K4me3 peaks overlapping or within 5Kb of the transcriptional start site determined by RNA-Seq reconstruction. (iv) The transcription factor binding locations and lincRNA promoter locations were intersected and the enrichment level of the peak overlapping a lincRNA promoter was assigned transcription factor binding enrichment for each lincRNA. We defined transcription factor binding locations for protein-coding genes in a comparable way. (v) To exclude the possibility that some of this binding might be due to transcription factor binding at distal enhancers, we excluded all binding events that showed evidence of P300, a protein associated with active enhancers68, localization. Altogether, we only identified ~5% of promoters overlapping with any P300 enrichment signal, a slightly lower percentage than identified for protein-coding gene promoters with detectable P300 signal.
