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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.

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Cumulative frequency distribution of the expression intensities of 21,928 rice transcriptional units (black line) and 258 bidirectional transcript pairs on the microarray (gray line). Signal intensity (x-axis) is plotted against the number of mRNAs with that signal intensity (bars) and also against the normalized cumulative frequency (lines).
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Figure 4: Cumulative frequency distribution of the expression intensities of 21,928 rice transcriptional units (black line) and 258 bidirectional transcript pairs on the microarray (gray line). Signal intensity (x-axis) is plotted against the number of mRNAs with that signal intensity (bars) and also against the normalized cumulative frequency (lines).

Mentions: A single-strand oligo microarray has been designed on the basis of 21,938 rice full-length cDNA sequences, which were determined and selected as transcriptional units in RFLSP [24,29]. Oligo microarray measurements that were performed by Agilent Technologies were in good agreement with Q-PCR measurements [30]. We used the microarray to investigate the expression of the bidirectional transcripts. Among 687 nonredundant bidirectional transcript pairs, 258 pairs were aligned on the oligo microarray. We hybridized mRNAs derived from eight kinds of libraries - young leaf (YL), germinating seed (GS), mature leaf (ML), panicle (P), root (R), apical meristem (Ap), callus (Ca), and primary callus (Pc) - on the microarray. Figure 4 shows the distribution of the expression intensities of 21,938 mRNAs derived from YL and 956 mRNAs of the bidirectional transcripts derived from YL. The expression intensities of all mRNAs and of mRNAs of bidirectional transcripts were not clearly divided into low and high intensities, but were distributed broadly from low to high intensity and varied among libraries. We therefore normalized the expression intensities by subtracting the median expression intensity of 315 negative controls instead of the median of the 21,938 mRNAs from the intensities of the bidirectional transcripts. As a result, all bidirectional transcripts on the microarray were expressed with more than the median intensity of the negative controls. We divided the expression intensities into three categories: high (++), low (+) and not detected (-); we defined mRNAs that were expressed in greater amount than the median of the expression intensities of all 21,928 mRNAs on the microarray as having high expression, those lower than the median and higher than the median intensities of the negative controls as low, and those lower than the median as not detected. Among 258 nonredundant bidirectional transcript pairs on the microarray, in 82 (32%) both transcripts showed high expression intensity in at least one of the eight libraries, and in 176 (68%) at least one transcript showed low expression intensity in eight libraries. The numbers of bidirectional transcripts in each category showing each level of expression intensity are shown in Figure 1. The bidirectional transcripts in categories 1 and 3 included 122 and 23 intronless transcripts in each category; all intronless transcripts in nonredundant bidirectional transcript pairs were more highly expressed than the median of the negative controls; and 46 (38%) intronless transcripts in categories 1 and 16 (70%) in category 3 were expressed at high intensity. This shows that the intronless bidirectional transcripts are not the contamination of the genome sequences but mRNAs. The expression intensities of all bidirectional transcript pairs including redundant pairs on the microarray are available from our website [27].


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)

Cumulative frequency distribution of the expression intensities of 21,928 rice transcriptional units (black line) and 258 bidirectional transcript pairs on the microarray (gray line). Signal intensity (x-axis) is plotted against the number of mRNAs with that signal intensity (bars) and also against the normalized cumulative frequency (lines).
© Copyright Policy
Related In: Results  -  Collection

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

Figure 4: Cumulative frequency distribution of the expression intensities of 21,928 rice transcriptional units (black line) and 258 bidirectional transcript pairs on the microarray (gray line). Signal intensity (x-axis) is plotted against the number of mRNAs with that signal intensity (bars) and also against the normalized cumulative frequency (lines).
Mentions: A single-strand oligo microarray has been designed on the basis of 21,938 rice full-length cDNA sequences, which were determined and selected as transcriptional units in RFLSP [24,29]. Oligo microarray measurements that were performed by Agilent Technologies were in good agreement with Q-PCR measurements [30]. We used the microarray to investigate the expression of the bidirectional transcripts. Among 687 nonredundant bidirectional transcript pairs, 258 pairs were aligned on the oligo microarray. We hybridized mRNAs derived from eight kinds of libraries - young leaf (YL), germinating seed (GS), mature leaf (ML), panicle (P), root (R), apical meristem (Ap), callus (Ca), and primary callus (Pc) - on the microarray. Figure 4 shows the distribution of the expression intensities of 21,938 mRNAs derived from YL and 956 mRNAs of the bidirectional transcripts derived from YL. The expression intensities of all mRNAs and of mRNAs of bidirectional transcripts were not clearly divided into low and high intensities, but were distributed broadly from low to high intensity and varied among libraries. We therefore normalized the expression intensities by subtracting the median expression intensity of 315 negative controls instead of the median of the 21,938 mRNAs from the intensities of the bidirectional transcripts. As a result, all bidirectional transcripts on the microarray were expressed with more than the median intensity of the negative controls. We divided the expression intensities into three categories: high (++), low (+) and not detected (-); we defined mRNAs that were expressed in greater amount than the median of the expression intensities of all 21,928 mRNAs on the microarray as having high expression, those lower than the median and higher than the median intensities of the negative controls as low, and those lower than the median as not detected. Among 258 nonredundant bidirectional transcript pairs on the microarray, in 82 (32%) both transcripts showed high expression intensity in at least one of the eight libraries, and in 176 (68%) at least one transcript showed low expression intensity in eight libraries. The numbers of bidirectional transcripts in each category showing each level of expression intensity are shown in Figure 1. The bidirectional transcripts in categories 1 and 3 included 122 and 23 intronless transcripts in each category; all intronless transcripts in nonredundant bidirectional transcript pairs were more highly expressed than the median of the negative controls; and 46 (38%) intronless transcripts in categories 1 and 16 (70%) in category 3 were expressed at high intensity. This shows that the intronless bidirectional transcripts are not the contamination of the genome sequences but mRNAs. The expression intensities of all bidirectional transcript pairs including redundant pairs on the microarray are available from our website [27].

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