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Antisense transcripts with rice full-length cDNAs.

Osato N, Yamada H, Satoh K, Ooka H, Yamamoto M, Suzuki K, Kawai J, Carninci P, Ohtomo Y, Murakami K, Matsubara K, Kikuchi S, Hayashizaki Y - Genome Biol. (2003)

Bottom Line: Both sense and antisense strands of 594 pairs (86%) had coding potential.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory for Genome Exploration Research Group, RIKEN Genomic Science Center (GSC), RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan 230-0045.

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.

Show MeSH
Frequency distribution of ESTs having homology to the bidirectional transcript pairs. The number of cDNAs (y axis) is plotted against the number of ESTs showing homology to each bidirectional transcript pair cDNA (x axis).
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Figure 3: Frequency distribution of ESTs having homology to the bidirectional transcript pairs. The number of cDNAs (y axis) is plotted against the number of ESTs showing homology to each bidirectional transcript pair cDNA (x axis).

Mentions: To confirm the reproducibility of the bidirectional transcript pairs, we used FASTA [26] to search for them against 32,718 rice 5'-EST sequences in the GenBank database, 91,425 rice 5'- and 175,642 rice 3'-EST sequences sequenced by the RFLSP. Among the 687 bidirectional transcript pairs identified, 642 showed homology to at least one EST sequence, not including the 5'- and 3'-EST sequences of the bidirectional transcript pairs themselves. Among these 642 pairs, 342 contained sequences homologous to at least one EST sequence on both strands of the pair; 300 contained such sequences on just one strand. The number of bidirectional transcript pairs in each category with EST support is shown in Figure 1 (the complete EST support dataset is available on our website [27]). The frequency distribution of EST matches on bidirectional transcript pair cDNA sequences is presented in Figure 3. Among 1,374 sequences of bidirectional transcript pairs, 931 sequences contain contiguous exons that are separated by a putative intron in the genomic sequence, and thus underwent splicing; therefore these pairs could not have been derived from contamination of the genome sequences.


Antisense transcripts with rice full-length cDNAs.

Osato N, Yamada H, Satoh K, Ooka H, Yamamoto M, Suzuki K, Kawai J, Carninci P, Ohtomo Y, Murakami K, Matsubara K, Kikuchi S, Hayashizaki Y - Genome Biol. (2003)

Frequency distribution of ESTs having homology to the bidirectional transcript pairs. The number of cDNAs (y axis) is plotted against the number of ESTs showing homology to each bidirectional transcript pair cDNA (x axis).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC395737&req=5

Figure 3: Frequency distribution of ESTs having homology to the bidirectional transcript pairs. The number of cDNAs (y axis) is plotted against the number of ESTs showing homology to each bidirectional transcript pair cDNA (x axis).
Mentions: To confirm the reproducibility of the bidirectional transcript pairs, we used FASTA [26] to search for them against 32,718 rice 5'-EST sequences in the GenBank database, 91,425 rice 5'- and 175,642 rice 3'-EST sequences sequenced by the RFLSP. Among the 687 bidirectional transcript pairs identified, 642 showed homology to at least one EST sequence, not including the 5'- and 3'-EST sequences of the bidirectional transcript pairs themselves. Among these 642 pairs, 342 contained sequences homologous to at least one EST sequence on both strands of the pair; 300 contained such sequences on just one strand. The number of bidirectional transcript pairs in each category with EST support is shown in Figure 1 (the complete EST support dataset is available on our website [27]). The frequency distribution of EST matches on bidirectional transcript pair cDNA sequences is presented in Figure 3. Among 1,374 sequences of bidirectional transcript pairs, 931 sequences contain contiguous exons that are separated by a putative intron in the genomic sequence, and thus underwent splicing; therefore these pairs could not have been derived from contamination of the genome sequences.

Bottom Line: Both sense and antisense strands of 594 pairs (86%) had coding potential.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory for Genome Exploration Research Group, RIKEN Genomic Science Center (GSC), RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan 230-0045.

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.

Show MeSH