Epigenomic reconfiguration during aging of rod photoreceptors

Abstract

Purpose : Aging is characterized by altered homeostasis and reconfiguration of the epigenetic landscape, including changes in DNA methylation. The contribution of the epigenome to age-dependent functional decline and susceptibility to disease is poorly understood. Our aim is to identify biological pathways prone to DNA methylation changes during aging of rod photoreceptors.

Methods : 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 and analyzed using Homer. Gene Ontology (GO) analysis was performed using GOrilla and transcription factor (TF) motif enrichment using Genomatix.

Results : 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. A group of DMRs that changed progressively with age (271) were enriched in mitochondrial 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 and protein degradation pathways were dysregulated with age.

Conclusions : DNA methylation pattern of rods is dynamic during aging with a preferential loss of methylation in neuronal and mitochondrial 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.

This is an abstract that was submitted for the 2018 ARVO Annual Meeting, held in Honolulu, Hawaii, April 29 - May 3, 2018.