Hematopoietic stem cells (HSCs) are responsible for continually replenishing the blood system with mature cells, ensuring immune competence and tissue homeostasis. However, during ageing, HSCs have reduced regenerative potential, skewed differentiation toward the myeloid lineage, and heightened susceptibility to clonal expansions and malignancies. Recent studies have illuminated the role of three-dimensional (3D) genome architecture as an additional, critical layer of stem cell regulation. Techniques such as Hi-C can capture how chromosomes fold within the nucleus, revealing interactions between genes and their regulatory elements. We examine the 3D genome organisation and gene regulatory network changes in young versus aged murine HSCs using in situ Hi-C to map the interactions between chromatin regions, then integrated this with gene expression and chromatin accessibility data.
Similar to results in other ageing cell types, our Hi-C analysis of aged vs young HSCs show erosion of topologically associating domain (TAD) boundaries, shifts between active (A) and inactive (B) compartments, and reorganised enhancer–promoter loops. These 3D structural changes are often closely tied to age-related activation & myeloid pathways and altered regions additionally show enrichment for certain transcription factor motifs. However, there is also an age-associated increase in informational (Shannon) entropy and a reorganisation of chromatin associated with lineage-inappropriate gene expression of non-HSC genes. Our work further demonstrates that age-related epigenetic changes likely contribute to HSC ageing and functional decline while highlighting the role of certain transcription factors as potential targets for cell reprogramming interventions to restore the gene regulatory network to a more youthful state.