RNA-directed DNA methylation(Rd DM) is a plant-specific de novo DNA methylation pathway,which has extensive cross-talk with histone modifications. Here, we report that the maize RdDM regulator SAWADEE HOMEODOMAIN HOMO...RNA-directed DNA methylation(Rd DM) is a plant-specific de novo DNA methylation pathway,which has extensive cross-talk with histone modifications. Here, we report that the maize RdDM regulator SAWADEE HOMEODOMAIN HOMOLOG 2(SHH2) is an H3 K9 me1 reader. Our structural studies reveal that H3 K9 me1 recognition is achieved by recognition of the methyl group via a classic aromatic cage and hydrogen-bonding and salt-bridge interactions with the free protons of the mono-methyllysine. The di-and tri-methylation states disrupt the polar interactions, decreasing the binding affinity. Our study reveals a monomethyllysine recognition mechanism which potentially links RdDM to H3 K9 me1 in maize.展开更多
In Arabidopsis thaliana,METHYL-CpG-BINDING DOMAIN 7(MBD7)and its associatedα-crystallin domain(ACD)proteins form a complex that interprets DNA methylation to prevent the silencing of methylated luciferase(LUC)reporte...In Arabidopsis thaliana,METHYL-CpG-BINDING DOMAIN 7(MBD7)and its associatedα-crystallin domain(ACD)proteins form a complex that interprets DNA methylation to prevent the silencing of methylated luciferase(LUC)reporter transgenes.However,the mechanism by which the MBD7 complex effectively targets methylated transgenes remains largely unclear.Here,we identify a novel role for SAWADEE HOMEODOMAIN HOMOLOG 1(SHH1),extending its function beyond the canonical RNA-directed DNA methylation(RdDM)pathway.We demonstrate that SHH1 prevents the transcriptional silencing of methylated LUC transgenes and a subset of endogenous genes by acting in concert with MBD7 within the same regulatory pathway.SHH1 co-localizes with MBD7 at nuclear foci and physically interacts with it to enhance its stability.Furthermore,SHH1 binds to methylated loci via its SAWADEE domain,which recognizes the H3K9me2 histone mark.This interaction promotes the reciprocal recruitment of SHH1 and MBD7 to methylated loci,revealing a cooperative mechanism that maintains transcriptional activity at promoter-methylated genes.Collectively,our findings unveil a dynamic,mutually reinforcing SHH1-MBD7 module that enhances the expression of promoter-methylated genes,likely by facilitating effective binding to chromatin marked by repressive epigenetic modifications.This work provides important insights into how DNA methylation fine-tunes gene expression in plants by balancing between transcriptional repression and activation.展开更多
基金supported by National Natural Science Foundation of China(31770782)the Ministry of Science and Technology of China(2016YFA0503200)+1 种基金the Shenzhen Science and Technology Program(JCYJ20200109110403829 and KQTD20190929173906742)Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes(2019KSYS006)to J.D.
文摘RNA-directed DNA methylation(Rd DM) is a plant-specific de novo DNA methylation pathway,which has extensive cross-talk with histone modifications. Here, we report that the maize RdDM regulator SAWADEE HOMEODOMAIN HOMOLOG 2(SHH2) is an H3 K9 me1 reader. Our structural studies reveal that H3 K9 me1 recognition is achieved by recognition of the methyl group via a classic aromatic cage and hydrogen-bonding and salt-bridge interactions with the free protons of the mono-methyllysine. The di-and tri-methylation states disrupt the polar interactions, decreasing the binding affinity. Our study reveals a monomethyllysine recognition mechanism which potentially links RdDM to H3 K9 me1 in maize.
基金supported by the National Natural Science Foundation of China(32160143,31960135,and 31801064)the Inner Mongolia Autonomous Region Natural Science Fund(2021ZD04)+5 种基金the Central Government Guiding Special Funds for the Development of Local Science and Technology(2020ZY0005)the Young Science and Technology Talents Cultivation Project of Inner Mongolia University(21400-5223711)awarded to D.L.by the Inner Mongolia Autonomous Region Natural Science Fund(2023QN03024)the National Natural Science Foundation of China(32560913)awarded to X.Y.by the National Natural Science Foundation of China(32470303)awarded to X.L.and by the Inner Mongolia Autonomous Region Natural Science Fund(2025QN03037)awarded to S.J.
文摘In Arabidopsis thaliana,METHYL-CpG-BINDING DOMAIN 7(MBD7)and its associatedα-crystallin domain(ACD)proteins form a complex that interprets DNA methylation to prevent the silencing of methylated luciferase(LUC)reporter transgenes.However,the mechanism by which the MBD7 complex effectively targets methylated transgenes remains largely unclear.Here,we identify a novel role for SAWADEE HOMEODOMAIN HOMOLOG 1(SHH1),extending its function beyond the canonical RNA-directed DNA methylation(RdDM)pathway.We demonstrate that SHH1 prevents the transcriptional silencing of methylated LUC transgenes and a subset of endogenous genes by acting in concert with MBD7 within the same regulatory pathway.SHH1 co-localizes with MBD7 at nuclear foci and physically interacts with it to enhance its stability.Furthermore,SHH1 binds to methylated loci via its SAWADEE domain,which recognizes the H3K9me2 histone mark.This interaction promotes the reciprocal recruitment of SHH1 and MBD7 to methylated loci,revealing a cooperative mechanism that maintains transcriptional activity at promoter-methylated genes.Collectively,our findings unveil a dynamic,mutually reinforcing SHH1-MBD7 module that enhances the expression of promoter-methylated genes,likely by facilitating effective binding to chromatin marked by repressive epigenetic modifications.This work provides important insights into how DNA methylation fine-tunes gene expression in plants by balancing between transcriptional repression and activation.
