Fig. 4: Functional and structural consequences upon disrupting heterochromatin structure.

a, b Representative two-color STORM images showing the spatial relationship between DNA and active (phosphorylated) RNAP II in control NIH-3T3 cells and those cells with SUV39h1 knockdown (siSUV39h1). Green: phosphorylated RNAP II (labeled by Alexa 647); Red: DNA (labeled by CF568). Scale bars, 4 µm and 500 nm in the original and magnified images, respectively. c Local density map of DNA (quantified by Voronoi polygon density) of control and SUV39h1 knockdown cells. d Average histogram distribution of intra-nuclear local density of control and SUV39h1 knockdown cells. The solid curve shows the average RDF from all measured nuclei and the shaded area shows the standard error. e Western blotting of H3K9me3 and phosphorylated RNAP II with tubulin as an internal reference in control cells and those cells with SUV39h1 knockdown (siSUV39h1). f–h Quantitative analysis of DNA nanodomain size (n = 12 and 24 cells, respectively), active RNAP II (n = 24 and 24 cells, respectively) cluster size and the percentage of DNA that overlaps with active RNAP II (n = 14 and 27 cells, respectively) in control and cells with SUV39h1 knockdown. i γH2AX immunofluorescence and quantification of γH2AX foci numbers in control (n = 43 cells) and cells with SUV39h1 knockdown (n = 29 cells). Error bars: mean ± 95% CI. All P values were determined using Mann−Whitney test. j Cytogenetic analysis of chromosomal aberration in control cells or SUV39h1 knockdown cells. The enlarged regions showed chromosomes with breaks pointed by red arrows. Error bars: mean ± standard error, over 30 cells were counted per group in four randomly assigned groups. The full western blots are provided as Source data.