Bioinformatics Identifies CIS-Regulatory Elements in Retinoic Acid-Responsive Genes of the Xenopus Embryo

Retinoic acid (RA) signaling plays a key role in early development and is essential for immune function, blood cell development, reproduction and other important functions. Retinoid receptors are nuclear proteins that respond to signals from fat-soluble ligands for the purpose of regulating gene expression. We seek to discover regions of DNA (cis-regulatory elements) which are bound by proteins that control the expression of a set of genes upregulated by RA. These genes belong to a synexpression group (i.e., they display similar spatial and temporal expression patterns in the neural tube, neural crest, and optic anlagen of the frog embryo). We hypothesize that synexpression implies coregulation, and that the same cis-regulatory elements will be found in each gene of the synexpression group.

Each gene belonging to the synexpression group was analyzed through in silico comparison of upstream, downstream, and intronic sequence. Phylogenetic footprinting enabled the “filtering” of a large sequence input to reveal evolutionarily-conserved sequences in each gene. These conserved sequences were then fed into de novo motif finding algorithms to identify statistically significant sequences that occurred in all genes of the synexpression group. We have identified several putative cis-regulatory elements that are both evolutionarily conserved and shared by each gene of the synexpression group. These in silico data set the stage for future, in vivo experiments aimed at determining whether the elements are necessary and sufficient to mediate the expression and RA responsiveness of the synexpression group genes.