Phylogenetic footprinting: a boost for microbial regulatory genomics

Abstract

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of homologous regulatory regions, usually collected from multiple species. It does so by identifying the best conserved motifs in those homologous regions. There are two popular sets of methods-alignment-based and motif-based, which are generally employed for phylogenetic methods. However, serious efforts have lacked to develop a tool exclusively for phylogenetic footprinting, based on either of these methods. Nevertheless, a number of software and tools exist that can be applied for prediction of phylogenetic footprinting with variable degree of success. The output from these tools may get affected by a number of factors associated with current state of knowledge, techniques and other resources available. We here present a critical apprehension of various phylogenetic approaches with reference to prokaryotes outlining the available resources and also discussing various factors affecting footprinting in order to make a clear idea about the proper use of this approach on prokaryotes.

Genome-scale exploration of transcriptional regulation in the nisin Z producer Lactococcus lactis subsp. lactis IO-1

“…Identification of phylogenetically conserved cis-regulatory motifs. Phylogenetic footprinting is a computational procedure of cis-regulatory motif identification in orthologous promoter regions of multiple genomes and is based on the principle that regulatory sequences in promoters are more conserved than the nonfunctional sequences since they evolve at a lower rate 79 . Generally, during this process the set of orthologous promoters are aligned and this alignment is then scanned for conserved motif finding.…”

Genome-wide prediction of transcription factor binding sites in cassava via phylogenetic footprinting between plants in Euphorbiaceae family

“…In order to unravel the systems regulation, several computation approaches have been applied to predict TFBSs and their transcription factors (TFs), for example, TFBS scan based on sequence similarity between known TFBSs of model organisms and promoter sequences of interested organisms. To overcome the limitation of TFBS information, phylogenetic footprinting approach was proposed under the hypothesis that the regulatory elements will be conserved across the related species via evolutionary conservation [1,2]. Methods and Algorithms: Therefore, in this work, the phylogenetic footprinting approach was applied to identify all putative transcription factor binding sites (TFBSs) in cassava, the emphasized plant for food and energy security in the 21 st century.…”

Evolutionary genomics of Borrelia burgdorferi sensu lato: Findings, hypotheses, and the rise of hybrids

“…Phylogenetic footprinting is a computational approach for ab initio prediction of gene-regulatory elements in intergenic spacer (IGS) regions by identifying excessively conserved sequences (Brohée et al, 2011; Katara et al, 2012). The basic assumption of phylogenetic footprinting is that cis -regulatory sequences and non-coding RNAs (ncRNAs) are subject to purifying selection and therefore evolve at a lower rate than less functional, more neutrally evolving intergenic sequences (Eddy, 2005).…”

“…For example, phylogenomics (Box 1) is an evolution-informed approach to annotate functions of unknown genes based on identification of gene orthology and signatures of adaptive evolution (Eisen, 1998; Kumar et al, 2012). Also based on evolutionary principles, phylogenetic footprinting (Box 1) is a computational approach for ab initio identification of gene-regulatory elements in non-coding parts of a genome (Brohée et al, 2011; Degnan et al, 2011; Katara et al, 2012). By generating and testing specific expectations on the level and pattern of sequence variability, evolutionary analyses are powerful to distinguish biologically important genome variations from a noisy background of stochastic neutral or nearly neutral variations.…”