Critical function of DNA methyltransferase 1 in tomato development and regulation of the DNA methylome and transcriptome

ABSTRACT: DNA methylation confers epigenetic regulation on gene expression and thereby on various biological processes. Tomato has emerged as an excellent system to study the function of DNA methylation in plant development. In contrast to recent discoveries that DNA demethylation is critical for tomato fruit ripening, regulation and function of DNA methylation maintenance remains unclear in tomato plants. Here we report the critical function of tomato (Solanum lycopersicum) Methyltransferase 1 (SlMET1) in plant development and DNA methylome and transcriptome regulation. Using CRISPR-Cas9 gene editing, we generated slmet1 mutants and discovered that SlMET1 is required for normal development of flowers and seeds in tomato. Mutations in SlMET1 caused CG hypomethylation and CHH hypermethylation on a whole-genome scale, leading to a disturbed transcriptome including defects in the expression of key genes involved in meristem formation, seed development and fruit ripening. Consistently, the slmet1 mutants showed impaired flower production, elevated lycopene levels in fruits, and pathenocarpic fruits. In the slmet1 mutants, hypomethylated CG and hypermethylated CHH cytosines are preferentially located in genes and transposable elements (TEs), respectively. Neither the CG hypomethylation nor CHH hypermethylation in the slmet1 mutants is related to tissue culture-induced non-CG hypomethylation, which prefers genes over TEs and is more stable in the former regions than the latter during subsequent inbreeding. Our results depict SlMET1- and tissue culture-dependent tomato DNA methylomes, and that SlMET1 is required for normal development of flowers and seeds, thereby highlighting a role of DNA methylation in determining the yield of normal tomato fruits.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE102273 | GEO | 2019/01/22

REPOSITORIES: GEO