@article{Cao01012019,
author = {Cao, Yaqiang and Chen, Guoyu and Wu, Gang and Zhang, Xiaoli and McDermott, Joseph and Chen, Xingwei and Xu, Chi and Jiang, Quanlong and Chen, Zhaoxiong and Zeng, Yingying and Ai, Daosheng and Huang, Yi and Han, Jing-Dong J.}, 
title = {Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions},
volume = {29}, 
number = {1}, 
pages = {40-52}, 
year = {2019}, 
doi = {10.1101/gr.235747.118}, 
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.}, 
URL = {http://genome.cshlp.org/content/29/1/40.abstract}, 
eprint = {http://genome.cshlp.org/content/29/1/40.full.pdf+html}, 
journal = {Genome Research} 
}