We aimed to assess the extent of experimental support for transcriptionally permissive chromatin configurations across all TFBSs enriched at lncRNA promoters. We reasoned that binding sites should have an open chromatin configuration in the cell or tissue types where binding occurs. We leveraged the empirical genome-wide catalog of DNase I hypersensitive sites, indicative of open chromatin, derived for 125 human cell types by the ENCODE Consortium [61]. We found that 67 of the 140 lncRNA-TSS-enriched TFBSs were significantly associated with hypersensitive sites in one or more cell types. This presence of DNase I hypersensitivity sites in lncRNA promoters supports the regulatory potential of such regions in at least one of the 125 studied cell types, despite the repressed chromatin conditions at their promoters in the eight cell types with available data in the CS analysis above.
