Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE

Abstract

SUMMARY In Arabidopsis, CHG DNA methylation is controlled by the H3K9 methylation mark through a self-reinforcing loop between DNA methyltransferase CHROMOMETHYLASE3 (CMT3) and H3K9 histone methyltransferase KRYPTONITE/SUVH4 (KYP). We report on the structure of KYP in complex with methylated DNA, substrate H3 peptide and cofactor SAH, thereby defining the spatial positioning of the SRA domain relative to the SET domain. The methylated DNA is bound by the SRA domain with the 5mC flipped out of the DNA, while the H3(1-15) peptide substrate binds between the SET and post-SET domains, with the ε-ammonium of K9 positioned adjacent to bound SAH. These structural insights complemented by in vivo functional data on key mutants of residues lining the 5mC and H3K9-binding pockets within KYP, establish how methylated DNA recruits KYP to the histone substrate. Together, the structures of KYP and previously reported CMT3 complexes provide insights into molecular mechanisms linking DNA and histone methylation.

Dicer-independent RNA-directed DNA methylation in Arabidopsis

“…Instead, it appears that the Pol IV transcript is mainly converted into dsRNA or amplified by RDR6, and RDR6-generated dsRNA or amplified transcript is required for DNA methylation. DNA methylation was also unaffected in the ago4/6 double mutant or any of the ago1, 2,3,5,7,8,9 or 10 single mutants, consistent with the hypothesis that 24-nt siRNAs are not required for DNA methylation at this locus ( Figure 1A and Supplementary information, Figure S1C). DNA methylation was also not affected in nrpe1 or nrpb2 mutants ( Figure 1A), indicating that Pol V or Pol II are not required at this locus.…”

“…CHG methylation is tightly linked to histone methylation and is maintained by a positive feedback loop. The histone methyltransferases KYP, SUVH5 and SUVH6 bind to methylated CHG and catalyze methylation on histone H3 lysine 9 (H3K9me2) [7][8][9]; the plant-specific DNA methyltransferase CMT3 binds to this mark and promotes CHG methylation [10,11]. The asymmetric CHH methylation is maintained by two different DNA methyltransferases, CMT2 and DRM2.…”

Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000

“…Additionally the SET-domain containing genes KRYPTONITE (SDG33) and ASHH1 (SDG26) were induced early in infection. These encode H3K9MTs implicated in crosstalk between DNA and histone methylation (Du et al, 2014) and in transcription regulation and flowering time control (Berr et al, 2015). Thus, the suppression of histone-encoding genes and the selective induction of genes involved in covalent modification of histones evidenced from this study is consistent with an early pathogen strategy to render stretches of DNA more accessible to TFs.…”

Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing inArabidopsis thalianaF1 epihybrids

“…Maintenance of non-CG methylation is more complex and involves the partially redundant activities of the DNA methyltransferases DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), CHROMOMETHYLASE 2 (CMT2), and CHROMOMETHYLASE 3 (CMT3). The three proteins act in self-reinforcing methylation and silencing loops that also rely on histone H3 methylation at lysine 9 (H3K9me) and small RNAs of 24 nt in length (9)(10)(11)(12). The interplay between chromatin and methylation is also apparent from the activity of the DECREASE IN DNA METHYLATION 1 (DDM1) chromatin remodeler, which seems to control access of methyltransferases to their H1-containing heterochromatic DNA targets (10).…”