ArticleNucleic acids research2017
Computational prediction of regulatory, premature transcription termination in bacteria.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 45 citations in OpenAlex.
- Expression of conjugation genes is controlled by a novel zipper-type transcriptional attenuation mechanism.Nucleic acids research · 2026Article
- Systems-level analysis predicts no autotrophy-linked protein-RNA interactions in Clostridium autoethanogenum.Nature communications · 2026Article
- Canonical transcription termination mechanisms explain a minority of operons in cyanobacteria.mSystems · 2026Article
- TerminatorNet: comprehensive identification of intrinsic transcription terminators in bacteria.Bioinformatics (Oxford, England) · 2026Article
- Functional analysis of thiamine pyrophosphate-responsive riboswitches in human bacterial pathogens of the ESKAPE group using a dual-luciferase reporter gene assay.Journal of bacteriology · 2025Article
- Canonical transcription termination mechanisms explain a minority of operons in cyanobacteria.bioRxiv : the preprint server for biology · 2025Article
- Temperature-dependent regulation of bacterial cell division hydrolases by the coordinated action of a regulatory RNA and the ClpXP protease.Cell surface (Amsterdam, Netherlands) · 2025Article
- BacTermFinder: a comprehensive and general bacterial terminator finder using a CNN ensemble.NAR genomics and bioinformatics · 2025Article
- PIPETS: a statistically informed, gene-annotation agnostic analysis method to study bacterial termination using 3'-end sequencing.BMC bioinformatics · 2024Article
- The DeoR-like pleiotropic regulator SCO1897 controls specialised metabolism, sporulation, spore germination, and phosphorus accumulation in Streptomyces coelicolor.Communications biology · 2024Article
- PIPETS: A statistically informed, gene-annotation agnostic analysis method to study bacterial termination using 3'-end sequencing.bioRxiv : the preprint server for biology · 2024Article
- Rli51 Attenuates Transcription of theInternational journal of molecular sciences · 2024Article
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- Mapping the Complex Transcriptional Landscape of the Phytopathogenic Bacterium Dickeya dadantii.mBio · 2022Article
- The SCO2102 Protein Harbouring a DnaA II Protein-Interaction Domain Is Essential for the SCO2103 Methylenetetrahydrofolate Reductase Positioning atInternational journal of molecular sciences · 2022Article
- Prediction of bone metastasis in non-small cell lung cancer based on machine learning.Frontiers in oncology · 2022Article
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- Quantitative mapping of mRNA 3' ends in Pseudomonas aeruginosa reveals a pervasive role for premature 3' end formation in response to azithromycin.PLoS genetics · 2021Article
- Extensive Reannotation of the Genome of the Model StreptomyceteFrontiers in microbiology · 2021Article
- The iron-dependent repressor YtgR is a tryptophan-dependent attenuator of the trpRBA operon in Chlamydia trachomatis.Nature communications · 2020Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
A common strategy for regulation of gene expression in bacteria is conditional transcription termination. This strategy is frequently employed by 5'UTR cis-acting RNA elements (riboregulators), including riboswitches and attenuators. Such riboregulators can assume two mutually exclusive RNA structures, one of which forms a transcriptional terminator and results in premature termination, and the other forms an antiterminator that allows read-through into the coding sequence to produce a full-length mRNA. We developed a machine-learning based approach, which, given a 5'UTR of a gene, predicts whether it can form the two alternative structures typical to riboregulators employing conditional termination. Using a large positive training set of riboregulators derived from 89 human microbiome bacteria, we show high specificity and sensitivity for our classifier. We further show that our approach allows the discovery of previously unidentified riboregulators, as exemplified by the detection of new LeuA leaders and T-boxes in Streptococci Finally, we developed PASIFIC (www.weizmann.ac.il/molgen/Sorek/PASIFIC/), an online web-server that, given a user-provided 5'UTR sequence, predicts whether this sequence can adopt two alternative structures conforming with the conditional termination paradigm. This webserver is expected to assist in the identification of new riboswitches and attenuators in the bacterial pan-genome.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.