Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data

BMC Bioinformatics

Research

Ethan C. Rath¹  Stephanie Pitman¹  Kyu Hong Cho¹  Yongsheng Bai² 

[1] Department of Biology, Indiana State University, 47809, Terre Haute, IN, USA;Department of Biology, Indiana State University, 47809, Terre Haute, IN, USA;The Center for Genomic Advocacy, Indiana State University, 47809, Terre Haute, IN, USA;

关键词: Streptococcus pyogenes;    Small RNAs;    RNase III;    RNA sequencing;    Bioinformatics;   

DOI  :  10.1186/s12859-017-1897-0

来源: Springer

【 摘 要 】

BackgroundSmall noncoding regulatory RNAs (sRNAs) are post-transcriptional regulators, regulating mRNAs, proteins, and DNA in bacteria. One class of sRNAs, trans-acting sRNAs, are the most abundant sRNAs transcribed from the intergenic regions (IGRs) of the bacterial genome. In Streptococcus pyogenes, a common and potentially deadly pathogen, many sRNAs have been identified, but only a few have been studied. The goal of this study is to identify trans-acting sRNAs that can be substrates of RNase III. The endoribonuclease RNase III cleaves double stranded RNAs, which can be formed during the interaction between an sRNA and target mRNAs.ResultsFor this study, we created an RNase III null mutant of Streptococcus pyogenes and its RNA sequencing (RNA-Seq) data were analyzed and compared to that of the wild-type. First, we developed a custom script that can detect intergenic regions of the S. pyogenes genome. A differential expression analysis with Cufflinks and Stringtie was then performed to identify the intergenic regions whose expression was influenced by the RNase III gene deletion.ConclusionThis analysis yielded 12 differentially expressed regions with >|2| fold change and p ≤ 0.05. Using Artemis and Bamview genome viewers, these regions were visually verified leaving 6 putative sRNAs. This study not only expanded our knowledge on novel sRNAs but would also give us new insight into sRNA degradation.

【 授权许可】

CC BY   
© The Author(s). 2017