Extended Data Fig. 3: Epigenomic features of human and chimpanzee iPSC-induced neurons.
From: Comparative characterization of human accelerated regions in neurons
a, Histograms showing the number of interactions for promoters in human and chimpanzee neurons. b, Cumulative distribution function (CDF) plots of chromatin interaction distances in human and chimpanzee neurons. c, Summary of the percentage of chromatin interactions corresponding to promoters with distal regions (XOR) and promoters with promoters (AND). d, Comparison of shared interactions between human and chimpanzee neurons. e, Bootstrap distribution of shared interaction ratios calculated between shuffled interactions (shuffled 1000 times) and human or chimpanzee interactions. The red dashed line indicates the actual shared interaction ratio between human and chimpanzee interactions. f, Comparison of shared accessible peaks between human and chimpanzee neurons. g, Bootstrap distribution of shared accessible peak ratios calculated between shuffled accessible peaks (shuffled 1000 times) and human or chimpanzee accessible peaks. The red dashed line indicates the actual shared accessible peaks ratio. h, Numbers of accessible peaks overlapping with H3K4me3-associated interactions in human and chimpanzee neurons. i, Bootstrap distribution of shared accessible peaks ratios related to H3K4me3-marked interaction calculated between shuffled accessible peaks (shuffled 1000 times) and human or chimpanzee accessible peaks related to H3K4me3-marked interactions. The red dashed line indicates the actual shared accessible peak ratios related to H3K4me3-associated interactions. j, Bar graph of the proportion of interactions in each study related to HAR sequences. k, Venn diagram shows the overlapping chromatin interactions with HARs between different studies24,25. l, Gene Ontology enriched terms for HAR- and HAR ortholog-interacting genes. P-values of enrichment analyses were conducted with the enrichGO with Benjamini-Hochberg adjustment. m, Linear regression analysis of gene expression associated with HARs and their orthologs in humans and chimpanzees. Coefficient values for both gene groups and OCNSs were calculated based on Meyer et al.55. Group I includes 374 and 377 genes interacting with accessible HARs or HAR orthologs, Group II includes 346 and 274 genes interacting with non-accessible HARs or HAR orthologs, and Group III includes 999 and 974 genes close to HARs or HAR orthologs but without interaction in human and chimpanzee neurons, respectively. n, Human and chimpanzee allele frequencies for 20,020 variants across 3,257 HARs based on the gnomAD database71.
