Fig. 5: PmutNgn2 enhances 3D genome and DNA methylation changes.

a, Contact probability as a function of the genomic distance. Lines: mean values from biological replicates; semi-transparent ribbons: s.e.m. obs/sum (obs), normalized contact probability. b, Knight–Ruiz balanced contact matrices for Chr 3 at 250-kb resolution (top) and DNA methylation (bottom). c, Average contact enrichment between pairs of 250-kb loci arranged by their eigenvalue (shown on top). Numbers represent the compartment strength. d, Average contact enrichment (top) and DNA methylation levels (bottom) across TADs. e, Aggregated Hi-C plots between intra-TAD pairs of the top 5,000 Ngn2 ChIP-seq peaks. f, Quantification of the interaction strength of intra-TAD contact pairs depicted in e (n = 6,888 pairs). g, Average DNA methylation plots at the distal regions within the top 5,000 Ngn2 ChIP-seq peaks. h, Quantification of the average DNA methylation at the sites depicted in g (n = 4,125 regions). i, Box plots depicting the interaction strength of intra-TAD cluster-specific positively correlated EGPs (n = 1,853, 1,795 and 3,852 pairs, respectively). j, Average DNA methylation plots at enhancers belonging to cluster-specific EGPs. k, Quantification of DNA methylation levels at enhancers belonging to cluster-specific EGPs (n = 1,568, 1,661 and 3,275 regions, respectively). l, Density scatter plots showing iN_2 E–P contact strengths. m, Same as l but for DNA methylation. n, Contact map (top) and aggregated accessibility of matched single-cell ATAC-seq clusters (bottom) at the Mdga1 locus. Depicted are the identified linked enhancers (arcs), colored by the Pearson correlation of the enhancer accessibility and Mdga1 expression. Dashed circles highlight dynamic E–P interactions. The shaded region highlights the Mdga1 locus and its associated contact map (top) and the aggregated accessibility of matched single-cell ATAC-seq clusters (bottom). Statistical significance in f, h–i and k was calculated using a two-sided paired Wilcoxon rank-sum test. Obs and exp refer to observed and expected chromatin contacts, respectively. All box plots display median (line), 25th or 75th percentiles (box) and 10th or 90th percentiles (whiskers). All experiments were performed with murine cells.