Regulatory element copy number differences shape primate expression profiles

Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across 3 primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs which were processed pseudogenes and some of which were expressed. Furthermore, there were copy number different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA. 17 primate samples were run on a custom Agilent arrayCGH platform against a single human reference (HapMap sample, NA10851). The array is designed based on human genome build hg18. All probes on the array have 100% identity to the human, chimpanzee, and rhesus macaque reference genomes. Thus, hybridization bias between the human reference and nonhuman primate samples should be minimized. These arrayCGH runs were used to determine copy number differences between species in order to study their role on gene expression differences between the same species.