Figure 6. PRDM9-bound regions (H3K4me3 and H3K36me3) are a stronger recruiter of ZCWPW1 than promoters (H3K4me3 only).

For any given level of H3K4me3 (x-axis), ZCWPW1 enrichment (y-axis) is higher at PRDM9-bound regions (red) than regions with pre-existing H3K4me3 (promoters, blue). H3K4me3 and ZCWPW1 were force called in 100bp windows across all autosomes. These windows were split into two sets defined as indicated in the legend (where ‘p’ is the p-value from peak-calling required for a window to be included in the subset) with the additional constraint of requiring input fragment coverage >5 for ZCWPW1 and >15 for H3K4me3. p: p-value for non-zero level of input corrected coverage in that bin. ‘pre-existing H3K4me3’ refers to H3K4me3 that is present without transfection (of either PRDM9 or ZCWPW1), which is mainly found at promoter regions. For each subset, H3K4me3 was split into 25 bins with equal number of data points. Horizontal bars: two standard errors of the mean. Vertical dotted bars: upper and lower quartiles. Grey ribbons show two standard errors for a Generalized additive model on log(mean H3K4me3 enrichment + 0.1). Dashed black horizontal line highlights that the mean enrichment of the highest bin for promoters is similar to that of the lowest bin for PRDM9-bound sites.

Figure 6—figure supplement 1. ZCWPW1 binding is positively associated with levels of both H3K4me3 and H3K36me3 marks.

Fraction of ZCWPW1 peaks (co-transfected with PRDM9 with input coverage of at least 5) that overlap either (A) H3K4me3 or (B) H3K36me3 peaks, for different bins of ZCWPW1 enrichment (100 equal sample size bins of increasing ZCWPW1 enrichment). Error bars show ±2 s.e. of the proportion. ‘Randomised’ shows expected proportions when x-axis regions are randomly shifted within a range of 100 million bases (or the chromosome size if lower). Dotted lines show overall means for each colour.

Figure 6—figure supplement 2. Enrichment from 100-bp non-overlapping windows, genome-wide, is binned into 100 equal sample size bins by either.

(A) H3K4me3 or (B) H3K36me3 levels, and mean enrichment of ZCWPW1 co-transfected with PRDM9 is plotted for each bin (error bars show ±2 s.e. of the mean). This is in some sense opposite (but complementary) to Figure 6—figure supplement 1 in which the subject of the axis is reversed. Windows with evidence of PRDM9-independent H3K4me3 have been removed from the H3K4me3 plot. Additionally, x-axis regions were removed if input reads were <15 and y-axis regions if <5. 0.01 has been added to the x-axis values in order to display enrichment estimates of zero on the log scale.