Irastorza-Azcarate Ibai, Kukalev Alexander, Kempfer Rieke, Thieme Christoph J, Mastrobuoni Guido, Markowski Julia, Loof Gesa, Sparks Thomas M, Brookes Emily, Natarajan Kedar Nath, Sauer Stephan, Fisher Amanda G, Nicodemi Mario, Ren Bing, Schwarz Roland F, Kempa Stefan, Pombo Ana
Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, 10115, Berlin, Germany.
Humboldt-Universität zu Berlin, Berlin, Germany.
Mol Syst Biol. 2025 May 6. doi: 10.1038/s44320-025-00107-3.
Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high density of single-nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, and with Polycomb occupancy. We show that histone genes are expressed with allelic imbalance in mESCs, and are involved in haplotype-specific chromatin contacts marked by H3K27me3. Conditional knockouts of Polycomb enzymatic subunits, Ezh2 or Ring1, show that one-third of ASE genes, including histone genes, is regulated through Polycomb repression. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.
遗传变异和三维染色质结构在基因调控中起主要作用。由于在以单倍型特异性分辨率绘制染色质构象方面存在挑战，遗传序列变异对三维基因组结构和基因表达失衡的影响仍未得到充分研究。在这里，我们将基因组架构图谱（GAM）应用于具有高密度单核苷酸多态性（SNP）的杂交小鼠胚胎干细胞（mESC）系。GAM以高灵敏度解析了单倍型特异性三维基因组结构，揭示了染色质区室、拓扑相关结构域（TAD）、长程增强子-启动子相互作用和CTCF环中的广泛等位基因差异。结构差异通常与基因表达中的等位基因特异性差异以及多梳蛋白占据情况一致。我们表明，组蛋白基因在mESC中以等位基因失衡的方式表达，并参与以H3K27me3标记的单倍型特异性染色质相互作用。多梳蛋白酶亚基Ezh2或Ring1的条件性敲除表明，包括组蛋白基因在内的三分之一的等位基因特异性表达（ASE）基因是通过多梳蛋白抑制来调控的。我们的工作揭示了同源染色体之间高度不同的三维折叠结构，并突出了它们与等位基因表达的复杂联系。
