Abstract Plant embryogenesis is a critical process characterized by extensive cellular differentiation and morphogenesis, regulated by complex epigenetic mechanisms. However, dynamic changes of DNA methylation during Arabidopsis early embryo development remain to be elucidated. In this study, Arabidopsis hybrid embryos from 2/4-cell to globular stage were subject to bisulfite sequencing and RNA-seq analysis. Our results revealed a local remodeling of DNA methylation during early embryogenesis, represented by a remarkable gain of CHH methylation and the progressive loss of CHG methylation. Genes with differential methylation were found to participate in cell division, morphogenesis, pattern specification and auxin signaling, indicating their potential role in embryo development. At globular stage, CHH hyper-methylation exhibited a notable association with TE repression. The divergences between allelic methylation primarily lied in CG context which increased with embryogenesis. CHH methylation variations between parental alleles underwent reprogramming. Our results implied a negative relevance between allele-specific expression and methylation at CHG sites in early embryos. This work provides new insights into DNA methylation remodeling and its association with transcriptional changes during Arabidopsis early embryogenesis, laying a foundation for future functional studies.
Wang et al. (Fri,) studied this question.