ArticleNature communications2016
Global repositioning of transcription start sites in a plant-fermenting bacterium.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 30 citations in OpenAlex.
- Systems-level analysis predicts no autotrophy-linked protein-RNA interactions in Clostridium autoethanogenum.Nature communications · 2026Article
- TSSpredator-Web: A web-application for transcription start site prediction and exploration.PloS one · 2026Article
- Refining the transcriptional landscapes for distinct clades of virulent phages infectingmicroLife · 2024Article
- Bradyrhizobium ottawaense efficiently reduces nitrous oxide through high nosZ gene expression.Scientific reports · 2023Article
- Review
- Tuning of Gene Expression inACS synthetic biology · 2022Article
- Genome-Wide TSS Distribution in Three Related Clostridia with Normalized Capp-Switch Sequencing.Microbiology spectrum · 2022Article
- Promotech: a general tool for bacterial promoter recognition.Genome biology · 2021Article
- Cappable-Seq Reveals Specific Patterns of Metabolism and Virulence forInternational journal of molecular sciences · 2021Article
- Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria.The ISME journal · 2020Article
- Article
- ABC Transporters Required for Hexose Uptake by Clostridium phytofermentans.Journal of bacteriology · 2019Article
- Capping-RACE: a simple, accurate, and sensitive 5' RACE method for use in prokaryotes.Nucleic acids research · 2018Article
- Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes.BMC genomics · 2018Article
- Metagenomic mining of regulatory elements enables programmable species-selective gene expression.Nature methods · 2018Article
- BAC-BROWSER: The Tool for Visualization and Analysis of Prokaryotic Genomes.Frontiers in microbiology · 2018Article
- Evolution of a Biomass-Fermenting Bacterium To Resist Lignin Phenolics.Applied and environmental microbiology · 2017Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacteria respond to their environment by regulating mRNA synthesis, often by altering the genomic sites at which RNA polymerase initiates transcription. Here, we investigate genome-wide changes in transcription start site (TSS) usage by Clostridium phytofermentans, a model bacterium for fermentation of lignocellulosic biomass. We quantify expression of nearly 10,000 TSS at single base resolution by Capp-Switch sequencing, which combines capture of synthetically capped 5' mRNA fragments with template-switching reverse transcription. We find the locations and expression levels of TSS for hundreds of genes change during metabolism of different plant substrates. We show that TSS reveals riboswitches, non-coding RNA and novel transcription units. We identify sequence motifs associated with carbon source-specific TSS and use them for regulon discovery, implicating a LacI/GalR protein in control of pectin metabolism. We discuss how the high resolution and specificity of Capp-Switch enables study of condition-specific changes in transcription initiation in bacteria.
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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.