Epigenetic and transcriptional changes in aging mouse rod photoreceptors [CUT&RUN]

Aging-associated functional decline and disease susceptibility are believed to be mediated, at least in part, through alterations in the epigenome. To explore epigenetic changes that might influence visual function with advanced age, we performed whole genome bisulfite sequencing of purified mouse rod photoreceptors at four different ages and identified 2054 genomic regions that gain or lose DNA methylation. Differentially methylated regions (DMRs) clustered at chromosomal hotspots, especially on Chromosome 10 that included a longevity interactome. DMRs were preferentially detected at an early stage of aging in long neuronal genes and in rod-specific regulatory regions containing open chromatin domains and H3K27 acetylation. Integration of methylome to age-related transcriptome changes, chromatin signatures and first order protein-protein interactions uncovered an enrichment of DMRs in pathways associated with aging, longevity, synaptic function, and energy homeostasis. In concordance, we detected reduced mitochondrial maximum reserve capacity with retinal age in ex vivo assays. Our study reveals age-dependent genomic and chromatin features susceptible to DNA methylation changes in rod photoreceptors and identifies associations with established and cell type-specific pathways altered in aging. Overall design: Flow-sorted rod photoreceptors from 3M male mice (H3K27ac: n = 4, H3K27me3: n = 6) were cryopreserved in a solution of HBSS containing 10% DMSO and slowly frozen using a Mr.FrostyTM container (Invitrogen, CA, USA). CUT&RUN was performed as previously described (Skene and Henikoff 2017) using 200-300,000 cells per experiment.