Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation - PubMed (original) (raw)

Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation

Chih-Hung Jen et al. Genome Biol. 2005.

Abstract

Background: Overlapping transcripts in antisense orientation have the potential to form double-stranded RNA (dsRNA), a substrate for a number of different RNA-modification pathways. One prominent route for dsRNA is its breakdown by Dicer enzyme complexes into small RNAs, a pathway that is widely exploited by RNA interference technology to inactivate defined genes in transgenic lines. The significance of this pathway for endogenous gene regulation remains unclear.

Results: We have examined transcription data for overlapping gene pairs in Arabidopsis thaliana. On the basis of an analysis of transcripts with coding regions, we find the majority of overlapping gene pairs to be convergently overlapping pairs (COPs), with the potential for dsRNA formation. In all tissues, COP transcripts are present at a higher frequency compared to the overall gene pool. The probability that both the sense and antisense copy of a COP are co-transcribed matches the theoretical value for coexpression under the assumption that the expression of one partner does not affect the expression of the other. Among COPs, we observe an over-representation of spliced (intron-containing) genes (90%) and of genes with alternatively spliced transcripts. For loci where antisense transcripts overlap with sense transcript introns, we also find a significant bias in favor of alternative splicing and variation of polyadenylation.

Conclusion: The results argue against a predominant RNA degradation effect induced by dsRNA formation. Instead, our data support alternative roles for dsRNAs. They suggest that at least for a subgroup of COPs, antisense expression may induce alternative splicing or polyadenylation.

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Figures

Figure 1

Figure 1

A comparison of the arrangements of overlapping gene pairs in Arabidopsis thaliana. A and A' label the start and end of the sense transcript, B' and B label the start and end of the antisense transcript. The total number of genes involved in group 1, 2 and 3 is 2,157, of which 2,147 are unique; the remaining 10 comprise four genes that are members of both group 1 and group 2 pairs, five genes that are members of both group 1 and group 3 pairs, and 1 gene that is a member of both a group 1 and group 3 pair.

Figure 2

Figure 2

The organization of convergent overlapping gene pairs with respect to the protein coding capacity of the sense and antisense transcripts.

Figure 3

Figure 3

Illustration of the distance between the end of the antisense transcript and the last intron-exon boundary of the sense transcript. Negative values refer to a termination of the antisense transcript 5' to the intron-exon boundary.

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