GSE158027
Ectopic targeting of CG DNA methylation in Arabidopsis with the bacterial SssI methyltransferase.
Targeting of epigenetic marks like DNA methylation to specific loci to manipulate gene expression is important in both basic research and in crop plant engineering. However, the extent to which targeted DNA methylation can be heritable is unknown. Here, we show that targeting the CG-specific methyltransferase M.SssI (SssI) from Spiroplasma sp. strain MQ1 with an artificial zinc finger (ZF) protein can establish heritable CG methylation and silencing of the targeted loci in Arabidopsis. This occurs even in the absence of a functional RNA-directed DNA methylation pathway, which is usually required for de novo methylation. In addition to the locus-specific targeted CG methylation, we observed widespread ectopic CG methylation throughout the genome that was highly heritable over generations, even in the absence of the effector transgene. A comparison with other epigenetic features showed that this ectopic methylation occurred preferentially at less open chromatin regions that were lacking in positive epigenetic histone marks. Although ectopic CG methylation was highly enriched over gene body regions, it showed little effect on transcription of these genes. However, we observed a mild but significant reduction in the histone variant H2A.Z and H3K27me3 over genes with ectopic CG methylation. These results outline general principals of the interaction of CG methylation with other epigenomic features that should help guide future efforts to engineer epigenomes. Overall design: This dataset contains 9 BSPCR-seq, 32 WGBS, 35 RNA-seq, 30 ChIP-seq and 3 ATAC-seq data.