To understand the biological context of the heterochromatin CS enrichment at lncRNA gene promoters, we analyzed histone modification marks (HMs) in the ENCODE Tier 1 cell line GM12878. LncRNA gene promoters were significantly depleted of almost all histone modification marks, except for H3K27me3 and H3K9me3 (Figure 2, Figure S4). H3K27me3 contributes to maintenance of ‘bivalent domains’, transcriptionally-poised regions combining activating and repressing histone marks [50], [51], suggesting that lncRNA promoters are not permanently repressed and could be subject to activation under specific conditions. H3K9me3 marks transcriptional repression [52] but is also found in certain transcribed regions [53], and may be involved in elongation [54]. After the subsets of lncRNA and protein-coding genes with non-zero and similar expression levels in different cell lines were selected, lncRNA gene promoters demonstrated enrichment for H3K9me3 and surprisingly for H3K36me3 in all tested cell types. H3K36me3 is a mark of transcriptional elongation [55], [56]. Interestingly, lncRNA gene promoters demonstrate a decreased level of H3K27me3 and, in H1-hESC, an increased level of H3K27ac, a mark of active promoters and enhancers [57]. Taken together, these results support active chromatin organization of lncRNA promoters, yet distinct from the one of protein-coding genes.
