Evidence for a preferential targeting of 3′-UTRs by cis-encoded natural antisense transcripts

Although both the 5′- and 3′-untranslated regions (5′- and 3′-UTRs) of eukaryotic mRNAs may play a crucial role in posttranscriptional gene regulation, we observe that cis-encoded natural antisense RNAs have a striking preferential complementarity to the 3′-UTRs of their target genes in mammalian (human and mouse) genomes. A null neutral model, evoking differences in the rate of 3′-UTR and 5′-UTR extension, could potentially explain high rates of 3′-to-3′ overlap compared with 5′-to-5′ overlap. However, employing a simulation model we show that this null model probably cannot explain the finding that 3′-to-3′ overlapping pairs have a much higher probability (>5 times) of conservation in both mouse and human genomes with the same overlapping pattern than do 5′-to-5′ overlaps. Furthermore, it certainly cannot explain the finding that overlapping pairs seen in both genomes have a significantly higher probability of having co-expression and inverse expression (i.e. characteristic of sense–antisense regulation) than do overlapping pairs seen in only one of the two species. We infer that the function of many 3′-to-3′ overlaps is indeed antisense regulation. These findings underscore the preference for, and conservation of, 3′-UTR-targeted antisense regulation, and the importance of 3′-UTRs in gene regulation.