Epigenetic reprogramming in the Arabidopsis germline

Epigenetic inheritance is more widespread in plants than in mammals, in part because mammals erase epigenetic information each generation by germline reprogramming. To assess the extent of germline reprogramming in plants, we sequenced the methylome from sperm cells (SC), the vegetative nucleus (VN), and the precursor microspore from developing haploid pollen. We found that asymmetric CHH methylation is lost in microspores and sperm cells, but restored in the VN and in fertilized seed, guided by 24nt small interfering RNA (siRNA). In the VN symmetric CG methylation is lost from targets of the DNA glycosylases DEMETER (DME) and REPRESSOR OF SILENCING 1 (ROS1). Methylation at these targets is retained in sperm cells, and many accumulate corresponding siRNA. These targets include maternally expressed imprinted genes, and recurrent epialleles that are pre-methylated in sperm and inherited in the next generation. In contrast, active transposons give rise to 21nt “epigenetically activated” small RNA in DECREASE IN DNA METHYLATION 1 (DDM1) mutants, in tissue culture and in the vegetative nucleus, and accumulate in sperm cells. Biogenesis requires miRNA and RNA DEPENDENT RNA POLYMERASE 6, which partially antagonizes 24nt siRNA biogenesis and RNA dependent DNA methylation (RdDM). 21nt easiRNA also arise in interspecific hybrids when maternal 24nt siRNA fail to recognize foreign transposons. Thus genome reprogramming in pollen contributes to epigenetic inheritance, transposon silencing, and imprinting, guided by small RNA.