603
33. Lanz RB Razani B Goldberg AD O'Malley BW Distinct RNA motifs are important for coactivation of steroid hormone receptors by steroid receptor RNA activator (SRA) Proc Natl Acad Sci USA 2002 99 16081-16086 138568 12444263 10.1073/pnas.192571399
34. Girard G Roussis A Gultyaev AP Pleij CWA Spaink HP Structural motifs in the RNA encoded by the early nodulation gene enod40 of soybean Nucleic Acids Res 2003 31 5003-5015 212817 12930950 10.1093/nar/gkg721
35. Takizawa PA Sil A Swedlow JR Herskowitz I Vale RD Actin-dependent localization of an RNA encoding a cell-fate determinant in yeast Nature 1997 389 90-93 10.1038/38015 9288973
36. Long RM Singer RH Meng X Gonzalez I Nasmyth K Jansen RP Mating type switching in yeast controlled by asymmetric localization of ASH1 mRNA Science 1997 277 383-387 10.1126/science.277.5324.383 9219698
37. Gonsalvez GB Urbinati CR Long RM RNA localization in yeast: Moving towards a mechanism Biol Cell 2005 97 75-86 10.1042/BC20040066 15601259
38. Corral-Debrinski M Blugeon C Jacq C In yeast, the 3′ untranslated region or the presequence of ATM1 is required for the exclusive localization of its mRNA to the vicinity of mitochondria Mol Cell Biol 2000 20 7881-7892 86399 11027259 10.1128/MCB.20.21.7881-7892.2000
39. Margeot A Blugeon C Sylvestre J Vialette S Jacq C Corral-Debrinski M In Saccharomyces cerevisiae, ATP2 mRNA sorting to the vicinity of mitochondria is essential for respiratory function EMBO J 2002 21 6893-6904 139110 12486010 10.1093/emboj/cdf690
40. Jang SK Kräusslich HG Nicklin MJ Duke GM Palmenberg AC Wimmer E A segment of the 5′ nontranslated region of encephalomyocarditis virus RNA directs internal entry of ribosomes during in vitro translation J Virol 1988 62 2636-2643 253694 2839690
41. Crucs S Chatterjee S Gavis ER Overlapping but distinct RNA elements control repression and activation of nanos translation Mol Cell 2000 5 457-467 10.1016/S1097-2765(00)80440-2 10882131
42. Hentze MW Kühn LC Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress Proc Natl Acad Sci USA 1996 93 8175-8182 38642 8710843 10.1073/pnas.93.16.8175
43. Mignone F Gissi C Liuni S Pesole G Untranslated regions of mRNAs Genome Biol 2002 3 0004 10.1186/gb-2002-3-3-reviews0004
44. Shalgi R Lapidot M Shamir R Pilpel Y A catalog of stability-associated sequence elements in 3′ UTRs of yeast mRNAs Genome Biol 2005 6 R86 1257469 16207357 10.1186/gb-2005-6-10-r86
45. Sylvestre J Margeot A Jacq C Dujardin G Corral-Debrins M The role of the 3′ untranslated region in mRNA sorting to the vicinity of mitochondria is conserved from yeast to human cells Mol Biol Cell 2003 14 3848-3856 196577 12972568 10.1091/mbc.E03-02-0074
46. Sylvestre J Vialette S Debrinski MC Jacq C Long mRNAs coding for yeast mitochondrial proteins of prokaryotic origin preferentially localize to the vicinity of mitochondria Genome Biol 2003 4 R44 193631 12844360 10.1186/gb-2003-4-7-r44
47. Martens JA Laprade L Winston F Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene Nature 2004 429 571-574 10.1038/nature02538 15175754
48. Martens JA Wu PY Winston F Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae Genes Dev 2005 19 2695-2704 1283962 16291644 10.1101/gad.1367605
49. Thomas M Chédin S Carles C Riva M Famulok M Sentenac A Selective targeting and inhibition of yeast RNA polymerase II by RNA aptamers J Biol Chem 1997 272 27980-27986 10.1074/jbc.272.44.27980 9346949
50. Allen TA VonKaenel S Goodrich JA Kugel J The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock Nat Struct Mol Biol 2004 11 816-821 10.1038/nsmb813 15300240
51. Espinoza CA Allen TA Hieb AR Kugel JF Goodrich JA B2 RNA binds directly to RNA polymerase II to repress transcript synthesis Nat Struct Mol Biol 2004 11 822-829 10.1038/nsmb812 15300239
52. Barrick JE Sudarsan N Weinberg Z Ruzzo WL Breaker RR 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter RNA 2005 11 774-784 1370762 15811922 10.1261/rna.7286705
53. Trotochaud AE Wassarman KM A highly conserved 6S RNA structure is required for regulation of transcription Nat Struct Mol Biol 2005 12 313-319 10.1038/nsmb917 15793584
54. Feng J Bi C Clark BS Mady R Shah P Kohtz JD The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator Genes Dev 2006 20 1470-1484 1475760 16705037 10.1101/gad.1416106
55. Kiyosawa H Yamanaka I Osato N Kondo S Hayashizaki Y RIKEN GER Group GSL Members Antisense transcripts with FANTOM2 clone set and their implications for gene regulation Genome Res 2003 13 1324-1234 403655 12819130 10.1101/gr.982903
56. Chen J Sun M Kent WJ Huang X Xie H Wang W Zhou G Shi RZ Rowley JD Over 20% of human transcripts might form sense-antisense pairs Nucleic Acids Res 2004 32 4812-4820 519112 15356298 10.1093/nar/gkh818
57. Blanchette M Kent WJ Riemer C Elnitski L Smit AFA Roskin KM Baertsch R Rosenbloom K Clawson H Green ED Haussler D Miller W Aligning multiple genomic sequences with the threaded blockset aligner Genome Res 2004 14 708-715 383317 15060014 10.1101/gr.1933104
58. UCSC Genome Browser http://genome.ucsc.edu/
59. Washietl S Hofacker IL Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics J Mol Biol 2004 342 19-30 10.1016/j.jmb.2004.07.018 15313604
60. Kent WJ BLAT - the BLAST-like alignment tool Genome Res 2002 12 656-664 187518 11932250 10.1101/gr.229202. Article published online before March 2002
61. Saccharomyces Genome Database http://www.yeastgenome.org/
62. Stein LD Mungall C Shu S Caudy M Mangone M Day A Nickerson E Stajich JE Harris TW Arva A Lewis S The generic genome browser: A building block for a model organism system database Genome Res 2002 12 1599-1610 187535 12368253 10.1101/gr.403602
63. Pearson WR Lipman DJ Improved tools for biological sequence comparison Proc Natl Acad Sci USA 1988 85 2444-2448 280013 3162770 10.1073/ pnas.85.8.2444
64. GO-TermFinder http://search.cpan.org/dist/GO-TermFinder/
65. Predicted RNA Yeast Genome Browser http://www-ps.informatik.uni-tuebingen.de/cgi-bin/ncrna/index.pl
66. Hinrichs AS Karolchik D Baertsch R Barber GP Bejerano G Clawson H Diekhans M Furey TS Harte RA Hsu F The UCSC Genome Browser Database: update 2006 Nucleic Acids Res 2006 34 D590-D598 1347506 16381938 10.1093/ nar/gkj144