Novel small RNA (sRNA) landscape of the starvation-stress response transcriptome of Salmonella enterica serovar typhimurium.

Small RNAs (sRNAs) are short (∼50-200 nucleotides) noncoding RNAs that regulate cellular activities across bacteria. Salmonella enterica starved of a carbon-energy (C) source experience a host of genetic and physiological changes broadly referred to as the starvation-stress response (SSR). In an attempt to identify novel sRNAs contributing to SSR control, we grew log-phase, 5-h C-starved and 24-h C-starved cultures of the virulent Salmonella enterica subspecies enterica serovar Typhimurium strain SL1344 and comprehensively sequenced their small RNA transcriptomes. Strikingly, after employing a novel strategy for sRNA discovery based on identifying dynamic transcripts arising from "gene-empty" regions, we identify 58 wholly undescribed Salmonella sRNA genes potentially regulating SSR averaging an ∼1,000-fold change in expression between log-phase and C-starved cells. Importantly, the expressions of individual sRNA loci were confirmed by both comprehensive transcriptome analyses and northern blotting of select candidates. Of note, we find 43 candidate sRNAs share significant sequence identity to characterized sRNAs in other bacteria, and ∼70% of our sRNAs likely assume characteristic sRNA structural conformations. In addition, we find 53 of our 58 candidate sRNAs either overlap neighboring mRNA loci or share significant sequence complementarity to mRNAs transcribed elsewhere in the SL1344 genome strongly suggesting they regulate the expression of transcripts via antisense base-pairing. Finally, in addition to this work resulting in the identification of 58 entirely novel Salmonella enterica genes likely participating in the SSR, we also find evidence suggesting that sRNAs are significantly more prevalent than currently appreciated and that Salmonella sRNAs may actually number in the thousands.

Burgeoning evidence indicates that microRNAs were initially formed from transposable element sequences.

MicroRNAs (miRNAs) constitute a recently discovered class of noncoding RNAs that play key roles in the regulation of gene expression. Despite being only ~20 nucleotides in length, these highly versatile molecules have been shown to play pivotal roles in development, basic cellular metabolism, apoptosis, and disease. While over 24,000 miRNAs have been characterized since they were first isolated in mammals in 2001, the functions of the majority of these miRNAs remain largely undescribed. That said, many now suggest that characterization of the relationships between miRNAs and transposable elements (TEs) can help elucidate miRNA functionality. Strikingly, over 20 publications have now reported the initial formation of thousands of miRNA loci from TE sequences. In this review we chronicle the findings of these reports, discuss the evolution of the field along with future directions, and examine how this information can be used to ascertain insights into miRNA transcriptional regulation and how it can be exploited to facilitate miRNA target prediction.