MTHFD1 controls DNA methylation in Arabidopsis.

Martin Groth,Amala John,Carolina Garcia-Salinas,Jixian Zhai,Sylvain Bischof,Jeff A Long,Haifeng Wang,Steven E Jacobsen,Guillaume Moissiard,Shawn J Cokus,Danielle C Smith,Ruediger Hell,Christopher J Hale,Suhua Feng,Rocío I Díaz De La Garza,Perla A Ramos-Parra,Markus Wirtz

doi:10.1038/ncomms11640

Abstract

DNA methylation is an epigenetic mechanism that has important functions in transcriptional silencing and is associated with repressive histone methylation (H3K9me). To further investigate silencing mechanisms, we screened a mutagenized Arabidopsis thaliana population for expression of SDCpro-GFP, redundantly controlled by DNA methyltransferases DRM2 and CMT3. Here, we identify the hypomorphic mutant mthfd1-1, carrying a mutation (R175Q) in the cytoplasmic bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase (MTHFD1). Decreased levels of oxidized tetrahydrofolates in mthfd1-1 and lethality of loss-of-function demonstrate the essential enzymatic role of MTHFD1 in Arabidopsis. Accumulation of homocysteine and S-adenosylhomocysteine, genome-wide DNA hypomethylation, loss of H3K9me and transposon derepression indicate that S-adenosylmethionine-dependent transmethylation is inhibited in mthfd1-1. Comparative analysis of DNA methylation revealed that the CMT3 and CMT2 pathways involving positive feedback with H3K9me are mostly affected. Our work highlights the sensitivity of epigenetic networks to one-carbon metabolism due to their common S-adenosylmethionine-dependent transmethylation and has implications for human MTHFD1-associated diseases.

Highlights

DNA methylation is an epigenetic mechanism that has important functions in transcriptional silencing and is associated with repressive histone methylation (H3K9me)
Recruitment of Pol IV to heterochromatin is dependent on H3K9me interaction via SAWADEE HOMEODOMAIN HOMOLOGue 1 (SHH1), whereas Pol V is recruited via the non-catalytic SUV39 homologues SUVH2 and 9 that bind to methylated DNA via their SET and RINGassociated (SRA) domains[11]
Mutant #162 was identified by screening M2 seedlings of an EMS-mutagenized population of Arabidopsis that carried an SDCpro-GFP insertion event in WT background for individuals that showed GFP fluorescence (Fig. 1a)

Summary

Introduction

DNA methylation is an epigenetic mechanism that has important functions in transcriptional silencing and is associated with repressive histone methylation (H3K9me). To further investigate silencing mechanisms, we screened a mutagenized Arabidopsis thaliana population for expression of SDCpro-GFP, redundantly controlled by DNA methyltransferases DRM2 and CMT3. CHG methylation is maintained by a reinforcing loop between non-CG methylation and methylation of lysine 9 of histone H3 (H3K9me), which involves the histone methyltransferases KRYPTONITE/SUVH4, 5 and 6 These preferentially bind methylated non-CG sequences via their SRA domains and modify the wrapped nucleosome with H3K9me Genome-wide loss of CHG and CHH methylation, reduced H3K9me and derepression of TEs in the mthfd[1] mutant indicate that the Met cycle constitutes an ‘Achilles heel’ of the feedback mechanisms between DNA and histone methylation

Methods

Results

Conclusion