Datasets on DNA methylation levels, phenotypic measurements, and soil microbiome (and associated metadata) for Quercus lobata seedlings treated with 5-Azacytidine and controls
Abstract: Epigenetic
modifications such as DNA methylation, where methyl groups are added to
cytosine base pairs, have the potential to impact phenotypic variation and gene
expression, and could influence plant response to changing environments. One
way to test this impact is through the application of chemical demethylation agents,
such as 5-Azacytidine, which inhibit DNA methylation and lead to a partial
reduction in DNA methylation across the genome. In this study, we treated
5-month-old seedlings of the tree, Quercus
lobata, with foliar application of 5-Azacytidine to test whether a
reduction in genome-wide methylation would cause differential gene expression
and change phenotypic development. First, we demonstrate that demethylation
treatment led to 3-6% absolute reductions and 6.7-43.2% relative reductions in
genome-wide methylation across CG, CHG, and CHH sequence contexts, with CHH
showing the strongest relative reduction. Seedlings treated with 5-Azacytidine
showed a substantial reduction in new growth, which was less than half that of
control seedlings. We tested whether this result could be due to impact of the
treatment on the soil microbiome and found minimal differences in the soil
microbiome between two groups, although with limited sample size. We found no
significant differences in leaf fluctuating asymmetry (i.e., deviations
from bilateral symmetry), which has been found in other studies. Nonetheless,
treated seedlings showed differential expression of a total of 23 genes. Overall,
this study provides initial evidence that DNA methylation is involved in gene
expression and phenotypic variation in seedlings and suggests that removal of
DNA methylation affects plant development.