Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions
- Yaqiang Cao1,3,
- Guoyu Chen1,3,
- Gang Wu1,3,
- Xiaoli Zhang1,3,
- Joseph McDermott1,
- Xingwei Chen1,
- Chi Xu1,
- Quanlong Jiang1,
- Zhaoxiong Chen1,
- Yingying Zeng1,2,
- Daosheng Ai1,
- Yi Huang1 and
- Jing-Dong J. Han1
- 1CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China;
- 2School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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↵3 These authors contributed equally to this work.
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.235747.118.
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Freely available online through the Genome Research Open Access option.
- Received February 6, 2018.
- Accepted November 12, 2018.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
