A high resolution map of a cyanobacterial transcriptome

Genome Biol. 2011;12(5):R47. doi: 10.1186/gb-2011-12-5-r47. Epub 2011 May 25.


Background: Previous molecular and mechanistic studies have identified several principles of prokaryotic transcription, but less is known about the global transcriptional architecture of bacterial genomes. Here we perform a comprehensive study of a cyanobacterial transcriptome, that of Synechococcus elongatus PCC 7942, generated by combining three high-resolution data sets: RNA sequencing, tiling expression microarrays, and RNA polymerase chromatin immunoprecipitation sequencing.

Results: We report absolute transcript levels, operon identification, and high-resolution mapping of 5' and 3' ends of transcripts. We identify several interesting features at promoters, within transcripts and in terminators relating to transcription initiation, elongation, and termination. Furthermore, we identify many putative non-coding transcripts.

Conclusions: We provide a global analysis of a cyanobacterial transcriptome. Our results uncover insights that reinforce and extend the current views of bacterial transcription.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Chromatin / genetics
  • Chromatin Immunoprecipitation
  • Chromosome Mapping / methods*
  • DNA-Directed RNA Polymerases / genetics
  • Databases, Genetic
  • Gene Expression Profiling / methods
  • Genome, Bacterial*
  • Genomics / methods*
  • Oligonucleotide Array Sequence Analysis / methods
  • Operon / genetics
  • RNA, Messenger / chemistry
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • Regulatory Sequences, Nucleic Acid / genetics
  • Sequence Analysis, RNA
  • Synechococcus / genetics*
  • Transcriptome*


  • Chromatin
  • RNA, Messenger
  • DNA-Directed RNA Polymerases