Nucleic Acids Research Advance Access originally published online on August 12, 2006
Nucleic Acids Research 2006 34(14):3980-3987; doi:10.1093/nar/gkl563
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Nucleic Acids Research, 2006, Vol. 34, No. 14 3980-3987
© 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.
Computational Biology |
The distinctive signatures of promoter regions and operon junctions across prokaryotes
1 Department of Biology, Wilfrid Laurier University 75 University Avenue West, Waterloo, ON, Canada, N2L 3C5 2 Program of Computational Genomics, CCG-UNAM Apdo Postal 565-A, Cuernavaca, Morelos, 62100 Mexico 3 USDA-ARS Plant Genetic Resources Unit, Geneva NY 14456, USA 4 DOE Joint Genome Institute, 2800 Mitchell Drive Walnut Creek, CA 94598, USA
*To whom correspondence should be addressed. Tel: 519 884 0710 ext 2364; Fax: 519 746 0677; Email: gmoreno{at}wlu.ca
Received May 5, 2006. Revised June 27, 2006. Accepted July 19, 2006.
Here we show that regions upstream of first transcribed genes have oligonucleotide signatures that distinguish them from regions upstream of genes in the middle of operons. Databases of experimentally confirmed transcription units do not exist for most genomes. Thus, to expand the analyses into genomes with no experimentally confirmed data, we used genes conserved adjacent in evolutionarily distant genomes as representatives of genes inside operons. Likewise, we used divergently transcribed genes as representative examples of first transcribed genes. In model organisms, the trinucleotide signatures of regions upstream of these representative genes allow for operon predictions with accuracies close to those obtained with known operon data (0.8). Signature-based operon predictions have more similar phylogenetic profiles and higher proportions of genes in the same pathways than predicted transcription unit boundaries (TUBs). These results confirm that we are separating genes with related functions, as expected for operons, from genes not necessarily related, as expected for genes in different transcription units. We also test the quality of the predictions using microarray data in six genomes and show that the signature-predicted operons tend to have high correlations of expression. Oligonucleotide signatures should expand the number of tools available to identify operons even in poorly characterized genomes.
*Correspondence may also be addressed to Sarath Chandra Janga. Tel: +52 777 3132063; Fax: +52 777 3291694; Email: sarath{at}ccg.unam.mx
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  R. W. W. Brouwer, O. P. Kuipers, and S. A. F. T. v. Hijum The relative value of operon predictions Brief Bioinform, April 17, 2008; (2008) bbn019v1. [Abstract] [Full Text] [PDF]
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