While bacteria were long thought to rely primarily on transcriptional control, it is now well established that they also use numerous small RNAs to regulate mRNA translation and stability. There has recently been a surge in studies, including one by Waters et al (2017) in this issue of The EMBO Journal, that have used clever variations of the RNA‐seq technique to comprehensively map small RNA–target networks.
See also: SA Waters et al
A major recent shift in our view of gene expression is that even the simplest organisms—bacteria—extensively control their genes post‐transcriptionally using small noncoding RNAs (sRNAs). Of the >200 sRNAs expressed in Escherichia coli or Salmonella, many regulate target mRNAs via base pairing to alter translation or transcript stability; and those that act via the global RNA‐binding protein Hfq typically target multiple mRNAs. Understanding the components of such RNA regulons is not only important to dissect the regulatory circuits underlying bacterial physiology and virulence, but also to fathom where and why organisms favor regulatory RNA over proteins.
Global transcript profiling by RNA‐seq has been amply used to map bacterial regulons, but sRNA‐mediated control seldom causes strong alterations in transcript abundance and observed changes may not always be a direct consequence of sRNA activity. As a result, there has recently been a surge in variations of the RNA‐seq technique to map bacterial RNA regulons more directly.
Co‐immunoprecipitation of cellular RNA followed by deep sequencing (RIP‐seq) has yielded semi‐quantitative snapshots of sRNA and mRNA association patterns with Hfq in different growth phases of Salmonella (Chao et al, 2012). These patterns were refined by the inclusion of UV cross‐linking in vivo (Tree et al, 2014; Holmqvist et al, 2016), showing more precisely where Hfq recognizes its …
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