Abstract
BackgroundBacterial small regulatory RNAs (sRNAs) play important roles in sensing environment changes through sRNA-target mRNA interactions. However, the current strategy for detecting sRNA-mRNA interactions usually combines bioinformatics prediction and experimental verification, which is hampered by low prediction accuracy and low-throughput. Additionally, among the 4736 sequenced bacterial genomes, only about 2164 sRNAs from 319 strains have been described. Furthermore, target mRNAs of only 157 sRNAs have been uncovered. Obviously, highly efficient methods were required to detect sRNA-mRNA interactions in the sequenced genomes. This study aimed to apply a modified CLASH (cross-linking, ligation and sequencing hybrids) method to detect RNA-RNA interactions in E. coli, a model bacterial organism.ResultsStatistically significant interactions were detected in 29 transcript pairs. To the best of our knowledge, 24 pairs were reported for the first time and were novel RNA interactions, including tRNA-tRNA, tRNA-ncRNA (non-coding RNA), tRNA-rRNA, rRNA-mRNA, rRNA-ncRNA, rRNA-rRNA, rRNA-IGT (intergenic transcript), and tRNA-IGT interactions.ConclusionsDiscovery of novel RNA-RNA interactions in the present study demonstrates that RNA-RNA interactions might be far more complicated than ever expected. New methods may be required to help discover more novel RNA-RNA interactions. The present work describes a high-throughput protocol not only for discovering new RNA interactions, but also directly obtaining base-pairing sequences, which should be useful in assessing RNA structure and interactions.
Highlights
Bacterial small regulatory RNAs play important roles in sensing environment changes through Small regulatory RNA (sRNA)-target mRNA interactions
Following cell lysis and RNA extraction, DNA residues were digested by DNase I, and single strand RNAs and free RNA overhangs adjacent to duplexes were digested by RNase T1
No sRNA-mRNA interaction was found with statistically significance in this study, almost all functional classes of RNAs were detected to be involved in various inter-molecular RNA-RNA interactions, among which tRNA-tRNA, tRNA-Non-coding RNA (ncRNA), tRNArRNA, rRNA-mRNA, rRNA-ncRNA, rRNA-rRNA, rRNA-Intergenic transcript (IGT) and tRNA-IGT interactions were detected in a RNase E-CLASH study by Waters et al [24]. 5 interacting gene pairs discovered in Waters’s study were detected with statistical significance in this study, of which 1 is tRNA-transfer-messenger RNA (tmRNA) and 4 is tRNA-tRNA
Summary
Bacterial small regulatory RNAs (sRNAs) play important roles in sensing environment changes through sRNA-target mRNA interactions. Highly efficient methods were required to detect sRNA-mRNA interactions in the sequenced genomes. This study aimed to apply a modified CLASH (cross-linking, ligation and sequencing hybrids) method to detect RNA-RNA interactions in E. coli, a model bacterial organism. Detecting RRIs, The current bioinformatics methods for predicting RRIs take RNA sequences as input, and can be divided into two classes [8]. The first class comprises general models for the prediction of RRIs. For example, the earliest methods, e.g. RNAfold [4] or Mfold [5], detect RRIs by predicting the secondary structure of a combined RNA sequence, which is composed of two RNAs to be studied. Base-pairing regions between the two RNAs can demonstrate their interaction Complex models such as RNAcofold [4] and RNAplex [6] have been developed.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
