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Nucleic Acids Research Advance Access first published online on September 29, 2006
This version published online on October 5, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl649
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

In vivo DNase I sensitivity of the Streptomyces coelicolor chromosome correlates with gene expression: implications for bacterial chromosome structure

Michael McArthur* and Mervyn Bibb

Department of Molecular Microbiology, John Innes Centre Norwich, NR4 7UH, UK

*To whom correspondence should be addressed. Tel: +44 1603 450757; Fax: +44 1603 450778; Email: michael.mcarthur{at}bbsrc.ac.uk

Received June 23, 2006. Revised August 22, 2006. Accepted August 23, 2006.

For a bacterium, Streptomyces coelicolor A3(2) contains a relatively large genome (8.7 Mb) with a complex and adaptive pattern of gene regulation. We discovered a correlation between the physical structure of the S.coelicolor genome and the transcriptional activity of the genes therein. Twelve genes were surveyed throughout 72 h of growth for both in vivo sensitivity to DNase I digestion and levels of transcription. DNase I-sensitivity correlated positively with transcript levels, implying that it was predictive of gene expression, and indicating increased accessibility of transcribed DNA. The genome was fractionated based on the sensitivity to DNase I digestion, with the low molecular weight (frequently cut) fraction highly enriched for actively transcribed sequences when compared to the infrequently cut fraction, which was representative of the entire genome. This approach will allow comparison of nucleoid proteins, and any modifications thereof, associated with transcriptionally active and inactive regions of the bacterial genome.


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