This research proposal, submitted in response to NIH RFA HG-03-004 (Technologies to Find Functional Elements in Genomic DNA), describes the development of a novel assay technology to begin to unravel the complexities of alternative RNA splicing. The proposal seeks to develop a means of measuring, in parallel, all predicted exon-specific mRNA sequences coded by the 30MB ENCODE targeted genomic sequences for their presence in a given population of mRNA and their contextual linkage to other exons. These studies are critical to understanding how the human genome is transcribed and translated into an enormous repertoire of molecular diversity from an unexpectedly small set of identified human genes. ? ? The proposed assay, termed an """"""""Exon-Linkage Assay"""""""" will combine a variety of technological innovations to the high-throughput characterization of the human spliceome through the use of a strategy of dual, internal-primer mediated double-stranded cDNA synthesis on a spatially resolved solid phase. The assay leverages a highly adaptable DNA microarray synthesis technology to provide an RNA splicing analysis tool that would be labor or cost-prohibitive by other means. ? ? The described method has the potential to quickly identify differential pre-mRNA splicing patterns in different tissues as well as shifts in splicing (caused either by regulatory defects or genomic mutations) associated with human disease in a rapid, scalable assay platform. ? ?
