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, 6 (4), R30

Genome-wide Prediction and Identification of Cis-Natural Antisense Transcripts in Arabidopsis Thaliana

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Genome-wide Prediction and Identification of Cis-Natural Antisense Transcripts in Arabidopsis Thaliana

Xiu-Jie Wang et al. Genome Biol.

Abstract

Background: Natural antisense transcripts (NAT) are a class of endogenous coding or non-protein-coding RNAs with sequence complementarity to other transcripts. Several lines of evidence have shown that cis- and trans-NATs may participate in a broad range of gene regulatory events. Genome-wide identification of cis-NATs in human, mouse and rice has revealed their widespread occurrence in eukaryotes. However, little is known about cis-NATs in the model plant Arabidopsis thaliana.

Results: We developed a new computational method to predict and identify cis-encoded NATs in Arabidopsis and found 1,340 potential NAT pairs. The expression of both sense and antisense transcripts of 957 NAT pairs was confirmed using Arabidopsis full-length cDNAs and public massively parallel signature sequencing (MPSS) data. Three known or putative Arabidopsis imprinted genes have cis-antisense transcripts. Sequences and the genomic arrangement of two Arabidopsis NAT pairs are conserved in rice.

Conclusion: We combined information from full-length cDNAs and Arabidopsis genome annotation in our NAT prediction work and reported cis-NAT pairs that could not otherwise be identified by using one of the two datasets only. Analysis of MPSS data suggested that for most Arabidopsis cis-NAT pairs, there is predominant expression of one of the two transcripts in a tissue-specific manner.

Figures

Figure 1
Figure 1
Relationships between NAT pairs from different datasets. (a) Overlap between cDNA-NAT pairs and genomic-NAT pairs. Among the 332 cDNA-NAT pairs, 145 pairs have corresponding annotated genes for both transcripts. For the other 187 cDNA-NAT pairs, at least one transcript has no counterpart in the current Arabidopsis genome annotation. (b) Overlap between cDNA-, genomic- and genomic-cDNA-NAT pairs. All cDNA-NAT pairs are included in genome-cDNA-NAT pairs. Blue circle, cDNA-NATs; red circle, genomic-NATs; green circle, genomic-cDNA-NATs.
Figure 2
Figure 2
Distribution of genomic overlap lengths of NATs. The overlap length of each NAT pair in exons was calculated. The number of NAT pairs (y-axis) is plotted against the overlap lengths (in nucleotides) of exons in each NAT pair (x-axis).
Figure 3
Figure 3
Distribution of coexpressed and dominantly expressed NAT pairs in different libraries. The number of coexpressed NAT pairs in each library was shown in blue bar and that of dominantly expressed NAT pairs in red bar. See legend of Table 5 for library information.

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