Antisense transcripts with rice full-length cDNAs. Export

@article{citeulike:889466, abstract = {BACKGROUND: Natural antisense transcripts control gene expression through post-transcriptional gene silencing by annealing to the complementary sequence of the sense transcript. Because many genome and mRNA sequences have become available recently, genome-wide searches for sense-antisense transcripts have been reported, but few plant sense-antisense transcript pairs have been studied. The Rice Full-Length cDNA Sequencing Project has enabled computational searching of a large number of plant sense-antisense transcript pairs. RESULTS: We identified sense-antisense transcript pairs from 32,127 full-length rice cDNA sequences produced by this project and public rice mRNA sequences by aligning the cDNA sequences with rice genome sequences. We discovered 687 bidirectional transcript pairs in rice, including sense-antisense transcript pairs. Both sense and antisense strands of 342 pairs (50\%) showed homology to at least one expressed sequence tag other than that of the pair. Microarray analysis showed 82 pairs (32\%) out of 258 pairs on the microarray were more highly expressed than the median expression intensity of 21,938 rice transcriptional units. Both sense and antisense strands of 594 pairs (86\%) had coding potential. CONCLUSIONS: The large number of plant sense-antisense transcript pairs suggests that gene regulation by antisense transcripts occurs in plants and not only in animals. On the basis of our results, experiments should be carried out to analyze the function of plant antisense transcripts.}, address = {Laboratory for Genome Exploration Research Group, RIKEN Genomic Science Center (GSC), RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan 230-0045.}, author = {Osato, N. and Yamada, H. and Satoh, K. and Ooka, H. and Yamamoto, M. and Suzuki, K. and Kawai, J. and Carninci, P. and Ohtomo, Y. and Murakami, K. and Matsubara, K. and Kikuchi, S. and Hayashizaki, Y.}, citeulike-article-id = {889466}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/gb-2003-5-1-r5}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/14709177}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=14709177}, doi = {10.1186/gb-2003-5-1-r5}, issn = {1465-6914}, journal = {Genome Biol}, keywords = {antisense, expression, genome, rice, sense}, number = {1}, posted-at = {2006-10-08 13:59:54}, priority = {5}, title = {Antisense transcripts with rice full-length cDNAs.}, url = {http://dx.doi.org/10.1186/gb-2003-5-1-r5}, volume = {5}, year = {2003} }

TY - JOUR ID - citeulike:889466 L3 - citeulike-article-id:889466 N2 - BACKGROUND: Natural antisense transcripts control gene expression through post-transcriptional gene silencing by annealing to the complementary sequence of the sense transcript. Because many genome and mRNA sequences have become available recently, genome-wide searches for sense-antisense transcripts have been reported, but few plant sense-antisense transcript pairs have been studied. The Rice Full-Length cDNA Sequencing Project has enabled computational searching of a large number of plant sense-antisense transcript pairs. RESULTS: We identified sense-antisense transcript pairs from 32,127 full-length rice cDNA sequences produced by this project and public rice mRNA sequences by aligning the cDNA sequences with rice genome sequences. We discovered 687 bidirectional transcript pairs in rice, including sense-antisense transcript pairs. Both sense and antisense strands of 342 pairs (50%) showed homology to at least one expressed sequence tag other than that of the pair. Microarray analysis showed 82 pairs (32%) out of 258 pairs on the microarray were more highly expressed than the median expression intensity of 21,938 rice transcriptional units. Both sense and antisense strands of 594 pairs (86%) had coding potential. CONCLUSIONS: The large number of plant sense-antisense transcript pairs suggests that gene regulation by antisense transcripts occurs in plants and not only in animals. On the basis of our results, experiments should be carried out to analyze the function of plant antisense transcripts. IS - 1 JF - Genome Biol SN - 1465-6914 AD - Laboratory for Genome Exploration Research Group, RIKEN Genomic Science Center (GSC), RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan 230-0045. TI - Antisense transcripts with rice full-length cDNAs. VL - 5 KW - antisense KW - expression KW - genome KW - rice KW - sense AU - Osato, N AU - Yamada, H AU - Satoh, K AU - Ooka, H AU - Yamamoto, M AU - Suzuki, K AU - Kawai, J AU - Carninci, P AU - Ohtomo, Y AU - Murakami, K AU - Matsubara, K AU - Kikuchi, S AU - Hayashizaki, Y PY - 2003/// UR - http://dx.doi.org/10.1186/gb-2003-5-1-r5 ER -