ERV1 LTRs associate with lincRNA TSSs. We plotted the coverage of various TE families approaching lincRNA TSSs. The prevalent L1 and Alu families are depleted in lincRNAs. Accordingly, their coverage drops throughout lincRNA promoters leading up to the TSS. Alternatively, ERV1 elements are enriched in lincRNAs, and coverage of the transcription-promoting ERV1 LTRs peaks at the TSS. This pattern was not observed for mRNAs (Figure S11 in Additional file 1).
Kelley and Rinn Genome Biology 2012 13:R107 doi:10.1186/gb-2012-13-11-r107