Gene expression noise dynamics unveil functional heterogeneity of ageing hematopoietic stem cells

Summary Variability of gene expression due to stochasticity of transcription or variation of extrinsic signals, termed biological noise, is a potential driving force of cellular differentiation. While unicellular organisms exploit noise as a bet-hedging strategy, its role during multilineage differentiation of stem cells is underexplored. Utilizing single-cell RNA-sequencing to reconstruct cell state manifolds, we developed VarID2, a method for the quantification of biological noise at single-cell resolution. VarID2 reveals enhanced nuclear versus cytoplasmic noise across cell types of the peripheral blood, and distinct regulatory modes stratified by correlation between noise, expression, and chromatin accessibility. Noise levels are minimal in murine hematopoietic stem cells and increase during both differentiation and ageing. Differential noise identified myeloid-biased Dlk1+ long-term-HSCs in aged mice with enhanced quiescence and self-renewal capacity. VarID2 reveals fundamental properties of noise across cellular compartments, during stem cell differentiation and ageing, and uncovers distinct cellular sub-states invisible to conventional gene expression analysis.