Integrative analysis of transcriptome and metabolome reveals the effect of DNA methylation of chalcone isomerase gene in promoter region on Lithocarpus polystachyus Rehd flavonoids

Metabolite biosynthesis is regulated by gene expression, which is altered by DNA methylation in the promoter region. Chalcone isomerase (CHI) gene encodes a key enzyme in the Lithocarpus polystachyus Rehd flavonoid pathway, and the expression of L. polystachyus CHI (LpCHI) is closely related to the synthesis of flavonoid metabolites. In this study, we analyzed the DNA methylation site of the LpCHI promoter and its effect on gene expression and metabolite accumulation. The proportions of three types of LpCHI promoter DNA methylation are 7.5%, 68.75%, 18.75%, determined by bisulfite sequencing. Transcriptome sequencing shows that LpCHI is strongly up-regulated in LpCHI promoter methylation Type A but down-regulated in LpCHI promoter methylation Type B and Type C. The expression of LpCHI shows no significant difference between Type B and Type C. Moreover, nine kinds of differentially expressed transcription factors (DETFs) bind to seven CpG-sites of the LpCHI promoter region to regulate LpCHI expression. The results of metabolomics show that differentially accumulated flavonoids are higher in LpCHI promoter methylation Type A than in LpCHI promoter methylation Type B and Type C. Additionally, a positive correlation was found between the LpCHI expression and flavonoids accumulation. These results show that the effect of CpG site-specificity on gene transcription is great than that of overall promoter DNA methylation on gene transcription. The mechanisms of flavonoid genes regulating metabolite accumulation are further revealed.