Genome-wide identification of transcription start sites yields a novel thermosensing RNA and new cyclic AMP receptor protein-regulated genes in Escherichia coli

J Bacteriol. 2011 Jun;193(11):2871-4. doi: 10.1128/JB.00398-11. Epub 2011 Apr 1.


Intergenic regions often contain regulatory elements that control the expression of flanking genes. Using a deep-sequencing approach, we identified numerous new transcription start sites in Escherichia coli, yielding a new thermosensing regulatory RNA and seven genes previously unknown to be under the control of the global regulator CRP.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Base Sequence
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • DNA, Intergenic
  • DNA-Binding Proteins / metabolism*
  • Escherichia coli / genetics*
  • Escherichia coli / radiation effects
  • Escherichia coli Proteins / metabolism*
  • Gene Expression Regulation, Bacterial*
  • Genes, Bacterial
  • High-Throughput Nucleotide Sequencing
  • Nucleic Acid Conformation
  • RNA / metabolism*
  • Receptors, Cyclic AMP / metabolism*
  • Regulon*
  • Sequence Alignment
  • Temperature
  • Transcription Initiation Site*


  • DNA, Bacterial
  • DNA, Intergenic
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • Receptors, Cyclic AMP
  • cyclic AMP receptor protein, E coli
  • RNA