Universal and distinct features of intra-population heterogeneity between differentiated cells and pluripotent stem cells

Isogenic cells cultured in the same nutrient-rich environment show heterogeneity in their proliferation rate. To understand the differences between fast and slow-proliferating cells and to identify markers for proliferation rate that can be used at the single-cell level, we developed a method to sort cells by their proliferation rate, and performed RNA sequencing (RNA-Seq) on slow, medium and fast proliferating subpopulations of pluripotent mouse embryonic stem cells (mESCs) and immortalized mouse fibroblasts. We identified a core proliferation-correlated transcriptome that is common to both cell types, to yeast, and to cancer cells: fast proliferating cells have higher expression of genes involved in both protein synthesis and protein degradation. In contrast to cells sorted by proliferation rate, RNA-seq on cells sorted by mitochondria membrane potential revealed a highly cell-type specific mitochondria-state related transcriptome. mESCs with hyperpolarized mitochondria are fast proliferating, while the opposite is true for fibroblasts. In addition, cell-to-cell variation in proliferation rate is highly predictive of pluripotency state in mESCs, with cells of more naive pluripotent character having a slower proliferation rate. Finally, we show that the proliferation signature learned from sorted cells can predict proliferation from scRNAseq data in both mESCs and in the developing nematode. While the majority of the transcriptional-signature associated with cell-to-cell heterogeneity in proliferation rate is conserved from yeast to embryos to differentiated cells to cancer, the metabolic and energetic details of cell growth are highly cell-type specific.