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Precise Identification of Genome-Wide Transcription Start Sites in Bacteria by 5′-Rapid Amplification of cDNA Ends (5′-RACE)

  • Dominick Matteau
  • Sébastien RodrigueEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1334)

Abstract

Transcription start sites are commonly used to locate promoter elements in bacterial genomes. TSS were previously studied one gene at a time, often through 5′-rapid amplification of cDNA ends (5′-RACE). This technique has now been adapted for high-throughput sequencing and can be used to precisely identify TSS in a genome-wide fashion for practically any bacterium, which greatly contributes to our understanding of gene regulatory networks in microorganisms.

Key words

Transcription Promoter RNA polymerase holoenzyme Transcription start site Rapid amplification of cDNA ends 5′-RACE Genome wide Next-generation sequencing RNA-seq Transcriptomics 

Notes

Acknowledgment

We thank Pierre-Étienne Jacques for technical assistance, Thomas Knight Jr. for M. florum genome annotations, the Centre de calcul scientifique of Université de Sherbrooke for computational resources and technical support, and Vincent Baby for its precious comments on the manuscript. This work was supported by the Fonds québécois de la recherche sur la nature et les technologies through a MSc scholarship awarded to D.M. and a Projet de recherche en équipe grant awarded to S.R. and Vincent Burrus. S.R. holds a Chercheur-Boursier Junior 1 award from the Fonds de recherche Québec-Santé.

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Département de biologie, Faculté des sciencesUniversité de SherbrookeSherbrookeCanada

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