Bioinformatics Identifies Cis-Regulatory Elements in Retinoic Acid-Responsive Genes of the
Xenopus Embryo
Amanda Janesick
Mentor: Bruce Blumberg
Retinoid receptors are nuclear proteins that respond to signals from lipid-soluble ligands to
regulate gene transcription and expression. The precise regulation of retinoic acid (RA) levels is
critically important to the temporal and spatial expression of genes involved in vertebrate
development. Retinoid-responsive genes can be regulated directly (the immediate early genes) or
indirectly (the late response genes) by RA. Deciphering the regulatory networks that connect one
gene to another in the retinoic acid receptor (RAR) signaling cascade remains a significant
challenge. We address this by examining three distinct groups of retinoid-responsive genes using
bioinformatics: genes expressed in pre-placodal ectoderm (a region that possesses the correct
signals to become sensory organs), genes belonging to the same synexpression group, and
immediate early genes downstream of RARs. We assume that noncoding sequence of these
genes hold enough information to provide insight to whether the genes are regulated directly or
indirectly by retinoic acid, and what transcription factors interact with them. Unlike previous
studies that examine a few kilobases of noncoding sequence, our approach has been to examine
the entire gene, comprising 20 kb upstream of the translation initiation site, the coding sequence,
and 20 kb downstream of the stop codon. To our knowledge, comparable studies have not been
performed in any organism. Identifying regulatory elements in a eukaryotic organism in silico is
a powerful approach to focus and inform subsequent wet lab techniques (e.g., ChIP-CHIP) that
seek to accomplish the same goal. The results of this study will facilitate the elucidation of the
gene regulatory networks under the control of RA signaling. Moreover, the combination of
bioinformatic and experimental approaches will allow us to concentrate on conserved promoter
elements in the target genes and lead to rapid progress in the defining regulatory hierarchies
down stream of RAR.