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Fig. 7 | Genome Biology

Fig. 7

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

Fig. 7

EpiGo-KRAB induced de novo heterochromatin-like domain formation. a H3K9me3 states and RNA levels of region 1, region 2, and region 3 in EpiGo-Control (dCas9) and EpiGo-KRAB (dCas9-KRAB) cell lines. Region 1 (chr19: 48,800,000–51,200,000) representing an active region, region 2 (chr19: 51,200,001–52,300,000) representing a silenced region, and region 3 (chr19: 52,300,001–54,300,000) containing endogenous H3K9me3 was highlighted in cyan, pink, and yellow respectively. The target sites of C19Q repeats were shown in green. Oligopaint FISH probes were designed to detect region 1, region 2, and region 3 respectively. b Images of C19Q, HP1α and region 1, 2, or 3 in EpiGo-Control cell lines. C19Q (green) was labeled by GFP using CRISPR imaging, HP1α (magenta) was labeled by HaloTag, and region 1, 2, or 3 (blue) was labeled by in situ hybridization with DNA probes conjugated to the dye Alexa-647. The colocalization among C19Q, HP1α, and region 1, 2 or, 3 was shown in merged images. c Percentage of cells with one spot vs multiple spots in region 1, 2, or 3 of EpiGo-Control (dCas9) cell lines. n = 200 transfected cells in each experiment and the error bar is standard deviation (SD) from three independent experiments. d Percentage of foci association with HP1α in EpiGo-Control cell lines. The association or non-association is defined by overlapping (regardless of the degrees) or non-overlapping between foci and HP1α condensates. n = 16, 16, and 12 cells from left to right respectively. e Images of C19Q, HP1α and region 1, 2, or 3 in EpiGo-KRAB cell lines. All the conditions are the same as b except the dCas9 was replaced by dCas9-KRAB. f Percentage of cells with one spot vs multiple spots in region 1, 2, or 3 of EpiGo-KRAB (dCas9-KRAB) cell lines. n = 200 transfected cells in each experiment and the error bar is standard deviation (SD) from three independent experiments. g Percentage of foci association with HP1α in EpiGo-KRAB cell lines. The association or non-association is defined by overlapping (regardless of the degrees) or non-overlapping between foci and HP1α condensates. n = 10, 15, and 12 cells from left to right respectively

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