Pervasive transcription: detecting functional RNAs in bacteria

Abstract

Pervasive, or genome-wide, transcription has been reported in all domains of life. In bacteria, most pervasive transcription occurs antisense to protein-coding transcripts, although recently a new class of pervasive RNAs was identified that originates from within annotated genes. Initially considered to be non-functional transcriptional noise, pervasive transcription is increasingly being recognized as important in regulating gene expression. The function of pervasive transcription is an extensively debated question in the field of transcriptomics and regulatory RNA biology. Here, we highlight the most recent contributions addressing the purpose of pervasive transcription in bacteria and discuss their implications.

Keywords: Hfq; RNA; RNase III; antisense transcription; asRNA; asRNA, antisense RNA; double-stranded RNA; dsRNA, double-stranded RNA; intraRNA, intragenic RNA; ncRNA, non-coding RNA; pervasive transcription; promoter; sigma factor; spurious transcription; transcriptome.

Figure 1.

Mechanisms of dsRNA-mediated gene regulation. (A) dsRNA-mediated translation inhibition. An asRNA that overlaps the RBS of its cognate mRNA could prevent the ribosome from binding the RBS and inhibit translation; the dsRNA would then be degraded by RNase III, but the translational regulation would not be dependent on RNase III. (B) dsRNA-mediated translation stimulation. Translation could also be stimulated by dsRNA formation by releasing the RBS for ribosome binding. (C) dsRNA-mediated transcription attenuation. dsRNA formation could cause transcriptional attenuation and termination, also resulting in a dsRNA byproduct, which would be degraded by RNase III.