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Nucleic Acids Research Advance Access originally published online on June 15, 2009
Nucleic Acids Research 2009 37(15):4919-4931; doi:10.1093/nar/gkp490
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Nucleic Acids Research, 2009, Vol. 37, No. 15 4919-4931
© 2009 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.

Computational Biology

Gains and unexpected lessons from genome-scale promoter mapping

K. S. Shavkunov1, I. S. Masulis1, M. N. Tutukina1, A. A. Deev2 and O. N. Ozoline1,*

1Institute of Cell Biophysics and 2Institute of Theoretical and Experimental Biophysics, of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation

*To whom correspondence should be addressed. Tel: +7 4967 73 91 40; Fax: +7 4967 33 05 09; Email: ozoline{at}icb.psn.ru

Received December 3, 2008. Revised May 19, 2009. Accepted May 20, 2009.

Potential promoters in the genome of Escherichia coli were searched by pattern recognition software PlatProm and classified on the basis of positions relative to gene borders. Beside the expected promoters located in front of the coding sequences we found a considerable amount of intragenic promoter-like signals with a putative ability to drive either antisense or alternative transcription and revealed unusual genomic regions with extremely high density of predicted transcription start points (promoter ‘islands’), some of which are located in coding sequences. PlatProm scores converted into probability of RNA polymerase binding demonstrated certain correlation with the enzyme retention registered by ChIP-on-chip technique; however, in ‘dense’ regions the value of correlation coefficient is lower than throughout the entire genome. Experimental verification confirmed the ability of RNA polymerase to interact and form multiple open complexes within promoter ‘island’ associated with appY, yet transcription efficiency was lower than might be expected. Analysis of expression data revealed the same tendency for other promoter ‘islands’, thus assuming functional relevance of non-productive RNA polymerase binding. Our data indicate that genomic DNA of E. coli is enriched by numerous unusual promoter-like sites with biological role yet to be understood.


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