Single Cell-Type Analysis Reveals Unique Patterns of DNA Methylation in the Root Meristem

DNA methylation is an epigenetic marker of cell types, but the dynamics of DNA methylation changes between closely related cell types and its biological significance is unclear. Here, we report the genome-wide DNA methylomes, transcriptomes, and small RNA transcriptomes of six root cell types. We identified widespread cell type specific DNA methylomes, especially in CHH context. Columella genome is hypermethylated, accompanied by upregulation of RNA-directed DNA methylation related factors and 24 nt small RNA accumulation. Contradictory, nucleosome remodeler DDM1 required for DNA methylation is absent in columella. Low abundance of heterochromatin related factors indicates loss of heterochromatin in columella genome. We hypothesize that decondensed chromatin may allow access of RdDM factors to whole genome, producing excess 24 nt small RNAs  in columella.