Extensive folding variability between homologous chromosomes in mammalian cells [GAM]

Genetic variation and 3D chromatin structure have major roles in gene regulation. Structural differences between genotypically different chromosomes and their effects on gene expression remain ill understood, due to challenges in mapping 3D genome structure with allele-specific resolution. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (ESC) line with high SNP density. Given its high efficiency of haplotype phasing, GAM resolves allele-specific 3D genome structures with high sensitivity. We discovered extensive genotype-specific folding of chromosomes in compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts and CTCF loops, often coinciding with allele-specific gene expression in association with Polycomb repression. We show that histone genes are expressed with allelic imbalance and involved in allele-specific chromatin contacts marked by H3K27me3. Functional analysis through conditional Ezh2- or Ring1b-knockdown shows a role for Polycomb repression in tuning histone protein levels. Our work reveals that the homologous chromosomes have highly distinct 3D folding structures, and their intricate relationships with gene-specific mechanisms of allelic expression imbalance. Genome architecture mapping (GAM) of mouse embryonic stem cells F123 (a male, hybrid cell line, derived from S129/Jae and Cast). Two biological replicates were collected. '0NP' samples have no nuclear profiles and were collected as negative controls. ‘1NP’ samples that passed quality control were merged into in-silico 3NP samples at the level of sergregation table.