have yet to be identified by genome-wide Hidden Markov Model (HMM) based chromatin studies. One of the reasons for this may be a low level of all histone modification signals in lncRNA gene promoters corresponding to low expression of lncRNAs, making these promoters appear more heterochromatin-like than protein-coding gene promoters. Another possibility is that due to high tissue-specificity of lncRNA expression, most lncRNA genes are repressed in each cell type from the limited repertoire of cells that we analyzed. LncRNAs can impact regulatory outcomes despite their low expression levels; for instance, the XIST lncRNA, expressed as a single genomically-tethered copy, recruits repressive histone modifiers to the allele from which it was expressed, leading to the inactivation of nearly an entire X-chromosome [69]. Therefore, the promoter characteristics of low-abundance, but functional, lncRNAs merit inclusion in future global definitions of human promoterome properties. A growing number of lncRNAs has recently been shown to exert diverse regulatory functions. Our characterization of the global selective regulation of lncRNA genes places three known human transcription factors at the nexus of empirical and computational evidence for their role in such regulation, enhancing our understanding of how the relationship of TFs and their lncRNA gene targets impacts
