Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation

5-methyl cytosine is widespread in plant genomes in both CG and non-CG contexts. During replication, hemi-methylation on parental DNA strands guides symmetric CG methylation on nascent strands, but non-CG methylation requires modified histones and small RNA guides. Here, we used immortalized Arabidopsis cell suspensions to sort replicating nuclei and determine genome-wide cytosine methylation dynamics during the plant cell cycle. We find that symmetric mCG and mCHG are selectively retained in actively dividing cells in culture, while mCHH is depleted. mCG becomes transiently asymmetric during S phase but is rapidly restored in G2, while mCHG remains asymmetric throughout the cell cycle. Hundreds of loci gain ectopic CHG methylation, as well as 24-nt small-interfering RNAs and H3K9me2, without gaining CHH methylation. This suggests that spontaneous epialelles that arise in plant cell cultures are stably maintained by small RNA independently of the canonical RNA-directed DNA methylation pathway. In contrast, loci that fail to produce siRNA are targeted for demethylation when cell cycle arrests. Comparative analysis with methylomes of various tissues and cell types suggests that loss of small RNA-directed non-CG methylation during DNA replication promotes germline reprogramming and epigenetic variation in plants propagated as clones. Small RNA sequencing of Arabidopsis cell cultures