Extended Data Fig. 6: Rhi chromodomains associate with regions co-occupied by H3K9me3 and H3K27me3.
a, Schematic showing the experimental workflow and cartoon of the dual-CD constructs used in the assay. b, Venn diagram showing overlap between CD2xPc binding, H3K27me3, H3K9me3, and Rhi across 125,499 genomic 1 kb bins. Signal was considered to be present if the bin overlapped a MACS2 broad peak (q < 0.05, broad-cutoff<0.1) present in at least two biological replicates. c, Scatter plot depicting CUT&RUN signal (fpkm) of uniquely mapping reads in 1 kb bins of CD2xRhi versus CDPc-CBX1 in S2 cells (average of 2-3 replicate experiments each). d, Heatmap and hierarchical clustering (Euclidean distance) of CUT&RUN signal detected for the indicated chromodomain constructs and histone modifications [log10(fpkm)]. e, Same as d, but across a subset of the genome classified as heterochromatin (10,180 out of 125,499 1 kb bins). f, UpSet plot showing all major intersections ( > 100 1 kb bins) across the six indicated CUT&RUN experiments. g, as in c but showing CD2xRhi versus CD2xPc (average of 2 replicate experiments each). h, as in c but showing CD2xRhi versus CD2xCBX1 (average of 2 replicate experiments each). i, Western blot analyses showing Kipf expression in S2 cells (treated as indicated) or w1118 ovaries. Tubulin is shown as loading control (experiment was repeated twice with similar results). j, Western blot analyses showing the levels of the indicated chromodomain constructs (Flag) in S2 cells that were transfected with the corresponding plasmids. Tubulin is shown as loading control (similar results were obtained in two independent experiments). k, Scatter plot depicting CUT&RUN signal (fpkm) of uniquely mapping reads in 1 kb bins of CD2xCBX1 upon control or kipf knockdown in S2 cells (1 replicate experiment).l-n, as in k but depicting CD2xPc, CDPc-CBX1, and CD2xRhi, respectively (2-3 replicate experiments each, as indicated).
