GSE117939
High throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites
These data were obtained using a recently-developed high throughput method to probe regional RNA accessibility by mimicking in vivo antisense hybridization.  The method (INTERFACE) is an engineered RNA system (for use in E. coli) that exploits conserved bacterial mechanisms of translational stalling and Rho-dependent transcription termination mechanisms to quantify RNA hybridization (via an asRNA targeting an RNA region of interest) via a transcriptional elongation response. We first establish the high throughput system by evaluating the accessibility profile of a well-characterized gI intron (overexpressed).  We then apply this method with bioinformatics and machine learning approaches to profile over 900 RNA-interaction interfaces in 71 validated, but largely mechanistically under-characterized, sRNAs of Escherichia coli, in the presence and absence of a global regulator, Hfq. Importantly, we showcase the utility of INTERFACE in detecting RNA regions whose hybridization is Hfq-sensitive, finding two thirds of tested sRNAs with Hfq dependency. Further, we identify in vivo hybridization patterns that hallmark functional regions in 16 well-characterized sRNAs and couple these insights to a computational target prediction algorithm to identify novel mRNA targets for six under-characterized and two well-characterized sRNAs. Overall design: Evaluation of regional accessibility profiles of a library of sRNAs in E. coli