We additionally found that 14 FOX-family TFs, 6 SOX-family TFs, 3 members of the HOXD homeobox family, 3 members of the CEBP family, 3 NKX-family TFs, and 2 PPAR TFs (Table S2) demonstrate similar patterns of differential TFBS enrichment at lncRNA promoters. Several of these same TFs have been previously reported as regulatory targets of lncRNAs as well. NKX2-2 is endogenously regulated by a cis-antisense lncRNA at its own locus [37]. Similarly, the HOXD cluster is regulated in cis and in trans by multiple lncRNAs [38]–[40]. CEBPA is cis-regulated by an lncRNA as well [41]. Our in silico predicted binding site results for homeobox TFs at the promoters of lncRNA genes are consistent with a recent evolutionary study [42]. Summarily, the TF families that are characterized by TFBS enrichments at lncRNA promoters in our analysis include TFs that are known to be direct targets of lncRNAs from prior mechanistic studies.
