Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses
HERV-TFBSs and HSREs were identified separately using ENCODE and Roadmap datasets. HERV-TFBSs and HSREs were identified for all- and unique-read TFBSs. A) HERV-TFBSs were identified in respective cell types by examining overlaps between HERV/LTRs and TFBSs. HERV-TFBSs of each TF were merged among cell types (merged HERV-TFBSs). B) In each HERV/LTR type, MSA of HERV/LTR copies was constructed with the consensus sequence, and then the position of the merged HERV-TFBS was mapped on each HERV/LTR sequence in the MSA. Red and pink regions indicate HERV-TFBSs for TF X and Y, respectively. C) TF-binding motif was scanned in HERV-TFBS and mapped on each HERV/LTR sequence in the MSA. Star and triangle marks indicate TF-binding motifs for TF X and Y, respectively. A set of TF-binding motifs was regarded as HSRE if the TF-binding motifs were shared among greater than 60% of HERV-TFBSs at the same position in MSA. Boxed TF-binding motifs are HSREs for TF X and Y, respectively.