RT Journal Article
SR Electronic
T1 Transposable element exaptation is the primary source of novelty in the primate gene regulatory landscape
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 083980
DO 10.1101/083980
A1 Marco Trizzino
A1 YoSon Park
A1 Marcia Holsbach-Beltrame
A1 Katherine Aracena
A1 Katelyn Mika
A1 Minal Caliskan
A1 George H. Perry
A1 Vincent J. Lynch
A1 Christopher D. Brown
YR 2016
UL http://biorxiv.org/content/early/2016/10/27/083980.abstract
AB Gene regulation plays a critical role in the evolution of phenotypic diversity. We investigated the evolution of liver promoters and enhancers in six primate species. We performed ChIP-seq for two histone modifications and RNA-seq to profile cis-regulatory element (CRE) activity and gene expression. The primate regulatory landscape is largely conserved across the lineage. Conserved CRE function is associated with sequence conservation, proximity to coding genes, cell type specificity of CRE function, and transcription factor binding. Newly evolved CREs are enriched in immune response and neurodevelopmental functions, while conserved CREs bind master regulators. Transposable elements (TEs) are the primary source of novelty in primate gene regulation. Newly evolved CREs are enriched in young TEs that affect gene expression. However, only 17% of conserved CREs overlap a TE, suggesting that target gene expression is under strong selection. Finally, we identified specific genomic features driving the functional recruitment of newly inserted TEs.