Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E

• DOI: 10.15252/embj.201694639
• Publication Date: 2016-11-12T02:26:50Z
• Authors: Shafagh A Waters; Sean P McAteer; Grzegorz Kudla; Ignatius Pang; Nandan P Deshpande; Timothy G Amos; Kai Wen Leong; Marc R Wilkins; Richard Strugnell; David L Gally; David Tollervey; Jai J Tree
• Keywords: Interactome

Abstract RNA sequencing studies have identified hundreds of non‐coding s in bacteria, including regulatory small ( sRNA ). However, our understanding function has lagged behind their identification due to a lack tools for the high‐throughput analysis – interactions bacteria. Here we demonstrate that vivo mRNA duplexes can be recovered using UV ‐crosslinking, ligation and hybrids CLASH Many recruit endoribonuclease, RN ase E, facilitate processing s. We were able recover base‐paired association with allowing proximity‐dependent cognate pairs as chimeric reads. verified this approach captures bona fide interactions. Clustering analyses novel seed regions sets potentially co‐regulated target multiple targets pathotype‐specific Esr41, which was shown regulate colicin sensitivity iron transport E. coli . Numerous also s, tRNA demonstrating high complexity interactome.