Autophagy maintains metabolism and functional activity of a subset of aged hematopoietic stem cells [RRBS]

Autophagy is critical for protecting HSCs from metabolic stress. Here, we used a genetic approach to inactivate autophagy in adult HSCs by deleting the Atg12 gene. We show that loss of autophagy causes accumulation of mitochondria and an oxidative phosphorylation (OXPHOS)-activated metabolic state, which drives accelerated myeloid differentiation likely through epigenetic deregulations rather than transcriptional changes, and impairs HSC self-renewal activity and regenerative potential. To determine how loss of autophagy affects DNA methylation, we conducted enhanced reduce representation bisulfite sequencing (ERRBS) of purified control and Atg12 conditional knockout HSCs. Atg12flox/flox:Mx1-Cre conditional knockout mice and control Atg12flox/flox mice were injected with poly(I:C) at 4 week of age, and HSCs (Lin-/c-Kit+/Sca-1+/Flk2-/CD150+/CD48-) were isolated from the bone marrow of individual mice 2-3 months later. DNA was extracted from 4 mice per group, and ERRBS was conducted as described in the methods.