Utilizing bioinformatics approaches for identifying binding sites in the Drosophila genome for a developmentally important transcription factor protein

Regulation of gene expression, at the transcription level, in eukaryotes is largely dependent on regulatory proteins called transcription factors. Transcription factors bind to highly specific, short nucleotide sequences on the DNA and regulate transcription by facilitating or inhibiting the binding of RNA polymerase II, the enzyme that catalyzes transcription of eukaryote genes. We are using computational tools that use inherent pattern-searching algorithms to identify binding sites for the Stripe protein, an important transcription factor in Drosophila development. The binding sites for Stripe are expected to lie close to genes that are known to be regulated by this transcription factor. Identifying the locations of these binding sites can be useful in determining the biological significance of these sites through further functional analyses.