Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data.
Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data.
复制标题
DOI：
10.1186/s12859-017-1897-0
复制
发表时间：
2017-12-28
影响因子：
3
通讯作者：
Bai Y
中科院分区：
文献类型：
--
作者：
Rath EC;Pitman S;Cho KH;Bai Y
小分子非编码调控RNAs(SRNAs)是转录后调节因子，调节细菌中的mRNAs、蛋白质和DNA。其中一类sRNAs，反式作用sRNAs，是从细菌基因组的基因间隔区转录而来的最丰富的sRNAs。化脓性链球菌是一种常见的、具有潜在致命性的病原菌，已鉴定出许多sRNA，但研究的很少。本研究的目的是确定可以作为RNaseIII底物的反式作用sRNAs。内切核糖核酸酶RNaseIII裂解双链RNAs，双链RNAs可以在sRNA与靶mRNAs相互作用过程中形成。在本研究中，我们创建了化脓性链球菌RNaseIII缺失突变体，并对其RNA测序(RNA-Seq)数据进行了分析，并与野生型进行了比较。首先，我们开发了一个定制的脚本，可以检测化脓性链球菌基因组的基因间隔区。然后用袖扣和Stringtie进行差异表达分析，以确定其表达受RNaseIII基因缺失影响的基因间隔区。这一分析得到了12个差异表达区域，其中>；|2|折叠变化，p-≤=0.05.使用Artemis和Bamview基因组观察器，对这些区域进行了视觉验证，留下了6个推测的sRNA。这项研究不仅扩大了我们对新的sRNA的认识，也将使我们对sRNA的降解有新的认识。
Small 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. For 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. This 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.
登录
查看更多内容
影响因子：
64.5
作者：
Gan, JH;Tropea, JE;Ji, XH
通讯作者：
Ji, XH
DOI：
10.1073/pnas.89.13.6172
发表时间：
1992-07-01
影响因子：
11.1
作者：
HANSKI, E;CAPARON, M
通讯作者：
CAPARON, M
影响因子：
3.6
作者：
Dasgupta, S;Fernandez, L;Court, DL
通讯作者：
Court, DL
影响因子：
5.8
作者：
Leng, Ning;Dawson, John A.;Kendziorski, Christina
通讯作者：
Kendziorski, Christina
影响因子：
14.9
作者：
Calin-Jageman, I;Nicholson, AW
通讯作者：
Nicholson, AW