JB Accepts, published online ahead of print on 20 March 2009

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J. Bacteriol. doi:10.1128/JB.00122-09
Copyright (c) 2009, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

The Structure and Complexity of a Bacterial Transcriptome

Karla D. Passalacqua, Anjana Varadarajan, Brian D. Ondov, David T. Okou, Michael E. Zwick, and Nicholas H. Bergman^*

School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA; Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; Electro-Optical Systems Laboratory, Georgia Tech Research Institute, Atlanta, GA 30332, USA

^* To whom correspondence should be addressed. Email: nickbergman{at}gatech.edu.

Although gene expression has been studied in bacteria for decades, many aspects of the bacterial transcriptome remain poorly understood. Transcript structure, operon linkages, and absolute abundance information all provide valuable insights into gene function and regulation, but none has ever been determined on a genome-wide scale for any bacterium. Indeed, these aspects of the prokaryotic transcriptome have only been explored on a large scale in a few instances, and consequently little is known about the absolute composition of the mRNA population within a bacterial cell. Here we report the use of a high-throughput sequencing-based approach (RNA-Seq) in assembling the first comprehensive, single-nucleotide resolution view of a bacterial transcriptome. We sampled the Bacillus anthracis transcriptome under a variety of growth conditions, and showed that these data provide an accurate and high-resolution map of transcript start sites and operon structure throughout the genome. Further, the sequence data identified previously unannotated regions with significant transcriptional activity, and enhanced the accuracy of existing genome annotations. Finally, our data provide estimates of absolute transcript abundance, and suggest there is significant transcriptional heterogeneity within a clonal, synchronized bacterial population. Overall, our results offer an unprecedented view of gene expression and regulation in a bacterial cell.

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