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Journal of Bacteriology, May 2009, p. 3203-3211, Vol. 191, No. 10
0021-9193/09/$08.00+0     doi:10.1128/JB.00122-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Structure and Complexity of a Bacterial Transcriptome ^,

Karla D. Passalacqua,¹ Anjana Varadarajan,¹ Brian D. Ondov,¹ David T. Okou,² Michael E. Zwick,² and Nicholas H. Bergman^1,3*

School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332,¹ Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322,² Electro-Optical Systems Laboratory, Georgia Tech Research Institute, Atlanta, Georgia 30332³

Received 29 January 2009/ Accepted 6 March 2009

Although gene expression has been studied in bacteria for decades, many aspects of the bacterial transcriptome remain poorly understood. Transcript structure, operon linkages, and information on absolute abundance 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 been explored on a large scale in only 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 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 the data provide an accurate and high-resolution map of transcript start sites and operon structure throughout the genome. Further, the sequence data identified previously nonannotated regions with significant transcriptional activity and enhanced the accuracy of existing genome annotations. Finally, our data provide estimates of absolute transcript abundance and suggest that 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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* Corresponding author. Mailing address: School of Biology, Georgia Institute of Technology, 310 Ferst Dr., Rm. 231, Atlanta, GA 30332-0230. Phone: (404) 894-8418. Fax: (404) 894-0519. E-mail: nickbergman{at}gatech.edu

Published ahead of print on 20 March 2009.

Supplemental material for this article may be found at http://jb.asm.org/.

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Journal of Bacteriology, May 2009, p. 3203-3211, Vol. 191, No. 10
0021-9193/09/$08.00+0     doi:10.1128/JB.00122-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

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