Active chromatin lncRNAs
Characterization of repressive chromatin associated lncRNAs
Divergent XH lncRNAs are overrepresented in active chromatin compartments (WDR5 + H3K4me2). a) Scatter plot showing enrichment of WDR5 lncRNAs over nuclear input. The X-axis denotes log transformed expression and Y-axis denotes log-fold change of WDR5 lncRNAs over nuclear input. Venn diagram, in the Scatter plot, shows 209 lncRNAs that are commonly enriched in both H3K4me2 and WDR5 ChRIP pulldowns. b) Genomic organization of H3K4me2 lncRNAs (green bars) with respect to nearest protein-coding genes (grey bars). XH: where lncRNA shows Head-to-Head arrangement with nearby protein-coding gene. XT: lncRNA in Tail- to-Tail arrangement with protein-coding gene, XI: lncRNA located inside a protein- coding gene, XO: lncRNA located outside and covers the entire protein-coding gene. Sense pairs means lncRNAs in the same orientation as protein-coding gene. The notion of greater or less than 2 kb means that the partner genes (pPCGs) are located within 2 kb (<2 kb) or away from 2 kb (> 2 kb) but within 50 kb window with respect to H3K4me2 lncRNAs. c) Distribution of different patterns of genomic arrangements as described in (b) for active chromatin associated lncRNAs (WDR5 + H3K4me2) and non-chromatin associated lncRNAs (non-CAR).
Active chromatin associated lncRNA (Active lncCAR) regulating protein coding gene in cis via maintaining and establishing active chromatin marks
a) Enrichment of H3K4me2, H3K4me3, and WDR5 ChIP-seq signals over active chromatin associated lncRNAs (active XH lncCARs) (in green, n = 98) and non-CAR XH lncRNA (in black, n = 335) promoters (±2 kb) in BT-549 cells. The signals presented in the plots represent log2ratio between ChIP and input sample. TSS denotes the transcription start site of lncRNAs.
H3K4me2 and H3K4me3 occupancy upon WDR5 depletion. b) H3K4me2 and H3K4me3 ChIP-seq signals at the promoter regions (±2 kb) of active chromatin associated lncRNAs in Control and upon WDR5-esi depletion. The signals presented in the plots represent log2ratio between ChIP pull-down and input sample. TSS denotes the transcription start site of active XH lncCARs or non-CAR XH lncRNAs. The solid lines in the plot represents H3K4me2 and H3K4me3 signal in control esiRNA transfected cells and dotted lines represents WDR5 esiRNA transfection.