ArticleNucleic acids research2018
A multivariate prediction model for Rho-dependent termination of transcription.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 52 citations in OpenAlex.
- An intrinsically disordered domain of transcription terminator Rho governs genome-wide Rho utilization (Rut) site selection in Mycobacterium tuberculosis.Nucleic acids research · 2026Article
- Spiky Magnetic Titania Particles for Integrated Exosome Capture and Metabolic Profiling Toward Cancer Diagnosis.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- Conserved 3' stem-loop structures enable comprehensive analysis of bacterial transcription termination in metagenomes.Microbiome · 2026Article
- Purine bias in bacterial genes is driven by runaway transcription.Nature microbiology · 2026Article
- Rho-dependent transcription termination: mechanisms and roles in bacterial fitness and adaptation to environmental changes.RNA (New York, N.Y.) · 2025Review
- Comprehensive mapping of transcription terminator Rho utilization (Rut) sites across the Bacillus subtilis genome.Nucleic acids research · 2025Article
- Article
- BacTermFinder: a comprehensive and general bacterial terminator finder using a CNN ensemble.NAR genomics and bioinformatics · 2025Article
- Evolution of pH-sensitive transcription termination inProceedings of the National Academy of Sciences of the United States of America · 2024Article
- CryptKeeper: a negative design tool for reducing unintentional gene expression in bacteria.bioRxiv : the preprint server for biology · 2024Article
- Diversification of the Rho transcription termination factor in bacteria.Nucleic acids research · 2024Article
- Riboswitch and small RNAs modulate btuB translation initiation in Escherichia coli and trigger distinct mRNA regulatory mechanisms.Nucleic acids research · 2024Article
- Phase Variation of Flagella and Toxins in Clostridioides difficile is Mediated by Selective Rho-dependent Termination.Journal of molecular biology · 2024Article
- Evolution of pH-sensitive transcription termination during adaptation to repeated long-term starvation.bioRxiv : the preprint server for biology · 2024Article
- CryptKeeper: a negative design tool for reducing unintentional gene expression in bacteria.Synthetic biology (Oxford, England) · 2024Article
- Identification of a Rho-Dependent Termination SiteMicrobiology spectrum · 2023Article
- Comprehensive transcription terminator atlas for Bacillus subtilis.Nature microbiology · 2022Article
- A scalable framework for the discovery of functional helicase substrates and helicase-driven regulatory switches.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Article
- In vivo regulation of bacterial Rho-dependent transcription termination by the nascent RNA.The Journal of biological chemistry · 2022Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial transcription termination proceeds via two main mechanisms triggered either by simple, well-conserved (intrinsic) nucleic acid motifs or by the motor protein Rho. Although bacterial genomes can harbor hundreds of termination signals of either type, only intrinsic terminators are reliably predicted. Computational tools to detect the more complex and diversiform Rho-dependent terminators are lacking. To tackle this issue, we devised a prediction method based on Orthogonal Projections to Latent Structures Discriminant Analysis [OPLS-DA] of a large set of in vitro termination data. Using previously uncharacterized genomic sequences for biochemical evaluation and OPLS-DA, we identified new Rho-dependent signals and quantitative sequence descriptors with significant predictive value. Most relevant descriptors specify features of transcript C>G skewness, secondary structure, and richness in regularly-spaced 5'CC/UC dinucleotides that are consistent with known principles for Rho-RNA interaction. Descriptors collectively warrant OPLS-DA predictions of Rho-dependent termination with a ∼85% success rate. Scanning of the Escherichia coli genome with the OPLS-DA model identifies significantly more termination-competent regions than anticipated from transcriptomics and predicts that regions intrinsically refractory to Rho are primarily located in open reading frames. Altogether, this work delineates features important for Rho activity and describes the first method able to predict Rho-dependent terminators in bacterial genomes.
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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.