Web-Based Identification of Evolutionary Conserved DNA cis-Regulatory Elements

Transcription regulation on a gene-by-gene basis is achieved through transcription factors, the DNA-binding proteins that recognize short DNA sequences in the proximity of the genes. Unlike other DNA-binding proteins, each transcription factor recognizes a number of sequences, usually variants of a preferred, “consensus” sequence. The degree of dissimilarity of a given target sequence from the consensus is indicative of the binding affinity of the transcription factor–DNA interaction. Because of the short size and the degeneracy of the patterns, it is frequently difficult for a computational algorithm to distinguish between the true sites and the background genomic “noise.” One way to overcome this problem of low signal-to-noise ratio is to use evolutionary information to detect signals that are conserved in two or more species. FOOTER is an algorithm that uses this phylogenetic footprinting concept and evaluates putative mammalian transcription factor binding sites in a quantitative way. The user is asked to upload the human and mouse promoter sequences and select the transcription factors to be analyzed. The results’ page presents an alignment of the two sequences (color-coded by degree of conservation) and information about the predicted sites and single-nucleotide polymorphisms found around the predicted sites. This chapter presents the main aspects of the underlying method and gives detailed instructions and tips on the use of this web-based tool.