Putrescine treatment has a higher effect on 5mC DNA methylation profile of wheat leaves under white than under blue light conditions

Abstract

Polyamines play a pivotal role in plant growth and development by modulating primary metabolism and gene expression patterns. However, their regulatory effect on epigenetics is still not clear. The impact of exogenous putrescine in wheat leaves was investigated to reveal novel insights into the intricate relationship between polyamines and DNA methylation. Since the outcome of putrescine treatment may vary depending on the light quality, the experiment was performed under both white and blue light, and MeDIP-seq method was applied to reveal the global methylation profile. Metabolite profiling revealed distinct changes induced by blue light and/or putrescine, and that the effect of putrescine in most cases was dominant under blue light. Blue light also exerted strong effects on methylation, and putrescine application could slightly induce further changes. Putrescine had a higher impact under white light, namely parallel with increased leaf spermidine level, a lower level of up-methylated genes involved in cellular component, but a higher level of down-methylated genes involved in molecular function and biological processes occurred compared to the blue light. Our results demonstrated that putrescine excess has a regulatory role in DNA methylation. These findings are also useful in understanding the relationship between polyamine metabolism and light conditions.

Keywords: DNA methylation; Light quality; Metabolite profile; Polyamine; Wheat.

Fig. 1

Polyamine contents (DAP: 1,3-diaminopropane, PUT: putrescine, SPD: spermidine and SPM: spermine) without (C) or with (P) 0.5 mM putrescine pre-treatment under white (W) or blue (B) light conditions in the leaves (A) and roots (B) of wheat plants. Values are means ± SD. Statistically significant differences are indicated with different letters at p < 0.05 level.

Fig. 2

Gene expression level of spermidine synthase (TaSPDS) without (C) or with (P) 0.5 mM putrescine pre-treatment under white (W) or blue (B) light conditions in the leaves (A) and roots (B) of wheat plants. Values are means ± SD. Statistically significant differences are indicated with different letters at p < 0.05 level.

Fig. 3

The distribution of the localization of differentially methylated gene elements. Percentages are calculated from the overlapping and the total locus counts of the query genome.

Fig. 4

The number of overlaps of differentially methylated genes (DMGs) in cases of up- (A) and down-methylation (B). The black columns show the sizes of the input sets. The red columns indicate the number of overlaps between the treatment combinations. Blue bars indicate the combination of sets of each intersection.

Fig. 5

The PCA loading plots show the eigenvalues of the original variables on the PC1 and PC2 planes (Dims) for the up- (A) and down-methylated (B) datasets, based on the log₂FC values of the DMGs. Percentages represent the explained variance of the PCs. Cos2 scale means the accuracy of the representation on the PC planes.

Fig. 6

The names, IDs, and numbers of significant (FDR < 0.05) gene ontology (GO) terms in light and putrescine treatment combinations. The terms of the three major GO classes are shown: cellular component, molecular function and biological process. The numbers in the coloured bars mean the number of mapped counts compared to the background (reference). All parent and redundant terms have been truncated.

Fig. 7

Gene expression levels of genes selected according to the most characteristics differences in DNA methylation (log₂FC >|5|). Relative expression values were normalised for the wheat Ta2291 – ADP-ribosylation factor.