Global repositioning of transcription start sites in a plant-fermenting bacterium

Magali Boutard, Laurence Ettwiller, Tristan Cerisy, Adriana Alberti, Karine Labadie, Marcel Salanoubat, Ira Schildkraut and Andrew C. Tolonen ()
Additional contact information
Magali Boutard: 1CEA, DRF, IG, Genoscope
Laurence Ettwiller: New England Biolabs, Inc.
Tristan Cerisy: 1CEA, DRF, IG, Genoscope
Adriana Alberti: 1CEA, DRF, IG, Genoscope
Karine Labadie: 1CEA, DRF, IG, Genoscope
Marcel Salanoubat: 1CEA, DRF, IG, Genoscope
Ira Schildkraut: New England Biolabs, Inc.
Andrew C. Tolonen: 1CEA, DRF, IG, Genoscope

Nature Communications, 2016, vol. 7, issue 1, 1-9

Abstract: 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.

Date: 2016
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/ncomms13783 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms13783

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/ncomms13783

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().