Single-cell multiome uncovers differences in glycogen metabolism underlying species-specific speed of development [mTORi]

Embryos from different mammalian species develop at characteristic timescales. These timescales are recapitulated during the differentiation of pluripotent stem cells in vitro. Specific genes and molecular pathways that modulate cell differentiation speed between mammalian species remain to be identified. Here we use single-cell multi-omic analysis of neural differentiation of mouse, cynomolgus monkey and human pluripotent cells to identify new regulators for differentiation speed. We demonstrate that species-specific differences in transcriptome dynamics are mirrored at the chromatin level, but that, contrary to other developmental contexts, the speed of neural differentiation is insensitive to manipulations of cell growth and cycling. Exploiting the single-cell resolution of our data, we identify glycogen storage levels regulated by UGP2 expression as a new species-specific trait of pluripotent cells, and show that lowered glycogen storage in UGP2 mutant cells is associated with accelerated neural differentiation. The control of energy storage could be a general strategy for the regulation of cell differentiation speed. Neural differentiation of mouse, cynomolgus and human cells was assessed at day 0 (pluripotency), day 2 and day4. Upon the start of neural induction, 50 nM INK128 was added to half of the cells. To minimize batch effects, samples were multiplexed and pooled before mRNA capture and library preparation for each timepoint.