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Fig. 1 | Genome Biology

Fig. 1

From: PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications

Fig. 1

PIRCh-seq enables effective chromatin-RNA association in vivo. a Schematic representation of PIRCh approach followed by high-throughput sequencing. b The overall enrichment of the H3 PIRCh-seq signal (bottom) over input (top) of lncRNA XIST in human female fibroblasts (fold change = 19). Read counts were normalized to sequencing depth of 10 million. c PIRCh-qPCR analysis in mouse neuronal stem cells (NSCs, orange) and adult brain (purple) shows that Xist is enriched on chromatin H3 compared with Actin control. d, e Normalized input and PIRCh-seq profiles with histone modifications of H3K4me3, H3K27ac, and H3K27me3 at the lncRNA Xist (d) and lnc-Nr2f1 (e) locus in mouse neuronal precursor cells (NPC). Dash lines represent fold change of PIRCh-seq over input and smoothed by 500 bp sliding windows. The boxed region represents the RepC domain on Xist. f Normalized input and ChIRP-seq profiles of lncRNA lnc-Nr2f1 in NPC, and H3K4me3, H3K27ac, H3K4me1, and H3K27me3 ChIP-seq profiles in NPC. Showing Clcn4 gene locus as an example. g Normalized log2 fold change of ChIP-seq signal over input around (± 10 kb) lnc-Nr2f1 ChIRP-seq peaks in NPC

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