Epigenetic memory marks determine epiallele stability at loci targeted by de novo DNA methylation

The transgenerational stability of DNA methylation changes is important in setting up genomic DNA methylation patterns and in the formation and transmission of epialleles. It is generally assumed that DNA methylation changes at genomic regions targeted by the de novo, RNA-directed DNA methylation (RdDM) pathway are unstable. Here, we show that RdDM targets in Arabidopsis can be classified into two groups based on their transgenerational epiallele stability following restoration of NRPD1 function in nrpd1 mutant plants: remethylable loci and non-remethylable loci. Compared to the remethylable loci, non-remethylable ones contain higher levels of the euchromatic marks H3K4me3 and H3K18ac, which interferes with the recruitment of the RdDM molecular machinery and helps to recruit the DNA demethylase ROS1 to antagonize RdDM, respectively. Using targeted de-methylation by CRISPR/dCas9-TET1, we demonstrate that mCG and mCHG are memory marks required for targeting the RdDM machinery to remethylable loci. Our results show that histone and DNA methylation marks are critical in determining the capacity of RdDM target loci to form stable epialleles, and contribute to understanding the formation and transmission of epialleles. Overall design: MethylC-Seq: 12 samples examined, Col-0, nrpd1-3, nrpe1-11, rdr2-2, two NRPD1 complementation lines,two NRPE1 complementation lines, two RDR2 complementation lines, nrpd1-3xCol-0 F1 and reciprocal F1 hybrids. Small RNA-Seq: 4 samples examined, Col-0, nrpd1-3 and two NRPD1 complementation lines