Fig. 3: MSL2 maintains promoter–enhancer contacts.
a,c, ATAC–seq and histone modification ChIP–seq metagene profiles for bi-to-monoA1 genes in male CaBl (a) and bi-to-monoA2 genes in BlCa (c) WT (grey) and Msl2-KO (pink) NPCs. The log2[FC] of ChIP–seq levels (IP/input) are displayed with the standard error (shadows). b,d, RNA-seq, ATAC–seq, and H3K4me3 and H4K36me3 ChIP–seq tracks of Zfp560 in male CaBl (b) and BlCa (d) WT and Msl2-KO NPCs (left). The fold change of ChIP–seq (IP/input) is shown. Right, RNA expression (top) and chromatin accessibility (bottom) on WNN UMAPs for Decr1. e, The MSL2 ChIP–seq peak distribution in male CaBl and BlCa and female 9sCa WT NPCs at the promoters (TSS ± 1 kb) and enhancers identified in NPCs by EnhancerAtlas2.030. f, H3K4me3 HiChIP analysis identified promoter–enhancer contacts of Rab9 in the surrounding region (±550 kb) built from allele 1 (magenta) and allele 2 (cyan) and standard analysis (black) in female 9sCa WT and Msl2-KO NPCs. MSL2 ChIP–seq (IP/input) tracks and Hi-C data in female 9sCa WT NPCs are shown. g, Aggregation of in silico MSL2 HiChIP (MSL2 ChIP–seq + Hi-C) interactions (top) and randomly selected Hi-C interactions (bottom) at pairwise promoter–enhancer combinations of bi-to-mono genes in female 9sCa WT NPCs. h, MSL2 ChIP–seq (IP/input) metagene profiles in male CaBl and BlCa and female 9sCa WT NPCs at the enhancers and promoters of bi-to-monoA2 genes.
