Abstract: Fairbrother

Dr. William Fairbrother – Brown University

“Mapping Cis-Elements in the Genome: Development of high throughput binding assays to query nucleic acid/protein interactions”

My research utilizes computational and experimental methods to understand the sequence determinants of gene expression. Mostly we are concerned with splicing and finding the cis-elements that modulate splice site recognition. A significant part of the lab takes a computational approach to finding these signals however we are also interested in developing technologies to identify these elements biochemically. This talk describes the development
of a high throughput interaction assay to search genomic space for protein nucleic acid complexes. This work concerns the transcription factor Oct4 and searching within in vivo binding regions for precise sites of binding. Not only are these precise sites of Oct4 identified, the method also returns how Oct4 is binding (monomer or multimer or as a larger complex). We have also started to apply this method to find the binding sites of U1snRNP, PTB and ASF in genomic pre-mRNA.