Extended Data Fig. 7: Allele-specific analysis of H3K4me3 HiChIP and scATAC-seq data in WT and Msl2-KO NPCs.
(a) Scheme illustrating the allele-specific analysis for H3K4me3 HiChIP data. Our pipeline started off with an alignment and quality control with HiC-Pro, followed by SNP-based separation of aligned reads. The separated reads were then processed with the normal HiChIP pipeline using MAPS (see Methods). (b) Summary of the chromatin contacts between Vcan and Sox2 promoter and distal sites in the surrounding region (+/− 550 kb) in female 9sCa WT and Msl2-KO NPCs scored by H3K4me3 HiChIP. The height of chromatin contacts indicates the observed contacts number/maximum contacts number within the sample. (c) Proportion of genes with promoter-enhancer contacts in female 9sCa WT NPCs identified by H3K4me3 HiChIP. (d) Aggregation of H3K4me3 HiChIP interactions at pairwise promoter-enhancer combinations of bi-to-mono (top) and bi-to-bi-down (bottom) genes in female 9sCa WT and Msl2-KO NPCs. H3K4me3 HiChIP interactions are the mean observed over expected contact ratios of Hi-C matrices with a 10 kb bin size. The scale represents mean observed over expected chromatin contacts. (e) Changes in the numbers of promoter-enhancer contacts at bi-to-monoA2 and bi-to-monoA1 genes in female 9sCa WT and Msl2-KO NPCs (left). Changes in the distribution of the distance between promoters and enhancers at bi-to-monoA2 and bi-to-monoA1 genes in WT and Msl2-KO female 9sCa NPCs (right). Significance was determined by nonparametric Wilcoxon rank-sum test (two-sided), exact p-values are indicated in the figure. Sample sizes for statistical tests are bi-to-monoA2: n = 90 and bi-to-monoA1: n = 58. For details on the boxplots, see Methods. (f) Summary of enhancer-promoter contacts of the bi-to-monoA2 genes Mecp2 (top) and Morf4l2 (bottom) in the surrounding region (+/− 550 kb) in female 9sCa WT and Msl2-KO NPCs. For visualization, the height of the contacts indicates the number of enhancer-promoter contacts divided by the maximum enhancer-promoter contact number per sample. MSL2 ChIP-seq (IP/Input) tracks and HiC data in female 9sCa WT NPCs are indicated. (g) MSL2 ChIP-seq metagene profiles (IP/Input) in male CaBl/BlCa and female 9sCa WT NPCs for bi-to-monoA1 genes showing biallelic binding at enhancers and promoters. Shadows in the profiles represent standard errors. (h) Changes in the numbers and co-accessibility scores of promoter-enhancer contacts identified by scATAC-seq analysis at bi-to-monoA2/A1 and bi-to-bi-down genes in male CaBl (left) and BlCa (right) WT and Msl2-KO NPCs. Significance is determined by nonparametric Wilcoxon rank-sum test (two-sided), exact p-values are indicated in the figure (see Supplementary Fig. 6 for details on the analysis). Sample sizes for statistical tests are as follows: male CaBl NPCs (top to bottom): n = 73, 81, 143; male BlCa NPCs (top to bottom): n = 94, 76, 348. For details on the boxplots, see Methods. (i) Summary of the Cicero co-accessibility links between the promoter of indicated genes and distal sites in the surrounding region (+/− 550 kb) in male BlCa (left) and CaBl (right) WT and Msl2-KO NPCs. The height of contacts indicates the magnitude of the Cicero co-accessibility score between the connected peaks. Peaks constructed from allele 1 (magenta) and allele 2 (cyan) are indicated (see Supplementary Fig. 6 for details on the analysis). (j) Motifs of overrepresented transcription factors (see Fig. 4a) derived from motif enrichment analysis of enhancers (left) and promoters (right) on the remaining active allele of bi-to-mono genes in male CaBl/BlCa and female 9sCa Msl2-KO NPCs (see Methods).
