Multi-omic gene regulatory networks informed by 3D chromatin architecture reveal insights into hematopoietic stem cell ageing

During ageing, hematopoietic stem cells (HSCs) have reduced regenerative potential, skewed differentiation toward the myeloid lineage, and heightened susceptibility to clonal expansion and malignancy. While epigenetic alterations are well documented, the impact of aging on higher-order 3D chromatin architecture remains poorly understood. Here, we examined the 3D genome organisation of aged murine HSCs using in-situ Hi-C then integrated this with gene expression and chromatin accessibility data to build HiC-informed gene regulatory networks (GRNs). Aged HSCs display erosion of topologically associating domain (TAD) boundaries, A/B compartment switching, and reorganised enhancer-promoter loops associated with lineage-inappropriate gene expression. Our GRN analysis identifies a hierarchy of transcription factors, including a c-Maf-Lyl1-Mnt axis that orchestrates the transition from a youthful to aged state and a Gfi1-Sox4 axis in young HSCs that regulates Bach1. This study provides a structural blueprint for aging HSCs and defines specific regulatory targets for potential reprogramming interventions to restore hematopoietic youthfulness.