Regulatory element copy number differences shape primate expression profiles.

Rebecca C Iskow
Omer Gokcumen
Alexej Abyzov
Joanna Malukiewicz
Qihui Zhu
Ann T Sukumar
Athma A Pai
Ryan E Mills
Lukas Habegger
Darren A Cusanovich
Meagan A Rubel
George H Perry
Mark Gerstein
Anne C Stone
Yoav Gilad
Charles Lee, The Jackson Laboratory


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 three 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 that 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.