Bioinformatics Advance Access originally published online on May 14, 2004
Bioinformatics 2004 20(16):2719-2725; doi:10.1093/bioinformatics/bth317
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Bioinformatics vol. 20 issue 16 © Oxford University Press 2004; all rights reserved.
Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replication
ATGC, CNRS UMR 8071/genopole®, 523 Terrasses de l'Agora, 91000 Evry, France
Received on January 11, 2004; revised on April 19, 2004; accepted on April 26, 2004
Advance Access Publication May 14, 2004
Motivation: The costs of head-on versus codirectional collisions between the replication complex and the much slower transcription complex on the circular bacterial chromosomes are much debated. Although it is established that the number of genes on the leading strand is higher than on the lagging strand of replication, the consequences of collisions on the length of transcription units are unknown.
Results: Here, we show that transcription units are generally longer on the leading strand, in rough proportion to the bias in number of units between the two strands. We propose a statistical physics model, based on the assumption that the proportion of interrupted transcripts for each unit is the major factor contributing to these biases. Its main prediction is that a large replication/transcription speed ratio implies a low leading/lagging bias for transcription unit length and number. This model is validated by an analysis of proven and predicted units in Escherichia coli and Bacillus subtilis. The results are consistent with an equal cost of head-on versus codirectional collisions.
Contact: francois.kepes{at}genopole.cnrs.fr
* To whom correspondence should be addressed.
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