DNA methylation analysis of needle tissue from Pinus banksiana exposed to nickel sulfate, potassium sulfate and water

The conifer genome offers a novel system for understanding the integrative epigenomics of plants in response to heavy metals such as nickel. Recent research on Pinus banksiana shows an unorthodox approach to heavy metal detoxification that prompts research into corresponding methylation patterns. The objectives of this study were to 1) Evaluate the effect of excess nickel exposure on global methylation patterns in Pinus banksiana and 2) Identify and annotate differentially methylated regions (DMRs) elicited by nickel exposure in Pinus banksiana. Reduced representation bisulfite sequencing (RRBS) was used to assess alterations in global methylation patterns in nickel treated seedlings. Nickel sulfate had a mostly inert effect on global methylation but elicited high levels of methylation in specific areas of the genome. Most global increases in CG were attributed to hypermethylated DMRs which exhibited methylation levels over 80%. The high levels of methylation seem to be an intrinsic property of the genome that is not specific to nickel ions. Additionally, CHH islands were identified as a potential epigenetic player responding to nickel induced stress. Decreased methylation of CHH and a corresponding reduction in average methylation levels suggests the potential dysregulation of genes and transposable elements (TEs). Overall, 1173 DMRs were hypermethylated and 239 DMRs were hypomethylated. Moreover, 97% of DMRs were categorized as intergenic and exhibited high levels of CG methylation which suggests that these DMRs were located on transposable elements (TEs). Every DMR that was annotated to genes covered two areas of the gene body, demonstrating a strong bias for gene upregulation. DMR-covered genes were associated with stress mitigation and encoded for proteins such as DEAD-box ATP dependent RNA helicase, calcium/calmodulin dependent protein kinase and UDP-glycosyltransferase. In addition to upregulating gene expression, DMR coverage of introns and exons suggests that certain DMRs regulated alternative splicing mechanisms.