Phylogenetic footprinting is a technique used to identify transcription factor binding sites (TFBS) within a non-coding region of DNA of interest by comparing it to the orthologous sequence in different species. When this technique is used with a large number of closely related species, this is called phylogenetic shadowing.
Researchers have found that non-coding pieces of DNA contain binding sites for regulatory proteins that govern the spatiotemporal expression of genes. These transcription factor binding sites (TFBS), or regulatory motifs, have proven hard to identify, primarily because they are short in length, and can show sequence variation. The importance of understanding transcriptional regulation to many fields of biology has led researchers to develop strategies for predicting the presence of TFBS, many of which have led to publicly available databases. One such technique is Phylogenetic Footprinting.
Phylogenetic footprinting relies upon two major concepts:
- The function and DNA binding preferences of transcription factors are well-conserved between diverse species.
- Important non-coding DNA sequences that are essential for regulating gene expression will show differential selective pressure. A slower rate of change occurs in TFBS than in other, less critical, parts of the non-coding genome.