Extended Data Fig. 3: Genome-wide colocalization between H3K36me2 and DNMT3A2 in mouse ES cells.

a, Immunoblots of lysates generated from parental and sgDnmt3a mouse ES cells (termed mESCs in the Extended Data figures) that ectopically express HA-tagged DNMT3A2. Vinculin was used as a loading control. Endogenous expression of the long isoform (DNMT3A1) and the short isoform (DNMT3A2) of DNMT3A is indicated. Data are representative of two independent experiments. b, ChIP–seq normalized reads of HA-tagged DNMT3A2 in sgDnmt3a relative to parental ES cells for 100-kb non-overlapping bins (n = 26,181). Pearson’s correlation coefficient is indicated. c, Genome browser representation of ChIP–seq normalized reads for H3K36me3, H3K36me2, DNMT3A2 and DNMT3B in ES cells at Chr12: 86.6–87.5 Mb. RefSeq genes are annotated at the bottom. The shaded areas indicate H3K36me2-enriched intergenic regions (orange) and H3K36me3-enriched genic regions (green) in parental cells. For H3K36me2 and DNMT3A2, ChIP–seq was performed once and an independent ChIP was performed in which genomic regions of selective enrichment and depletion were confirmed by qPCR. H3K36me3 and DNMT3B ChIP–seq were performed once. d, ChIP–seq normalized reads per 10-kb bin for DNMT3A2 (y axis) and DNMT3B (x axis) in ES cells (n = 246,285). Bins (dots) are colour-coded on the basis of differences between H3K36me3 and H3K36me2 ChIP–seq reads, to show selective enrichment for H3K36me2 (orange) or H3K36me3 (green). e, De novo methylation per bin by DNMT3A2 (brown) or DNMT3B (grey) after reintroduction into Dnmt1, Dnmt3a and Dnmt3b triple-knockout ES cells relative to H3K36me3. To generate bins, 1-kb genomic tiles (n = 2,462,755) were ranked by H3K36me3 enrichment in ES cells and grouped into 1,000 bins, ordered by rank (2,463 tiles per group). The dashed lines indicate H3K36me3 enrichment per bin. Goodness of fit was computed using a quadratic model (red lines). For gel source data, see Supplementary Fig. 1.