HERVH elements associate with stem cell-specific lincRNA expression. (a) HERVH is a primate-specific 9 kb endogenous retrovirus containing the group specific antigen (Gag), protease (Pro), polymerase (Pol), and envelope (Env) proteins, surrounded on both sides by transcription-promoting LTRs. (b) 127 lincRNAs (columns) contain HERVH elements and expression of these lincRNAs (measured as log2(FPKM + 0.25)) across cell types (rows) is highly specific to the pluripotent H1-hESCs and iPSCs. (c) HERVH-lincRNAs are expressed at much greater levels than lincRNAs devoid of HERVH (dHERVH-lincRNAs) in ESCs, displayed here as the cumulative distribution of FPKM + 0.25. (d) ChIP-Seq read coverage indicates that HERVH-lincRNAs are marked by the activating histone modification H3K4me3 in H1-hESCs but not GM12878 where expression is low. (e) The transcription factor SP1 was previously found to be required for HERVH transcription. Accordingly, ChIP-Seq read coverage shows SP1 occupies the TSSs of HERVH-lincRNAs in H1-hESC but not GM12878.