ArticleActa biochimica et biophysica Sinica2016
An automated approach for global identification of sRNA-encoding regions in RNA-Seq data from Mycobacterium tuberculosis.
Article in Acta biochimica et biophysica Sinica, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Small RNA ASpks2 promotes Mycobacterium tuberculosis survival in macrophages via targeting polyketide synthase 2.The Journal of biological chemistry · 2026Article
- Identification of Small RNAs inInternational journal of molecular sciences · 2024Article
- Exploring the transcription start sites and other genomic features facilitates the accurate identification and annotation of small RNAs across multiple stress conditions in Mycobacterium tuberculosis.Functional & integrative genomics · 2024Article
- Transcriptome analysis and molecular characterization of novel small RNAs in Mycobacterium tuberculosis Lineage 1.World journal of microbiology & biotechnology · 2024Article
- Devising Isolation Forest-Based Method to Investigate the sRNAome ofBioinformatics and biology insights · 2024Article
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- Whole-genome sequencing and transcriptome-characterizedMicrobial genomics · 2023Article
- Omics analysis of Mycobacterium tuberculosis isolates uncovers Rv3094c, an ethionamide metabolism-associated gene.Communications biology · 2023Article
- Article
- Small Noncoding RNAs and Their Role in the Pathogenesis of Mycobacterium tuberculosis Infection.Biochemistry. Biokhimiia · 2021Review
- Genome-wide identification of the context-dependent sRNA expression in Mycobacterium tuberculosis.BMC genomics · 2020Article
- APERO: a genome-wide approach for identifying bacterial small RNAs from RNA-Seq data.Nucleic acids research · 2019Article
- On a stake-out:Non-coding RNA research · 2019Review
- Application of Transcriptomics to Enhance Early Diagnostics of Mycobacterial Infections, with an Emphasis onVeterinary sciences · 2019Review
- Small RNA profiling inProceedings of the National Academy of Sciences of the United States of America · 2018Article
- Article
- Expression, maturation and turnover of DrrS, an unusually stable, DosR regulated small RNA in Mycobacterium tuberculosis.PloS one · 2017Article
- Article
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Authors and funding
10 authors.
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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.
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