RT Journal
A1 Cao, Yaqiang
A1 Chen, Guoyu
A1 Wu, Gang
A1 Zhang, Xiaoli
A1 McDermott, Joseph
A1 Chen, Xingwei
A1 Xu, Chi
A1 Jiang, Quanlong
A1 Chen, Zhaoxiong
A1 Zeng, Yingying
A1 Ai, Daosheng
A1 Huang, Yi
A1 Han, Jing-Dong J.
T1 Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions
JF Genome Research 
JO Genome Research 
YR 2019 
FD January 01 
VO 29 
IS 1 
SP 40 
OP 52 
DO 10.1101/gr.235747.118 
UL http://genome.cshlp.org/content/29/1/40.abstract 
AB 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.