Hippocampal DNA methylation, DNAm age and spatial memory performance in young and old rats

Abstract

In humans and rats, aging is associated with a progressive deterioration of spatial learning and memory. These functional alterations are correlated with morphological and molecular changes in the brain, particularly in the hippocampus. Here, we assessed the age-related changes in the DNA methylation (DNAm) landscape in the rat hippocampus and assessed the correlation of spatial memory performance with hippocampal DNAm age in young (2.6 mo.) and old (26.6 mo.) rats. Spatial memory performance was assessed with a modified version of the Barnes maze test. In order to evaluate learning ability as well as spatial memory retention, we assessed the time spent (permanence) by animals in goal sector 1 (GS1) and 3 (GS3) when the escape box was removed. The rat pan-tissue clock was applied to DNA methylation profiles of hippocampal tissue. The bisulfite converted genomic DNA was analyzed by Illumina Infinium HorvathMammalMethylChip40. The Horvath Mammal Methyl Chip40 assay provides quantitative measurements of DNA methylation for 22528 CpG dinucleotides that map to the Rattus norvegicus UCSC 6.0 genome. An enrichment pathway analysis revealed that neuron fate commitment, brain development, and central nervous system development were processes whose underlying genes were enriched in positively methylated CpGs. In the old rat hippocampi, the methylation levels of CpGs proximal to transcription factors associated with genes Pax5, Lbx1, Nr2f2, Hnf1b, Zic1, Zic4, Hoxd9; Hoxd10, Gli3, Gsx1 and Lmx1b, and Nipbl showed a significant regression with spatial memory performance. Regression analysis of different memory performance indices with hippocampal DNAm age was significant when data from young and old rats were taken together. The above results suggest that age-related hypermethylation of certain gene families, like Zic and Gli, may play a causal role in the decline in spatial memory in old rats. Hippocampal DNAm age seems to be a reliable index of spatial memory performance in young and old rats.