ArticleNucleic acids research2019
APERO: a genome-wide approach for identifying bacterial small RNAs from RNA-Seq data.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 47 citations in OpenAlex.
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- Bacterial small RNAs and extracellular vesicles in inflammatory and osteoimmune diseases: regulatory mechanisms and host-microbe communication.Archives of microbiology · 2026Review
- Small regulatory RNAs modulate lactococcal susceptibility to cell wall-targeting antimicrobials.Nucleic acids research · 2026Article
- Hfq modulates system-wide regulatory networks controlling biocontrol property inSynthetic and systems biotechnology · 2026Article
- Symbionts with eroded genomes adjust gene expression according to host life-stage and environment.EMBO reports · 2025Article
- Harnessing Small RNAs as Synthetic Post-transcriptional Regulators in Bacteria.ACS synthetic biology · 2025Review
- Identification of Small RNAs inInternational journal of molecular sciences · 2024Article
- TSS-Captur: a user-friendly pipeline for characterizing unclassified RNA transcripts.NAR genomics and bioinformatics · 2024Article
- Coordinated adaptation ofmBio · 2024Article
- Characterisation of sRNAs enriched in outer membrane vesicles of pathogenicJournal of extracellular biology · 2024Article
- Devising Isolation Forest-Based Method to Investigate the sRNAome ofBioinformatics and biology insights · 2024Article
- Simultaneous carbon catabolite repression governs sugar and aromatic co-utilization inApplied and environmental microbiology · 2023Article
- CRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis.Journal of industrial microbiology & biotechnology · 2023Article
- Mapping the Complex Transcriptional Landscape of the Phytopathogenic Bacterium Dickeya dadantii.mBio · 2022Article
- Small regulatory RNAs of oral streptococci and periodontal bacteria.The Japanese dental science review · 2021Review
- Identification of BvgA-Dependent and BvgA-Independent Small RNAs (sRNAs) in Bordetella pertussis Using the Prokaryotic sRNA Prediction Toolkit ANNOgesic.Microbiology spectrum · 2021Article
- Methyltransferase-directed orthogonal tagging and sequencing of miRNAs and bacterial small RNAs.BMC biology · 2021Article
- Review
- RNA Chaperones Hfq and ProQ Play a Key Role in the Virulence of the Plant Pathogenic BacteriumFrontiers in microbiology · 2021Article
- Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study.Frontiers in cellular and infection microbiology · 2021Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small non-coding RNAs (sRNAs) regulate numerous cellular processes in all domains of life. Several approaches have been developed to identify them from RNA-seq data, which are efficient for eukaryotic sRNAs but remain inaccurate for the longer and highly structured bacterial sRNAs. We present APERO, a new algorithm to detect small transcripts from paired-end bacterial RNA-seq data. In contrast to previous approaches that start from the read coverage distribution, APERO analyzes boundaries of individual sequenced fragments to infer the 5' and 3' ends of all transcripts. Since sRNAs are about the same size as individual fragments (50-350 nucleotides), this algorithm provides a significantly higher accuracy and robustness, e.g., with respect to spontaneous internal breaking sites. To demonstrate this improvement, we develop a comparative assessment on datasets from Escherichia coli and Salmonella enterica, based on experimentally validated sRNAs. We also identify the small transcript repertoire of Dickeya dadantii including putative intergenic RNAs, 5' UTR or 3' UTR-derived RNA products and antisense RNAs. Comparisons to annotations as well as RACE-PCR experimental data confirm the precision of the detected transcripts. Altogether, APERO outperforms all existing methods in terms of sRNA detection and boundary precision, which is crucial for comprehensive genome annotations. It is freely available as an open source R package on https://github.com/Simon-Leonard/APERO.
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