The pattern of DNA methylation alteration, and its association with the changes of gene expression and alternative splicing during phosphate starvation in tomato. (30th September 2021)

• Record Type: Journal Article
• Authors: Tian, Peng; Lin, Zeteng; Lin, Dongbo; Dong, Shuangyu; Huang, Jianzi; Huang, Tengbo
• Is Part Of: Plant journal. Volume 108:Number 3(2021)
• Page Start: 841
• Page End: 858
• Publication Date: 2021-09-30
• Subjects: phosphate starvation -- DNA methylation -- differential gene expression -- alternative splicing -- Solanum lycopersicum; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.15486
• Languages: English
• ISSNs: 0960-7412

Abstract

SUMMARY: DNA methylation is changed and associates with gene expression alterations in plant response to phosphate starvation (Pi–), a common stress that impacts plant growth and productivity. However, in the horticultural model species Solanum lycopersicum (tomato), the dynamics of DNA methylation and its relationship with changes in gene transcription and alternative splicing (AS) under Pi– are unknown. Here, we performed integrative methylome and transcriptome analyses of tomato seedlings under Pi‐deficient and ‐sufficient conditions. We found Pi– caused a slight increase in the overall methylation level, with millions of differentially methylated cytosines (DmCs) and a few hundred differentially methylated regions (DMRs). We also identified thousands of differentially expressed (DE) and differential AS (DAS) genes induced by Pi–, and found that DmCs were more abundant in non‐expressed genes than in DE or DAS genes. Moreover, DNA methylation alterations weakly correlated with transcription changes but not with DAS events, and hyper‐CHH‐DMRs overlapping with transposable elements (TEs) were enriched in a subset of Pi starvation response (PSR) genes. We propose that changes in DNA methylation may be associated with the differential expression of some PSR genes, but that most of these changes probably control the expression of nearby TEs, rather than directly affecting the transcription or AS of PSR genes. Besides, the pattern of methylation changes upon Pi– may largely be shaped by TE distributions. Together, our study provides comprehensive insights into the association of DNA methylation with gene transcription and AS under Pi– in tomato and may contribute to unveiling novel roles of epigenetic mechanisms in plant stress response. Significance Statement: We conducted the first genome‐wide and integrative analysis of the changes of DNA methylation, gene transcription and alternative splicing, as well as their associations in tomato under Pi starvation. Our results revealed weak correlations in the DNA methylation dynamics of different cytosine contexts with transcriptional changes, but not with differential alternative splicing in PSR processes, and indicated that the pattern of methylation changes was largely influenced by TE distribution.