Abstract
STEREO is a novel algorithm that discovers cis-regulatory RNA interactions by assembling complete and potentially overlapping same-strand RNA transcripts from tiling expression data. STEREO first identifies coherent segments of transcription and then discovers individual transcripts that are consistent with the observed segments given intensity and shape constraints. We used STEREO to identify 1446 regions of overlapping transcription in two strains of yeast, including transcripts that comprise a new form of molecular toggle switch that controls gene variegation.
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References
Bolstad, B.: Probe Level Quantile Normalization of High Density Oligonucleotide Array Data. Technical report, Division of Biostatistics, University of California, Berkeley (2001)
Bumgarner, S.L., Dowell, R.D., Grisafi, P., Gifford, D.K., Fink, G.R.: Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast. Proceedings of the National Academy of Sciences 106(43), 18321–18326 (2009)
Camblong, J., Iglesias, N., Fickentscher, C., Dieppois, G., Stutz, F.: Antisense RNA Stabilization Induces Transcriptional Gene Silencing via Histone Deacetylation in S. cerevisiae. Cell 131, 706–717 (2007)
David, L., Huber, W., Granovskaia, M., Toedling, J., Palm, C.J., Bofkin, L., Jones, T., Davis, R.W., Steinmetz, L.M.: A high-resolution map of transcription in the yeast genome. PNAS 103(14), 5320–5325 (2006)
Dowell, R.D., Ryan, O., Jansen, A., Cheung, D., Agarwala, S., Danford, T.W., Bernstein, D., Rolfe, P.A., Fink, G.R., Gifford, D.K., Boone, C.: Genotype to Phenotype: A Comparison of Two Interbreeding Yeast Strains Reveals Complex Genetics of Conditional Essential Genes (in submission)
Hongay, C., Grisafi, P., Galitski, T., Fink, G.: Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell 127(4), 735–745 (2006)
Huber, W., Toedling, J., Steinmetz, L.: Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics 22(16), 1963–1970 (2006)
Hughes, T.A.: Regulation of gene expression by alternative untranslated regions. Trends in Genetics 22(3), 119–122 (2006)
Marioni, J., Mason, C., Mane, S., Stephens, M., Gilad, Y.: RNA-Seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Research 18, 1509–1517 (2008)
Martens, J.A., Laprade, L., Winston, F.: Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429, 571–574 (2004)
Martianov, I., Ramadass, A., Barros, A.S., Chow, N., Akoulitchev, A.: Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445, 666–670 (2007)
Miura, F., Kawaguchi, N., Sese, J., Toyoda, A., Hattori, M., Morishita, S., Ito, T.: A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. PNAS 103(47), 17486–17851 (2006)
Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., Snyder, M.: The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349 (2008) 1158441
Parkhomchuk, D., Borodina, T., Amstislavskiy, V., Banaru, M., Hallen, L., Krobitsch, S., Lehrach, H., Soldatov, A.: Transcriptome analysis by strand-specific sequencing of complementary dna. Nucleic Acids Research (July 2009)
Picard, F., Robin, S., Lavielle, M., Vaisse, C., Daudin, J.-J.: A Statistical Approach for Array CGH Data Analysis. BMC Bioinformatics 6(27) (February 2005)
Picard, F., Robin, S., Lebarbier, E., Daudin, J.-J.: A segmentation/clustering model for the analysis of array CGH data. Biometrics 63, 758–766 (2007)
Rochette, A., Raymond, F., Ubeda, J.M., Smith, M., Messier, N., Boisvert, S., Rigault, P., Corbeil, J., Ouellette, M., Papadopoulou, B.: Genome-wide gene expression profiling analysis of leishmania major and leishmania infantum developmental stages reveals substantial differences between the two species. BMC Genomics 9(255) (2008)
Royce, T., Rozowsky, J., Bertone, P., Samanta, M., Stolc, V., Weissman, S., Snyder, M., Gerstein, M.: Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends in Genetics 21(8), 466–475 (2005)
Urban, A.E., Korbel, J.O., Selzer, R., Richmond, T., Hacker, A., Popescu, G., Cubells, J.F., Green, R., Emanuel, B.S., Gerstein, M.B., Weissman, S.M., Snyder, M.: High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. PNAS 103(12), 4534–4539 (2006)
Wilhelm, B., Landry, J.R.: Rna-seq: quantitative measurement of expression through massively parallel rna-sequencing. Methods 48(3), 249–257 (2009)
Wilhelm, B., Marguerat, S., Watt, S., Schubert, F., Wood, V., Goodhead, I., Penkett, C., Rogers, J., Bahler, J.: Dynamic repertoire of a eukaryotic transcriptome surveyed at a single-nucleotide resolution. Nature 453, 1239–1243 (2008)
Zheng, S., Chen, L.: A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level. Nucleic Acids Research, 1–16 (2009)
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Danford, T., Dowell, R., Agarwala, S., Grisafi, P., Fink, G., Gifford, D. (2010). Discovering Regulatory Overlapping RNA Transcripts. In: Berger, B. (eds) Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science(), vol 6044. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-12683-3_8
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DOI: https://doi.org/10.1007/978-3-642-12683-3_8
Publisher Name: Springer, Berlin, Heidelberg
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