Sex matters in the birth of genes

Recent progress in technology has allowed an extraordinary refinement of our knowledge of transcriptomes, revealing their unexpected complexity. In addition to the large number of siRNAs and miRNAs, many noncoding RNA species are now known to be transcribed by RNA polymerase II (RNAPII), in proximity or overlapping to known transcription units in both sense and antisense orientations, as well as from DNA regions previously thought to be transcriptionally inert or silent. This phenomenon, dubbed 'pervasive' transcription, appears to be evolutionary conserved in all eukaryotes from yeast to human 1. These noncoding RNAs had previously escaped identification because of their very low abundance in cells grown under standard physiological conditions where they are eliminated by degradative machineries shortly after their transcription by RNAPII. Why cells even produce RNAs destined to degradation is an open question. However, it appears logic that cells use quality control mechanisms to rapidly target potentially hazardous transcripts to degradation while preserving proper expression of coding RNAs. Nevertheless, this is not the whole story, as in budding yeast several examples are beginning to emerge of noncoding RNAs that are involved in gene expression regulation, particularly those arising antisense to ORFs. So far, regulation by noncoding RNAs in S. cerevisiae relies on the RNA itself or the very act of its transcription generally leading to inhibition of the target gene through cis-acting transcriptional interference mechanisms, or by inducing repressive changes in chromatin structure in interesting analogy to RNAi mechanisms of higher eukaryotes. What these instances of noncoding RNA-mediated regulation tell us is that pervasive transcripts are not just noise but genetic material that can be tested by natural selection and eventually evolve specific functions and be exploited for regulatory purposes.