%0 Journal Article
%T Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions
%A Chi Xu
%A Daosheng Ai
%A Gang Wu
%A Guoyu Chen
%A Jing-Dong J. Han
%A Joseph McDermott
%A Quanlong Jiang
%A Xiaoli Zhang
%A Xingwei Chen
%A Yaqiang Cao
%A Yi Huang
%A Yingying Zeng
%A Zhaoxiong Chen
%J Genome Research
%D 2019
%R http://www.genome.org/cgi/doi/10.1101/gr.235747.118
%X Abstract A few families of transposable elements (TEs) have been shown to evolve into cis-regulatory elements (CREs). Here, to extend these studies to all classes of TEs in the human genome, we identified widespread enhancer-like repeats (ELRs) and find that ELRs reliably mark cell identities, are enriched for lineage-specific master transcription factor binding sites, and are mostly primate-specific. In particular, elements of MIR and L2 TE families whose abundance co-evolved across chordate genomes, are found as ELRs in most human cell types examined. MIR and L2 elements frequently share long-range intra-chromosomal interactions and binding of physically interacting transcription factors. We validated that eight L2 and nine MIR elements function as enhancers in reporter assays, and among 20 MIR-L2 pairings, one MIR repressed and one boosted the enhancer activity of L2 elements. Our results reveal a previously unappreciated co-evolution and interaction between two TE families in shaping regulatory networks
%U https://genome.cshlp.org/content/29/1/40.abstract