TY  - JOUR
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
Y1  - 2019/01/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 40 
EP  - 52 
DO  - 10.1101/gr.235747.118 
VL  - 29 
IS  - 1 
UR  - http://genome.cshlp.org/content/29/1/40.abstract 
N2  - 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. 
ER  -