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A high resolution map of a cyanobacterial transcriptome

Vikram Vijayan12, Isha H Jain2 and Erin K O'Shea12*

Author Affiliations

1 Graduate Program in Systems Biology, Harvard University, 52 Oxford Street, Northwest 445.40, Cambridge, MA 02138, USA

2 Howard Hughes Medical Institute, Harvard Faculty of Arts and Sciences Center for Systems Biology, Departments of Molecular and Cellular Biology and Chemistry and Chemical Biology, Harvard University, 52 Oxford Street, Northwest 445.40, Cambridge, MA 02138, USA

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Genome Biology 2011, 12:R47  doi:10.1186/gb-2011-12-5-r47

Published: 25 May 2011



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.


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.


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