Ectopic targeting of CG DNA methylation in Arabidopsis with the bacterial SssI methyltransferase

Wanlu Liu,Ming Wang,Peggy Hsuanyu Kuo,Zhenhui Zhong,Yuxing Zhou,Jason Gardiner,Steven E Jacobsen,Suhua Feng,Somsakul Pop Wongpalee,Javier Gallego-Bartolomé

doi:10.1038/s41467-021-23346-y

Abstract

The ability to target epigenetic marks like DNA methylation to specific loci is important in both basic research and in crop plant engineering. However, heritability of targeted DNA methylation, how it impacts gene expression, and which epigenetic features are required for proper establishment are mostly unknown. Here, we show that targeting the CG-specific methyltransferase M.SssI with an artificial zinc finger protein can establish heritable CG methylation and silencing of a targeted locus in Arabidopsis. In addition, we observe highly heritable widespread ectopic CG methylation mainly over euchromatic regions. This hypermethylation shows little effect on transcription while it triggers a mild but significant reduction in the accumulation of H2A.Z and H3K27me3. Moreover, ectopic methylation occurs preferentially at less open chromatin that lacks positive histone marks. These results outline general principles of the heritability and interaction of CG methylation with other epigenomic features that should help guide future efforts to engineer epigenomes.

Highlights

The ability to target epigenetic marks like DNA methylation to specific loci is important in both basic research and in crop plant engineering
To test whether SssI is capable of targeting CG DNA methylation in Arabidopsis, we fused SssI with a previously described artificial zinc finger (ZF) designed to target the FLOWERING WAGENINGEN (FWA) promoter[33]
In this study, we used the bacterial CG methyltransferase SssI fused to an artificial zinc finger protein to target CG methylation in Arabidopsis

Summary

Introduction

The ability to target epigenetic marks like DNA methylation to specific loci is important in both basic research and in crop plant engineering. We show that targeting the CG-specific methyltransferase M.SssI with an artificial zinc finger protein can establish heritable CG methylation and silencing of a targeted locus in Arabidopsis. We observe highly heritable widespread ectopic CG methylation mainly over euchromatic regions This hypermethylation shows little effect on transcription while it triggers a mild but significant reduction in the accumulation of H2A.Z and H3K27me[3]. DNA methylation is an evolutionarily conserved epigenetic modification that plays critical roles in silencing transposable elements and in regulating gene expression[1,2,3]. Methylation over heterochromatic regions occurs in CG, CHG, and CHH contexts and plays an important role in transcriptional silencing of transposable elements and repetitive sequences[4,20]. Previous studies in different organisms have used the Spiroplasma sp. strain MQ1 CG methyltransferase M.SssI (SssI) to target methylation[39,40]

Methods

Results

Conclusion