RESEARCH ARTICLE Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses Jumpei Ito1,2, Ryota Sugimoto1, Hirofumi Nakaoka1,2, Shiro Yamada3, Tetsuaki Kimura1, Takahide Hayano1, Ituro Inoue1,2* 1 Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, Japan, 2 Department of Genetics, School of Life Science, SOKENDAI (The Graduate a1111111111 University for Advanced Studies), 1111 Yata, Mishima, Shizuoka, Japan, 3 Department of Pediatrics, Tokai a1111111111 University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, Japan a1111111111 a1111111111 *
[email protected] a1111111111 Abstract Human endogenous retroviruses (HERVs) and other long terminal repeat (LTR)-type OPEN ACCESS retrotransposons (HERV/LTRs) have regulatory elements that possibly influence the tran- Citation: Ito J, Sugimoto R, Nakaoka H, Yamada S, scription of host genes. We systematically identified and characterized these regulatory ele- Kimura T, Hayano T, et al. (2017) Systematic ments based on publicly available datasets of ChIP-Seq of 97 transcription factors (TFs) identification and characterization of regulatory provided by ENCODE and Roadmap Epigenomics projects. We determined transcription elements derived from human endogenous retroviruses. PLoS Genet 13(7): e1006883. https:// factor-binding sites (TFBSs) using the ChIP-Seq datasets and identified TFBSs observed doi.org/10.1371/journal.pgen.1006883 on HERV/LTR sequences (HERV-TFBSs). Overall, 794,972 HERV-TFBSs were identified. Editor: CeÂdric Feschotte, University of Utah School Subsequently, we identified ªHERV/LTR-shared regulatory element (HSRE),º defined as a of Medicine, UNITED STATES TF-binding motif in HERV-TFBSs, shared within a substantial fraction of a HERV/LTR type.