Prediction of Co-Regulated Genes in Eubacterial Genomes by Phylogenetic Footprinting

摘要

Since co-regulated genes are recognized by the same transcription factor, they must have the same motif in their upstream sequences. Thus, in principle, we can expect to understand the co-regulation relationship of genes by finding their common motif.However, it is generally difficult to find unknown motifs because they are usually short and are not strictly conserved. One way to reduce unavoidable noises is to use the evolutionary information. Namely, we can postulate that most binding sites of transcription factors are phylogenetically conserved (the method is often called the phylogenetic footprinting). In a previous work, we used such an approach to three closely-related species of Bacillus genus and could successfully identify many plausible cis-elements and co-regulated genes (regulons). A preliminary work to apply the same approach into the analysis of another genera was reported last year by us. In this work, we report more comprehensive results on Mycoplasma, Chlamydia and Mycobacterium genera.