Locating Genetic Determinants Of Translational Significance Using The Rat Genome

Genome-wide association studies (GWAS) have detected associations of genetic elements on human chromosome 2 with hypertension but lack the ability to discern whether these associations are/are not causal factors for hypertension. Using rat genetic models of hypertension, we have identified that factors linked to the inheritance of hypertension map to rat chromosome 9, which is homologous to human chromosome 2. Here we report that by applying high resolution mapping approaches, we have prioritized two regions on rat chromosome 9, one spanning < 788kb and a second region spanning < 81.8kb, as genomic segments containing novel inherited genetic elements controlling blood pressure. The <788kb region contains 3 protein coding genes, Trmp8 , Spp2 and Arl4c , which are also associated with human hypertension. Of these, there was only one nonsynonymous polymorphism within the gene Spp2 between the Dahl S and S.SHR strains used to map this locus. The expression of Spp2 was significantly higher in the S.SHR rat compared with S. We therefore prioritize Spp2 as a positional candidate for the <788kb region. The <81.8kb region contains no known/predicted protein-coding genes. We hypothesized that polymorphisms within gene regulatory elements underlie the <81.8kb locus. By combining the locations of the relevant polymorphisms with promoters predicted by the Proscan promoter prediction software, 5 regions were prioritized for further analysis. Alleles from the normotensive R rat from 1 out of these 5 regions had a 5.14 fold higher luciferase activity compared with that of the hypertensive S rat alleles (p<0.05). This region maps from chr9:80880396 to chr9:80882643 (Rnor5.0) on the rat genome. The downstream target for this promoter activity is unknown. Interestingly, within 110,419bp downstream of this region, there is a predicted long non-coding RNA in the mouse (AK079660) and in humans ( DIRC4) . By RT-PCR using rat kidney, we detected a novel rat transcript that is potentially a rat homologue of the mouse and human predictions. Collectively, these data point to conserved syntenic regions in rats and humans that contain novel promoter sequence variants and variants within the conserved gene, Spp2 , as potential quantitative trait nucleotides for blood pressure regulation.