title: An automated approach for global identification of sRNA-encoding regions in RNA-Seq data from Mycobacterium tuberculosis.
abstract: Deep-sequencing of bacterial transcriptomes using RNA-Seq technology has made it possible to identify small non-coding RNAs, RNA molecules which regulate gene expression in response to changing environments, on a genome-wide scale in an ever-increasing range of prokaryotes. However, a simple and reliable automated method for identifying sRNA candidates in these large datasets is lacking. Here, after generating a transcriptome from an exponential phase culture of Mycobacterium tuberculosis H37Rv, we developed and validated an automated method for the genome-wide identification of sRNA candidate-containing regions within RNA-Seq datasets based on the analysis of the characteristics of reads coverage maps. We identified 192 novel candidate sRNA-encoding regions in intergenic regions and 664 RNA transcripts transcribed from regions antisense (as) to open reading frames (ORF), which bear the characteristics of asRNAs, and validated 28 of these novel sRNA-encoding regions by northern blotting. Our work has not only provided a simple automated method for genome-wide identification of candidate sRNA-encoding regions in RNA-Seq data, but has also uncovered many novel candidate sRNA-encoding regions in M. tuberculosis, reinforcing the view that the control of gene expression in bacteria is more complex than previously anticipated.
authors.affiliation: Key Laboratory of Non-Coding RNA & State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Wang
authors.affiliation: Key Laboratory of Non-Coding RNA & State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Joy
authors.initials: J
authors.lastname: Fleming
authors.affiliation: Beijing Chest Hospital, Capital Medical University, Beijing 101149, China.
authors.forename: Zihui
authors.initials: Z
authors.lastname: Li
authors.affiliation: Beijing Chest Hospital, Capital Medical University, Beijing 101149, China.
authors.forename: Chuanyou
authors.initials: C
authors.lastname: Li
authors.affiliation: Key Laboratory of Non-Coding RNA & State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Hongtai
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Non-Coding RNA & State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Yunxin
authors.initials: Y
authors.lastname: Xue
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Maoshan
authors.initials: M
authors.lastname: Chen
authors.affiliation: Beijing Chest Hospital, Capital Medical University, Beijing 101149, China.
authors.forename: Zongde
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Non-Coding RNA & State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China blj@sun5.ibp.ac.cn zhangxe@sun5.ibp.ac.cn.
authors.forename: Xian-En
authors.initials: XE
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Non-Coding RNA & State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China Guangdong Province Key Laboratory of TB Systems Biology and Translational Medicine, Foshan 528000, China blj@sun5.ibp.ac.cn zhangxe@sun5.ibp.ac.cn.
authors.forename: Lijun
authors.initials: L
authors.lastname: Bi
mesh_terms: D057205:Automation, Laboratory; D002874:Chromosome Mapping; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D009169:Mycobacterium tuberculosis / Q000235:genetics*; D012329:RNA, Bacterial / Q000235:genetics*; D058727:RNA, Small Untranslated / Q000235:genetics*; D012343:RNA, Transfer / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome
chemical_list: D012329:RNA, Bacterial; D058727:RNA, Small Untranslated; D012343:RNA, Transfer
keywords: Mycobacterium tuberculosis; RNA-Seq; non-coding RNA; transcriptome