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Fig. 6 | Genome Biology

Fig. 6

From: Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription

Fig. 6

EpiGo-KRAB-mediated H3K9me3 deposit does not result in widespread gene silencing. a H3K9me3 and RNA levels in EpiGo-Control (dCas9) and EpiGo-KRAB (dCas9-KRAB) cell lines. ChIP-seq of H3K9me3 and RNA-seq were performed in these two cell lines. Region 1 (chr19: 48,800,000–51,200,000, cyan) or region 2 (chr19: 51,200,001–52,300,000, pink) of C19Q-1 with different transcriptional states was highlighted with cyan or pink respectively. b H3K9me3, H3K4me3, H3K27ac states and RNA level in region 1. ChIP-seq of H3K9me3, H3K4me3, H3K27ac, and RNA-seq were performed in EpiGo-Control (dCas9) and EpiGo-KRAB (dCas9-KRAB) cell lines. KDELR1 gene or CYTH2 gene were highlighted with light orange or light green respectively. c H3K9me3, H3K4me3, H3K27ac states and RNA levelin region 2. KLK6 gene or CTU1 gene were highlighted with light orange or light green respectively. d Fold changes of mRNA level and H3K9me3 in the EpiGo-KRAB targeted genes. The active genes (FPKM ≥ 1) targeted by EpiGo-KRAB were chosen for the analysis. The five genes (KCNN4, KDELR1, HSD17B14, KLK6, and TNNT1) with most reduction in mRNA levels were marked in red. e Fold changes of mRNA level and H3K4me3 in the EpiGo-KRAB targeted genes. f Fold changes of mRNA level and H3K27ac in the EpiGo-KRAB targeted genes

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