Naturally occurring antisense: transcriptional leakage or real overlap?

Abstract

Naturally occurring antisense transcription is associated with the regulation of gene expression through a variety of biological mechanisms. Several recent genome-wide studies reported the identification of potential antisense transcripts for thousands of mammalian genes, many of them resulting from alternatively polyadenylated transcripts or heterogeneous transcription start sites. However, it is not clear whether this transcriptional plasticity is intentional, leading to regulated overlap between the transcripts, or, alternatively, represents a "leakage" of the RNA transcription machinery. To address this question through an evolutionary approach, we compared the genomic organization of genes, with or without antisense, between human, mouse, and the pufferfish Fugu rubripes. Our hypothesis was that if two neighboring genes overlap and have a sense-antisense relationship, we would expect negative selection acting on the evolutionary separation between them. We found that antisense gene pairs are twice as likely to preserve their genomic organization throughout vertebrates' evolution compared to nonantisense pairs, implying an overlap existence in the ancestral genome. In addition, we show that increasing the genomic distance between pairs of genes having a sense-antisense relationship is selected against. These findings indicate that, at least in part, the abundance of antisense transcripts observed in expressed data represents real overlap rather than transcriptional leakage. Moreover, our results imply that natural antisense transcription has considerably affected vertebrate genome evolution.

Figure 1.

The TP53BP1-76P sense-antisense locus (Yelin et al. 2003). Two alternatively polyadenylated transcripts of TP53BP1 (above DNA) and three alternatively polyadenylated transcripts of 76P (below DNA). The abundant transcripts of both genes are the short variants; overlap is only possible when the longer form of one of the genes is produced.

Figure 2.

Identification of conserved consecutive gene pairs between human and Fugu genomes. An orthology between human and Fugu proteins (light and dark boxes, respectively) was defined using BLASTP as described in Methods; mappings of proteins to the human and Fugu genomes (light and dark boxes, respectively) were used to define a consecutive pair and to calculate the distance between the coding sequence coordinates in each pair (d_H and d_F for human and Fugu, respectively).

Figure 3.

Antisense and gene distance expansion. (A) Average genomic distances (in kb) between pairs of genes in human and Fugu genomes. (B) Relationship between the human and Fugu genomic distances. For this analysis, only the 50 “antisense” and 120 “same-strand” pairs with distance on Fugu <5 kb were taken. While the “same-strand” group shows large distance expansion in human, the distance of pairs in the “antisense” group is almost unvaried between the two genomes. Distances appear in kb. Note the scale difference between the two axes.