Prevalence of small base-pairing RNAs derived from diverse genomic loci

Abstract

Small RNAs (sRNAs) that act by base-pairing have been shown to play important roles in fine-tuning the levels and translation of their target transcripts across a variety of model and pathogenic organisms. Work from many different groups in a wide range of bacterial species has provided evidence for the importance and complexity of sRNA regulatory networks, which allow bacteria to quickly respond to changes in their environment. However, despite the expansive literature, much remains to be learned about all aspects of sRNA-mediated regulation, particularly in bacteria beyond the well-characterized Escherichia coli and Salmonella enterica species. Here we discuss what is known, and what remains to be learned, about the identification of regulatory base-pairing RNAs produced from diverse genomic loci including how their expression is regulated. This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F. Repoila.

Keywords: RNA-seq; UTR; sRNA biogenesis; small RNAs.

Figure 1.

Origin of sRNAs from diverse genomic loci. (A) antisense (B) intergenic (C) operon- derived (D) 5′ derived (E) intragenic (F) 3′ derived (G) tRNA-derived. Coding sequences are denoted in gray, sRNA sequences in red, tRNA sequences in green, and regulatory tRNA sequences in purple. Processing cleavage sites are indicated with an “x”. Instances of known transcription termination are indicated by a hairpin. 3′ ends corresponding to known processed RNAs are blunt. An arrow is used if the mechanism of 3′ end generation is unknown.