Epigenomic reconfiguration during aging of rod photoreceptors reveals a crosstalk between DNA methylation and stress pathways

Authors

• X Corso-Diaz
• R Rebernick
• C Jaeger
• F van Asten
• A Swaroop

Abstract

Aging is characterized by altered homeostasis and reconfiguration of the epigenetic landscape, including changes in histone and DNA chemical modifications. Although both stochastic and deterministic changes in DNA methylation have been observed in multiple mammalian tissues, the contribution of this modification to age-dependent functional decline and susceptibility to disease is poorly understood. Furthermore, most studies have used tissues containing mixed cell populations, which interferes with the identification of DNA methylation changes in cell-type specific loci. Visual function decline is evident in the aging human and mouse retina, and is accompanied by cellular and structural changes with photoreceptors being highly affected. Our aim is to identify biological pathways prone to DNA methylation changes during aging in purified rod photoreceptors. Genomic DNA from flow-sorted rod photoreceptors of 3 month (3M), 12M, 18M and 24M-old old male mice (n=3) was used for whole genome bisulfite sequencing (WGBS) to assess DNA methylation at single nucleotide resolution. Differentially methylated regions (DMRs) were identified using the R-package BSmooth. RNA-seq was performed for purified rods at corresponding ages. Open chromatin regions in 3M-old mice were assessed by ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) and analyzed using Homer. Gene Ontology (GO) analysis was performed using GOrilla and transcription factor (TF) motif enrichment using Genomatix. Aging rods (24M) exhibited more variability in their methylation pattern compared to younger rods (3M) and harbored 1160 DMRs (q < 0.01). Most DMRs were hypomethylated (1037/1160), localized to coding regions (685), and were enriched in neuronal genes. DMRs harbored TFs involved in chromatin architecture and oxidative stress, and 10% of intergenic DMRs were present in open chromatin regions, indicating dysfunction of distal regulatory elements. RNA-seq revealed that mitochondrial metabolism, protein degradation and neuronal function pathways were dysregulated with age. In summary, the DNA methylation pattern of rods is dynamic during aging with a preferential loss of methylation in neuronal genes and suggests a crosstalk with stress pathways and chromatin architecture. Our study sheds light into epigenetic mechanisms contributing to functional decline in the aging retina.

Scientific Focus Area: Genetics and Genomics

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