Predicting Transcription Factor Binding Sites in Upstream and Intronic Regions of Rx1
Regulated Genes in Xenopus laevis
Degl’Innocenti A (1), Perrotta M (2), Biasci D (1,3), Giudetti G (1,4), Giannaccini M (1,5), Andreazzoli M
(1)
(1) Department of Biology, University of Pisa, Pisa
(2) Faculty of Engineering, University of Pisa, Pisa
(3) Cambridge Institute for Medical Research, University of Cambridge, Cambridge
(4) European Commission, Ispra, Varese
(5) Scuola Superiore Sant\'Anna, Pisa "
Contact: [email protected]; [email protected]
Motivation
Validated microarray experiments on Xenopus laevis embryonic cDNA led to the definition of a list of
genes potentially regulated by Rx1, a key factor in eye development. Transcriptomic analyses, typically
produce huge amounts of information, thus bioinformatic approaches can be of great help to fully
exploit this kind of output. In particular, here we focused on the prediction of Rx1 Transcription Factor
Binding Sites (TFBSs) in order to obtain a first individuation of Rx1 directly targeted genes. Moreover,
to identify other transcription factors potentially able to regulate the same set of genes, we searched
for the presence of other TFBSs.
Methods
We designed a pipeline to look for TFBSs in promoter/upstream regions as well as intronic regions of
the corresponding genes in Xenopus tropicalis, a near and genetically better characterized species,
using a Position-Specific Weight Matrices (PSWMs)-based method. We used the JASPAR Rax mouse
matrix as an input for MEME Suite's FIMO (Find Individual Motif Occurrence) tool, and the whole
JASPAR database as input for MotifViz's Clover (Cis-eLement OVERrepresentation) tool.
Results
Our work suggests that a subgroup of the listed genes are putative direct targets of Rx1 and indicates
the presence of binding sites for eye specific factors in some other genes of the list.