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A quantitative model of MET1-catalyzed establishment and epigenetic inheritance of DNA methylation

ABSTRACT: A quantitative model of MET1-catalyzed establishment and epigenetic inheritance of DNA methylation

PROVIDER: PRJNA842430 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19412800.fastq.gz	Fastqsanger.gz
	SRR19412801.fastq.gz	Fastqsanger.gz
	SRR19412802.fastq.gz	Fastqsanger.gz
	SRR19412803.fastq.gz	Fastqsanger.gz
	SRR19412804.fastq.gz	Fastqsanger.gz

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A quantitative model of MET1-catalyzed establishment and epigenetic inheritance of DNA methylation

Project description:Methylation of CG dinucleotides (mCG), which regulates genome function in eukaryotes, is epigenetically propagated by Dnmt1/MET1 methyltransferases via a semiconservative mechanism. How these enzymes accomplish stable epigenetic inheritance despite imperfect fidelity remains mysterious. Here we show that MET1 de novo activity, which is enhanced by existing proximate methylation, seeds and stabilizes mCG in Arabidopsis thaliana genes. MET1 activity is delimited by active DNA demethylation and counterbalanced by histone variant H2A.Z, natural variation in which accounts for high genic methylation in accessions from northern Sweden. Based on these observations, we develop a mathematical model that precisely recapitulates mCG inheritance dynamics and successfully predicts steady-state intragenic mCG patterns and their population-scale variation given only CG site spacing as input. Our results demonstrate how methylation patterns are created in plant genes, reconcile imperfect mCG maintenance with long-term stability, and establish a quantitative model for the epigenetic inheritance of mCG.

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Project description:Met1 type ubiquitination and deubiquitination are involved in the regulation of many fundamental processes such as inflammation and innate immunity, and their interference by pathogens can suppress immune responses in human cells. However, few plant-derived deubiquitinases (DUBs) against Met1 ubiquitin chains has been reported, and the selection mechanism for linkage-type of ubiquitin chains remains elusive, which greatly limits our understanding of the functions of plant-derived DUBs. Using a dehydroalanine (DHA)-bearing Met1 diubiquitin (Met1-diUb) suicide probe, synthesized in one-pot, we captured OTUB1 from Oryza sativa (OsOTUB1) and uncovered its ability to hydrolyze Met1 ubiquitin chains (Met1 activity). Further, by resolving the apo structure of OsOTUB1 and its complex with Met1-diUb, we found that Met1-specific motifs (N-handle motif and C-handle motif) in the S1’ pocket of OsOTUB1 confers its Met1 activity. Through large-scale sequence alignment and hydrolysis experiments, Met1-specific motifs in the S1' pocket of the OTUB subfamily (OTUBs) were found to determine the Met1 ability of OTUBs, regardless of species. Furthermore, by analyzing the species distribution of OTUBs capable of hydrolyzing Met1 ubiquitin chains, we found that whereas this activity does not exist in metazoans, it is conserved in green plants (Viridiplantae). This discovery may inform studies of the differentiation between primitive plants and animals.

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