GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs

Abstract

Transcriptional cis-regulatory control regions frequently are found within non-coding DNA segments conserved across multi-species gene orthologs. Adopting a systematic gene-centric pipeline approach, we report here the development of a web-accessible database resource--GenomeTraFac (http://genometrafac.cchmc.org)--that allows genome-wide detection and characterization of compositionally similar cis-clusters that occur in gene orthologs between any two genomes for both microRNA genes as well as conventional RNA-encoding genes. Each ortholog gene pair can be scanned to visualize overall conserved sequence regions, and within these, the relative density of conserved cis-element motif clusters form graph peak structures. The results of these analyses can be mined en masse to identify most frequently represented cis-motifs in a list of genes. The system also provides a method for rapid evaluation and visualization of gene model-consistency between orthologs, and facilitates consideration of the potential impact of sequence variation in conserved non-coding regions to impact complex cis-element structures. Using the mouse and human genomes via the NCBI Reference Sequence database and the Sanger Institute miRBase, the system demonstrated the ability to identify validated transcription factor targets within promoter and distal genomic regulatory regions of both conventional and microRNA genes.

Figure 1

(A) Regulogram depiction of shared cis-elements between two sequences in the context of their sequence similarity: The two sequences, mouse and human ITGB1BP2 (melusin), are represented as horizontal bars. The red colored segments on these bars are exons. The green colored bars shown parallel to the genomic sequences represent the repeat regions. The regions of sequence alignment are represented as different colored quadrilaterals that relate one sequence to another. Within each shaded block, the percent sequence similarity and the number of TF-binding sites are represented as two separate line graphs in the lower half. The frequencies of individual binding sites occurring in each of the sequences separately are shown as two running graphs in the top half of the pane. The percent similarity is the average sequence conservation as determined by the BlastZ algorithm and the shared cis-element hits are determined by an algorithm that uses a 200 bp moving window that looks through the cis-elements that are present within the conserved sequence block. Numbers are nucleotide positions. Regulogram can be clicked to zoom in or view the TF-binding sites that are in common between the two sequences at the click-point coordinate. (B) Example of GNF expression pattern for the human gene ITGBIBP2 showing very specific heart expression. The bar-graph is based on that from (C) Visualizing GenomeTrafac tracks on the UCSC Genome browser: The pink horizontal bars are the conserved TFBSs from GenomeTrafac. Image shown here corresponds to the flanking regions of the first exon of human gene ITGB1BP2. (D) TraFaC image of a cis-element dense upstream region of ITGB1BP2: The two gray vertical bars are the two genes (human and mouse ITGB1BP2) that are compared. The numbers represent the nucleotide positions with respect to the sequences used. The TF-binding sites occurring in both the genes are highlighted as various colored bars drawn across the two genes. The positional and extent of consecutive individual elements in potential regulatory clusters tend to be highly conserved. Putative binding sites for cardiogenic TFs (SRF, MEF2, GATA and HAND) are highlighted. This cardiogenic TFBSs cluster could be responsible for the cardiac overexpression (see panel B) of the human gene ITGB1BP2.