Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions
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 ELRs reliably mark cell identities, enriched for lineage-specific master transcription factor binding sites and 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 transcriptions factors. We validated 8 L2 and 9 MIR elements function as enhancers in reporter assays, and among 20 MIR-L2 pairings, 1 MIR repressed, and 1 boosted, the enhancer activity of L2 elements. Our results reveal a previously unappreciated coevolution and interaction between two TE families in shaping regulatory networks.
- Received February 6, 2018.
- Accepted November 12, 2018.
- Published by Cold Spring Harbor Laboratory Press
This manuscript is Open Access.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International license), as described at http://creativecommons.org/licenses/by-nc/4.0/.
