Supplementary Fig. 6: Locus-specific binding of MTHFD1.

ChIP-seq results for BRD4 and MTHFD1 immunoprecipitation in HAP1 WT (WT) and MTHFD1 knock-out (KO) cells. a, Number of ChIP-seq peaks detected for each protein in WT cells. b, Amount of overlap between peaks of MTHFD1, BRD4 or H3K27ac in WT or KO cells measured by the fractional overlap, total intersection or the Jaccard index (intersection over the union of peaks). c, GREAT enrichment analysis for binding sites of BRD4 and MTHFD1 in HAP1 WT cells. The hypergeometric test and Benjamini Hochberg multiple test correction were employed. d, Volcano and scatterplots comparing binding in KO to WT cells, with significantly bound sites (FDR adjusted p-value < 0.1 and absolute log2 fold change > 1) marked in red. Differential regions were discovered with the Wald test using the DiffBind package with n = 2 biologically independent experiments. P-values were adjusted with the Benjamini-Hochberg method. e, Normalized ChIP-seq signal in differential regions bound by MTHFD1 or BRD4; f, Global differences in differentially bound MTHFD1 or BRD4 sites upon MTHFD1 KO. A two-sided Mann-Whitney U-test was used to assess significance.