Impacts of Early Life Stress on the Methylome and Transcriptome of Atlantic Salmon

Abstract

Exposure to environmental stressors during early-life stages can change the rate and timing of various developmental processes. Epigenetic marks affecting transcriptional regulation can be altered by such environmental stimuli. To assess how stress might affect the methylome and transcriptome in salmon, fish were treated using cold-shock and air-exposure from the eye-stage until start-feeding. The fish were either stressed prior to hatching (E), post-hatching (PH), pre- and post-hatching (EPH) or not stressed (CO). Assessing transcriptional abundances just prior to start feeding, E and PH individuals were found to have modified the expression of thousands of genes, many with important functions in developmental processes. The EPH individuals however, showed expression similar to those of CO, suggesting an adaptive response to extended periods of stress. The methylome of stressed individuals differed from that of the CO, suggesting the importance of environment in shaping methylation signatures. Through integration of methylation with transcription, we identified bases with potential regulatory functions, some 10s of kb away from the targeted genes. We then followed fish growth for an additional year. Individuals in EPH showed superior growth compared to other treatment groups, highlighting how stress can potentially have long-lasting effects on an organism’s ability to adapt to environmental perturbations.

Changes in gene and genotype frequencies during the development of the grass carp Ctenopharyngodon idella

“…The genes for collagens, myosin light‐chain kinase, dynein, zinc finger protein, 5‐hydroxytryptamine receptor and glutamate metabotropic receptor have been reported to be associated with morphological changes in the nervous, muscular and cardiovascular systems (Xu et al ., ). The GO and KEGG enrichment analyses showed that the significantly enriched GO terms were involved in DNA replication, metabolic process and enzyme activity, which are significant processes during fish embryogenesis (Moghadam et al ., ). Therefore, it is not surprising that the changes in allele frequencies in these genes affect the embryogenesis of C. idella and the survival of fish larvae; however, further studies are required.…”

“…The GO and KEGG enrichment analyses showed that the significantly enriched GO terms were involved in DNA replication, metabolic process and enzyme activity, which are significant processes during fish embryogenesis (Moghadam et al, 2017). Therefore, it is not surprising that the changes in allele frequencies in these genes affect the embryogenesis of C. idella and the survival of fish larvae; however, further studies are required.…”

Parent and offspring genotypes influence gene expression in early life

“…These gene regulation studies primarily use changes in DNA methylation as an indicator of ELS (Murgatroyd et al 2009, Kinnally et al 2011, Lewis & Olive 2014) and recent work has expanded these approaches into non-mammalian organisms (e.g. Rubenstein et al 2016, Moghadam et al 2017, Pértille et al 2017, Gott 2018, Sheldon et al 2018). DNA methylation studies of ELS investigate changes to the structure of DNA, but are often limited in the functional implications of ELS (i.e.…”

“…Indeed, several studies have also taken candidate gene approaches to investigating gene expression in the context of ELS (Marco et al 2014, Diaz-Real et al 2017, Anastasiadi et al 2018, Reshetnikov et al 2018). However, very few studies assess genome-wide transcription under ELS (Moghadam et al 2017), particularly in the context of parental effects (but see: Weaver et al 2006).…”

Parent and offspring genotypes influence gene expression in early life

“…In particular, the quality of parental care can have strong impacts on offspring health resulting from epigenetic modifications (Liu et al, 1997;Meaney, 2001;Weaver et al, 2004). These gene regulation studies primarily use changes in DNA methylation as an indicator of ELS (Kinnally et al, 2011;Lewis & Olive, 2014;Murgatroyd et al, 2009) and recent work has expanded these approaches into nonmammalian organisms (e.g., Gott, 2018;Moghadam et al, 2017;Pértille et al, 2017;Rubenstein et al, 2016;Sheldon, Schrey, Ragsdale, & Griffith, 2018). DNA methylation studies of ELS investigate changes to the structure of DNA, but are often limited in the functional implications of ELS (i.e., transcription and translation).…”