Non-coding RNA Prediction and Verification in Saccharomyces Cerevisiae

Overview

Journal PLoS Genet

Specialty Genetics

Date 2009 Jan 3

PMID 19119416

Citations 15

Authors

Laura A Kavanaugh

Fred S Dietrich

Affiliations

Soon will be listed here.

Abstract

Non-coding RNA (ncRNA) play an important and varied role in cellular function. A significant amount of research has been devoted to computational prediction of these genes from genomic sequence, but the ability to do so has remained elusive due to a lack of apparent genomic features. In this work, thermodynamic stability of ncRNA structural elements, as summarized in a Z-score, is used to predict ncRNA in the yeast Saccharomyces cerevisiae. This analysis was coupled with comparative genomics to search for ncRNA genes on chromosome six of S. cerevisiae and S. bayanus. Sets of positive and negative control genes were evaluated to determine the efficacy of thermodynamic stability for discriminating ncRNA from background sequence. The effect of window sizes and step sizes on the sensitivity of ncRNA identification was also explored. Non-coding RNA gene candidates, common to both S. cerevisiae and S. bayanus, were verified using northern blot analysis, rapid amplification of cDNA ends (RACE), and publicly available cDNA library data. Four ncRNA transcripts are well supported by experimental data (RUF10, RUF11, RUF12, RUF13), while one additional putative ncRNA transcript is well supported but the data are not entirely conclusive. Six candidates appear to be structural elements in 5' or 3' untranslated regions of annotated protein-coding genes. This work shows that thermodynamic stability, coupled with comparative genomics, can be used to predict ncRNA with significant structural elements.

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References

Costa F . Non-coding RNAs: lost in translation?. Gene. 2006; 386(1-2):1-10. DOI: 10.1016/j.gene.2006.09.028. View

Lim L, Lau N, Weinstein E, Abdelhakim A, Yekta S, Rhoades M . The microRNAs of Caenorhabditis elegans. Genes Dev. 2003; 17(8):991-1008. PMC: 196042. DOI: 10.1101/gad.1074403. View

Storz G . An expanding universe of noncoding RNAs. Science. 2002; 296(5571):1260-3. DOI: 10.1126/science.1072249. View

Kapranov P, Drenkow J, Cheng J, Long J, Helt G, Dike S . Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res. 2005; 15(7):987-97. PMC: 1172043. DOI: 10.1101/gr.3455305. View

Eddy S . Non-coding RNA genes and the modern RNA world. Nat Rev Genet. 2001; 2(12):919-29. DOI: 10.1038/35103511. View

Gasch A, Spellman P, Kao C, Eisen M, Storz G, Botstein D . Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 2000; 11(12):4241-57. PMC: 15070. DOI: 10.1091/mbc.11.12.4241. View

Rhoades M, Reinhart B, Lim L, Burge C, Bartel B, Bartel D . Prediction of plant microRNA targets. Cell. 2002; 110(4):513-20. DOI: 10.1016/s0092-8674(02)00863-2. View

Kapranov P, Cawley S, Drenkow J, Bekiranov S, Strausberg R, Fodor S . Large-scale transcriptional activity in chromosomes 21 and 22. Science. 2002; 296(5569):916-9. DOI: 10.1126/science.1068597. View

Le S, Chen J, Maizel J . Thermodynamic stability and statistical significance of potential stem-loop structures situated at the frameshift sites of retroviruses. Nucleic Acids Res. 1989; 17(15):6143-52. PMC: 318267. DOI: 10.1093/nar/17.15.6143. View

10.

Xie X, Lu J, Kulbokas E, Golub T, Mootha V, Lindblad-Toh K . Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature. 2005; 434(7031):338-45. PMC: 2923337. DOI: 10.1038/nature03441. View

11.

Accardo M, Giordano E, Riccardo S, Digilio F, Iazzetti G, Calogero R . A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome. Bioinformatics. 2004; 20(18):3293-301. DOI: 10.1093/bioinformatics/bth394. View

12.

Chen J, Le S, Shapiro B, Currey K, Maizel J . A computational procedure for assessing the significance of RNA secondary structure. Comput Appl Biosci. 1990; 6(1):7-18. DOI: 10.1093/bioinformatics/6.1.7. View

13.

Livny J, Waldor M . Identification of small RNAs in diverse bacterial species. Curr Opin Microbiol. 2007; 10(2):96-101. DOI: 10.1016/j.mib.2007.03.005. View

14.

Miura F, Kawaguchi N, Sese J, Toyoda A, Hattori M, Morishita S . A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A. 2006; 103(47):17846-51. PMC: 1693835. DOI: 10.1073/pnas.0605645103. View

15.

Samanta M, Tongprasit W, Sethi H, Chin C, Stolc V . Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway. Proc Natl Acad Sci U S A. 2006; 103(11):4192-7. PMC: 1389707. DOI: 10.1073/pnas.0507669103. View

16.

Laslett D, Canback B, Andersson S . BRUCE: a program for the detection of transfer-messenger RNA genes in nucleotide sequences. Nucleic Acids Res. 2002; 30(15):3449-53. PMC: 137083. DOI: 10.1093/nar/gkf459. View

17.

Zhang Z, Dietrich F . Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. Nucleic Acids Res. 2005; 33(9):2838-51. PMC: 1131933. DOI: 10.1093/nar/gki583. View

18.

Mendes Soares L, Valcarcel J . The expanding transcriptome: the genome as the 'Book of Sand'. EMBO J. 2006; 25(5):923-31. PMC: 1409726. DOI: 10.1038/sj.emboj.7601023. View

19.

Mignone F, Gissi C, Liuni S, Pesole G . Untranslated regions of mRNAs. Genome Biol. 2002; 3(3):REVIEWS0004. PMC: 139023. DOI: 10.1186/gb-2002-3-3-reviews0004. View

20.

Terai G, Komori T, Asai K, Kin T . miRRim: a novel system to find conserved miRNAs with high sensitivity and specificity. RNA. 2007; 13(12):2081-90. PMC: 2080609. DOI: 10.1261/rna.655107. View