Extensive folding variability between homologous chromosomes in mammalian cells

Area of Science:

• Genomics
• Epigenetics
• Molecular Biology

Background:

• Genetic variation and 3D chromatin structure are crucial for gene regulation.
• Understanding how sequence variations affect 3D genome organization and gene expression imbalance is challenging due to limitations in haplotype-specific mapping.

Purpose of the Study:

• To investigate the impact of genetic variation on 3D genome structure and allele-specific gene expression using haplotype-resolved methods.
• To identify the role of Polycomb repression in regulating allele-specific gene expression.

Main Methods:

• Application of Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high single-nucleotide polymorphism (SNP) density.
• Analysis of haplotype-specific chromatin compartments, topologically associating domains (TADs), enhancer-promoter contacts, and CTCF loops.
• Investigation of Polycomb occupancy and the effects of Ezh2 and Ring1 knockouts on allele-specific expression (ASE).

Main Results:

• GAM successfully resolved haplotype-specific 3D genome structures with high sensitivity.
• Extensive allelic differences were observed in chromatin architecture, including compartments, TADs, and loops, often correlating with allele-specific gene expression and Polycomb occupancy.
• Histone genes exhibit allelic imbalance and haplotype-specific chromatin contacts marked by H3K27me3, with one-third of allele-specific expression genes regulated by Polycomb repression.

Conclusions:

• Homologous chromosomes exhibit distinct 3D folding structures.
• Genetic variation significantly influences 3D genome organization, leading to allele-specific gene expression.
• Polycomb repression plays a key role in regulating allele-specific gene expression, including that of histone genes.