Cerebral Methylome Analysis in a Model of Intergenerational Adaptive Epigenetics
Authors: Belmonte Krystal Courtney , Harman Jarrod , Lanson Nick , Gidday Jeff 
Published: June 2021

Several decades of research support the phenomenon of epigenetic conditioning, wherein a stressful, but not damaging, stimulus promotes a protective phenotype against an otherwise detrimental injury. Epigenetics involves changes in gene expression without changing DNA sequence, and occurs through three fundamental mechanisms: DNA methylation, histone modifications, and noncoding RNAs. Recent findings in our lab show that this induced adaptive response can be transmitted intergenerationally to first‐generation offspring. Specifically, using repetitive hypoxic conditioning (RHC) as an epigenetic stimulus, we documented reduced retinal ischemic injury not only in the animals that were treated with RHC, but also in their untreated F1 generation adult offspring. In this study, we investigate whether this adaptive response also occurs in the brain and how such epigenetic mechanisms manifest a protective effect within and across generations. Using methylated DNA immunoprecipitation and sequencing (meDIP‐seq), genome‐wide DNA methylation sites were identified in samples of cerebral cortex of the following animal groups: direct RHC‐treated F0 mice (F0‐RHC), their matched controls (F0‐CTL), the F1 mice derived from mating pairs of F0 RHC mice (F1‐RHC) and mating pairs of control mice (F1‐CTL). Differentially methylated regions (DMRs) on gene promoters were identified and compared between control and RHC‐treated mice at each generation. We identified 3059 DMRs (1549 hypermethylated, 1510 hypomethylated) between F0‐RHC and F0‐CTL in the F0 generation, and 4818 DMRs (2266 hypermethylated and 2552 hypomethylated) between F1‐RHC and F1‐CTL in the F1 generation. Subsequent bioinformatic analysis (Ingenuity Pathway Analysis [IPA], Qiagen) yielded 1405 differentially expressed (based on activated z‐scores) genes (719 down, 686 up) between RHC and control cortex in the F0 generation, with 220 unique molecules being enriched in 58 IPA‐designated pathways. In the F1 generation, 2105 differentially expressed genes (986 down, 1119 up) were identified between F1‐RHC and F1‐CTL, comprised of 317 unique molecules enriched in 79 IPA‐designated pathways. 52 of these genes were similarly hyper‐ or hypo‐methylated in each generation. Notably, both F0‐RHC and F1‐RHC generations exhibited a downregulation of pathways identified by IPA relating to “neurological disease.” However, further interrogation of these pathways reveal that directionally‐appropriate changes in ischemia‐related genes largely define the F0‐RHC cortex, whereas the F1‐RHC cortex is enriched in genes that collectively provide defense against broader categories of neurodegeneration. Thus, mechanisms underlying resilience in F0 cerebral cortex directly treated with our RHC stimulus are not directly replicated in the brain of animals that inherit resilience from their treated F0 parents. These results indicate that the cortical DNA methylome is responsive to our RHC stress, and thus may participate in the epigenetic establishment of injury‐resilient CNS phenotypes both within and between generations.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.