Dynamic DNA methylation reconfiguration during seed development and germination (MethylC-seq)

The life cycle of flowering plants ends and begins with seeds. Unlike animals, plants can pause their life cycle as dormant seeds during this transition. DNA methylation is involved in the regulation of gene expression and genome integrity. Reprogramming erases and re-establishes DNA methylation during development in animals. Knowledge of reprogramming or reconfiguration in plants has been limited to pollen and the central cell. To better understand epigenetic reconfiguration in the embryo, which forms the plant body, we compared dry and germinating seed time-series methylomes to publicly available seed development methylomes. Time-series whole genome bisulfite sequencing (WGBS) revealed extensive gain of CHH methylation during seed development and drastic loss of CHH methylation during germination. These dynamic changes in methylation mainly occur within transposable elements. Active DNA methylation during embryogenesis depends on both RNA-directed DNA methylation and heterochromatin formation pathways whereas global demethylation during germination occurs in a passive manner. However, an active DNA demethylation pathway is initiated during late embryogenesis, which contributes to the endosperm specific methylation patterns.This study provides new insights into dynamic DNA methylation reprogramming events during seed development and germination and suggests possible mechanisms of regulation. The observed sequential methylation/demethylation cycle suggests an important role of DNA methylation in seed dormancy. Overall design: MethylC-seq from dry and germinating seed of Arabidopsis