HP1a depletion and TGFß activation exert antagonistic effects on 3D genome organization

The three-dimensional (3D) organization of the human genome plays a critical role in regulating gene expression and is frequently disrupted in cancer. However, how key factors like Heterochromatin Protein 1 alpha (HP1a) and Transforming Growth Factor beta (TGFß) remodel this architecture to drive tumorigenesis remains poorly understood. We investigated the effects of HP1a knockdown and TGFß treatment on higher-order chromatin structure and gene expression in human mammary epithelial cells. Our findings reveal that HP1a depletion and TGFß stimulation exert distinct and opposing effects on genome compartmentalization and subcompartmentalization. HP1a knockdown drives a genome-wide shift of chromatin from transcriptionally inactive B compartments to active A compartments. This is accompanied by a stepwise redistribution of A subcompartments toward the most transcriptionally active state (A3), and the upregulation of oncogenic genes involved in EMT and proliferation. In contrast, TGFß treatment promotes chromatin compaction, increases the proportion of B compartments, and drives a stepwise reduction in active A subcompartments. Our results highlight the differential roles of HP1a and TGFß in shaping the 3D genome and underscore how precise, stepwise architectural changes contribute to malignant transformation. This study provides critical insight into how chromatin architecture acts as a regulatory layer in breast cancer development. Overall design: We generated Hi-C and RNA-seq datasets for MCF10A, MCF10A HP1a knockdown, and MCF10 treated with TGFB cell lines to investigate changes in 3D genome conformation and the impact on gene expression.