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Transposable element exaptation is the primary source of novelty in the primate gene regulatory landscape

By Marco Trizzino, YoSon Park, Marcia Holsbach-Beltrame, Katherine Aracena, Katelyn Mika, Minal Caliskan, George H. Perry, Vincent J. Lynch, Christopher D. Brown

Posted 27 Oct 2016
bioRxiv DOI: 10.1101/083980 (published DOI: 10.1101/gr.218149.116)

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.

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