Several TFs regulated by specific lncRNAs emerge as potential global regulators of lncRNA transcriptome in our analysis. A representative example is PGR (progesterone receptor), a nuclear hormone receptor (NHR), whose predicted TFBSs are differentially enriched at lncRNA promoters. The human PGR gene itself is cis-regulated by two lncRNAs: an lncRNA containing primate-specific repetitive elements provides transcriptional regulation [34], [35] and another cis-antisense transcript acts post-transcriptionally [36]. Here, we show widespread genome-wide association of lncRNA promoters with the same TF families that have been previously implicated as regulatory targets of lncRNAs. The human NHR superfamily provides the most abundant evidence of preferential involvement in genome-wide lncRNA cis-regulatory programs: the TFBSs of 13 (27%) of the 48 total known human NHRs (PGR, NR1I2, NR1I3, NR2C2, NR2E3, NR5A2, RARG, ESR2, PPARG, HNF4A, RXRB, ERR1, and ERR2) were differentially enriched at lncRNA promoters.
