Detecting RNA-RNA interactions in E. coli using a modified CLASH method

BMC Genomics

Research Article

Tao Liu¹  Song Xu¹  Wuju Li¹  Kaiyu Zhang¹  Zheng Wang¹  Hanjiang Fu²  Baolei Tian²  Xiaofei Zheng² 

[1] Beijing Institute of Basic Medical Sciences, Taiping Road 27, 100850, Beijing, Haidian district, China;Beijing Institute of Radiation Medicine, Taiping Road 27, 100850, Beijing, Haidian district, China;

关键词: RNA-RNA interaction;    High-throughput sequencing;    Bacteria;   

DOI  :  10.1186/s12864-017-3725-3

 received in 2017-01-19, accepted in 2017-04-25,  发布年份 2017

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© The Author(s). 2017