Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation.

Ira Alexandra Iosub,Sander Granneman,Stuart William Mckellar,Marta Marchioretto,Robert Willem Van Nues,Gabriella Viero,Karen Jule Nieken,Jai Justin Tree,Brandon Sy

doi:10.7554/elife.54655

Ira Alexandra Iosub, Sander Granneman + Show 7 more

Open Access

https://doi.org/10.7554/elife.54655

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Journal: eLife	Publication Date: May 1, 2020
Citations: 73	License type: CC BY 4.0

Affiliation: University of Edinburgh, UNSW Sydney

Abstract

By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt to changes in their environment. To better understand how Escherichia coli acclimatizes to nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) to uncover Hfq-associated RNA-RNA interactions at specific growth stages. We demonstrate that Hfq CLASH robustly captures bona fide RNA-RNA interactions. We identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA interactions and involving 3'UTR-derived sRNAs. We rediscovered known and identified novel sRNA seed sequences. The sRNA-mRNA interactions identified by CLASH have strong base-pairing potential and are highly enriched for complementary sequence motifs, even those supported by only a few reads. Yet, steady state levels of most mRNA targets were not significantly affected upon over-expression of the sRNA regulator. Our results reinforce the idea that the reproducibility of the interaction, not base-pairing potential, is a stronger predictor for a regulatory outcome.

Highlights

Microorganisms are renowned for their ability to adapt to environmental changes by rapidly rewiring their gene expression program
To generate high-quality Hfq CLASH data, we made a number of improvements to the original protocol used for RNase E CLASH (Waters et al, 2017)
Small RNAs and their associated RNA-binding proteins play a key role in this process

Summary

Introduction

Microorganisms are renowned for their ability to adapt to environmental changes by rapidly rewiring their gene expression program. These responses are mediated through integrated transcriptional and post-transcriptional networks. E. coli employs many post-transcriptional regulators, including small regulatory RNAs (sRNAs (Waters and Storz, 2009)), cis-acting RNAs (Kortmann and Narberhaus, 2012), and RNA binding proteins (RBPs) (Holmqvist and Vogel, 2018). By base-pairing with their targets, small RNAs can repress or stimulate translation and transcription elongation and control the stability of transcripts (Sedlyarova et al, 2016; Updegrove et al, 2016; Vogel and Luisi, 2011; Waters and Storz, 2009)

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