High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites

Mia K. Mihailovic, Jorge Vazquez-Anderson, Yan Li, Victoria Fry, Praveen Vimalathas, Daniel Herrera, Richard A. Lease, Warren B. Powell and Lydia M. Contreras ()
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Mia K. Mihailovic: University of Texas at Austin
Jorge Vazquez-Anderson: University of Texas at Austin
Yan Li: Princeton University
Victoria Fry: University of Texas at Austin
Praveen Vimalathas: University of Texas at Austin
Daniel Herrera: University of Texas at Austin
Richard A. Lease: The Ohio State University
Warren B. Powell: Princeton University
Lydia M. Contreras: University of Texas at Austin

Nature Communications, 2018, vol. 9, issue 1, 1-16

Abstract: Abstract Herein we introduce a high-throughput method, INTERFACE, to reveal the capacity of contiguous RNA nucleotides to establish in vivo intermolecular RNA interactions for the purpose of functional characterization of intracellular RNA. INTERFACE enables simultaneous accessibility interrogation of an unlimited number of regions by coupling regional hybridization detection to transcription elongation outputs measurable by RNA-seq. We profile over 900 RNA interfaces in 71 validated, but largely mechanistically under-characterized, Escherichia coli sRNAs in the presence and absence of a global regulator, Hfq, and find that two-thirds of tested sRNAs feature Hfq-dependent regions. Further, we identify in vivo hybridization patterns that hallmark functional regions to uncover mRNA targets. In this way, we biochemically validate 25 mRNA targets, many of which are not captured by typically tested, top-ranked computational predictions. We additionally discover direct mRNA binding activity within the GlmY terminator, highlighting the information value of high-throughput RNA accessibility data.

Date: 2018
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DOI: 10.1038/s41467-018-06207-z

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