yHSC AThi oHSC ATlo oHSC ATAC-Seq - Differences in Chromatin Accessibility in Autophagy engaging vs non-autophagy engaging old hematopoeitic stem cells (HSC) comapred to young HSC.
Experiment was designed to assess differences in chromatin accessibility across the three indicated HSC populations of interest. By ATAC-seq, we observed large differences in chromatin accessibility between young and old HSCs. However, we found that the chromatin accessibility landscape of AThi and ATlo oHSCs was largely conserved, with no statistically different peaks between the two oHSC subsets and predominantly shared peaks differentially accessible between oHSC subsets and yHSC. Both oHSC subsets had a unidirectional increase in peak accessibility across greater than four thousand statistically significant loci compared to yHSCs, indicating epigenetic de-repression with aging. Pathway analysis of ATAC-seq peaks differing between oHSCs and yHSCs revealed epigenetic poising towards engagement of inflammatory responses, cell stress, and altered metabolic programs in both AThi and ATlo oHSC subsets, with some of the most differentially accessible peaks located in the promoters of genes involved in lipid metabolism. These results suggest that cellular responses associated with oHSC dysfunction are, to some extent, embedded in their epigenetic state. Overall design: Paired AThi/ATlo oHSC biological replicates and 5 yHSC replicates were generated over 2 isolation and transposition days for ATAC-seq.