Environmental enrichment effect on DNA methylation
Our results revealed strong effect of environmental enrichment on brain DNA methylation patterns, with 1,854 differentially methylated cytosines (DMCs) (neighbouring or on gene bodies of 728 genes) between genetically uniform parents reared on enriched and poor environments. Several studies have reported effects of environmental enrichment on brain growth (Näslund et al. 2012), cell proliferation (von Krogh et al.2010), cognitive capacity (Salvaneset al. 2013; Spence et al.2011), and gene expression levels (Evanset al. 2015) in fish. The functional analysis of the genes affected by DMCs in the parents showed that among the most relevant biological regulation processes affected by environmental enrichment, 33 annotated genes were involved on signalling transduction, which involves transmembrane signal reception and regulation of downstream cellular processes. Among metabolic processes, 14 genes affected by DMCs were involved on the transcription by RNA polymerase II, suggesting that those could regulate differential gene expression levels in the brain of individuals reared in enriched and poor environments. Regarding pathways, Wnt and cadherin signalling pathways were shown to be the most representative. Wnts are growth factors signalling proteins which interact cadherin-mediated cell adhesion through β-catenin (Nelson & Nusse 2004). These two signalling pathways are known to converge and have crucial roles on gene expression, cell migration, proliferation, adhesion, differentiation and renewal (Cadigan & Nusse 1997). In the vertebrate brain, Wnt/cadherin signalling pathways regulate the patterns of axes (anterior-posterior and dorsal ventral) of neural regions, promote size expansion and brain morphogenesis (Ille & Sommer 2005; Nyholm et al. 2007). Therefore, the differential methylation patterns between rearing environments could be related to differential transcription levels (or transcriptional noise reduction, depending of the genetic context) (Evans et al. 2015) in pathways of the brain development that could be the basis of the physiological and behavioural differences observed between enriched and poor reared individuals. Further research targeting specific epigenetic variants (e. g. using CRISPR/Cas9 (2017)), would expand the information how the specific epigenetic variants found here may be affecting gene expression, and the consequent effects for downstream phenotypes.
Due to epigenetic reprogramming during embryogenesis, only a small subset of epigenetic variants on the parents are likely to be transmitted to the offspring (Burggren 2016; Illum et al. 2018). DNA methylation changes during embryogenesis in K . marmoratus has a longer and later DNA methylation reprogramming period when compared to other fish and mammals (Fellous et al. 2018), which might represent an epigenetic window of environmental sensitivity. In the offspring, most of our results indicated a stronger effect of their own rearing environment than that of their parents on DNA methylation patterns. Thus, although there were clear effects of environmental enrichment on the brain DNA methylation patterns of the parents, these changes may not have influenced the germline to the same extent, suggesting limited potential for epigenetically-mediated parental effects being transmitted trans-generationally and/or scape epigenetic reprogramming. Yet, three DMCs maintained the same methylation patterns in both parents and offspring while additional DMCs maintained the parental methylation patterns in the offspring in a more environment-specific manner. To our knowledge, this is the first evidence of parental effects on the offspring epigenetic patterns caused by environmental enrichment in fish, extending previous results in mice, in which parental enrichment has shown to affect offspring brain weight, global methylation levels (Mychasiuket al. 2012) and learning capacity (Arai & Feig 2011).
In summary, our results reveal behavioural and, limited but significant, epigenetic parental effects in the offspring caused by environmental enrichment which, if maintained, could have long-term evolutionary implications.