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.