ArticleScientific reports2021
Clusters of hairpins induce intrinsic transcription termination in bacteria.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Canonical transcription termination mechanisms explain a minority of operons in cyanobacteria.mSystems · 2026Article
- AnMicrobiology spectrum · 2026Article
- Single-Molecule Methods to Investigate Mechanisms of Transcription by RNA Polymerase ofbioRxiv : the preprint server for biology · 2026Article
- Review
- Canonical transcription termination mechanisms explain a minority of operons in cyanobacteria.bioRxiv : the preprint server for biology · 2025Article
- BacTermFinder: a comprehensive and general bacterial terminator finder using a CNN ensemble.NAR genomics and bioinformatics · 2025Article
- Characterization of the dual regulation by a c-di-GMP riboswitch Bc1 with a long expression platform fromMicrobiology spectrum · 2024Article
- Utilizing RNA-seq Data to Infer Bacterial Transcription Termination Sites and Validate Predictions.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Review
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2 authors.
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Abstract
Intrinsic transcription termination (ITT) sites are currently identified by locating single and double-adjacent RNA hairpins downstream of the stop codon. ITTs for a limited number of genes/operons in only a few bacterial genomes are currently known. This lack of coverage is a lacuna in the existing ITT inference methods. We have studied the inter-operon regions of 13 genomes covering all major phyla in bacteria, for which good quality public RNA-seq data exist. We identify ITT sites in 87% of cases by predicting hairpin(s) and validate against 81% of cases for which the RNA-seq derived sites could be calculated. We identify 72% of these sites correctly, with 98% of them located ≤ 80 bases downstream of the stop codon. The predicted hairpins form a cluster (when present < 15 bases) in two-thirds of the cases, the remaining being single hairpins. The largest number of clusters is formed by two hairpins, and the occurrence decreases exponentially with an increasing number of hairpins in the cluster. Our study reveals that hairpins form an effective ITT unit when they act in concert in a cluster. Their pervasiveness along with single hairpin terminators corroborates a wider utilization of ITT mechanisms for transcription control across bacteria.
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