Genomic analysis of mammalian imprinted loci

DESCRIPTION (provided by applicant): We have found imprinted genes in the human genome to have distinctive sequence characteristics in their flanking regions. This allows us to identify the other genes in the genome that resemble imprinted genes in terms of these discriminatory patterns, as a basis for predicting new imprinted loci. While the validation of such predictions can be difficult when imprinting occurs in a very tissue or developmental stage-limited manner, we have developed a powerful molecular assay that precisely quantifies expression from each parental allele. We present preliminary data of the analysis of 2 adjacent loci, Cdh8 and Cdh11, which are predicted to be non-imprinted and imprinted, respectively, based on the discriminatory sequence features we have identified. Our molecular analysis is in accord with these predictions, implicating CDH11 as the gene causing psoriatic arthropathy in humans. We propose to develop further our bioinformatics analyses, identifying the sequence features that discriminate imprinted loci even more strongly, providing further insights into the mechanism and evolution of imprinting. We will develop our imprinted gene discovery platform to allow the analysis of hundreds of loci during the funding period, focusing on regions for which imprinted genes have been implicated in growth, obesity and congenital malformations in humans. As the rate of imprinted gene discovery has declined in the last several years, we will make all of our data publiclyavailable on generation through a web server in order to facilitate imprinted gene discovery by other investigators. We will identify potential transcription factor binding sites using bioinformatic techniques and test whether these candidates bind to transcription factors using electrophoretic mobility shift assays. The major goal is to identify new imprinted genes, but the secondary goals that will build on this increased sample size involve disease gene discovery and more robust insights into the mechanistic mediators of genomic imprinting and the evolution of this epigenetic process.