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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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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.

2023-11-13 | GSE204837 | GEO

Deubiquitinases that digest Met1 chains in Rice

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.

2022-10-15 | PXD032822 | Pride

zhang-arabidopsis-met1 vs ws

Project description:Comparison of met1 mutant with control

2012-02-19 | E-MEXP-3120 | biostudies-arrayexpress

Whole-genome bisulphite sequencing of met1-3/+

Project description:14 F1 individuals that resulted from crosses between a 420-CEN3 reporter line and met1-3/+ plants were subject to whole-genome bisulphite sequencing alongside Col wild-type and met1-3/+ controls

2015-10-10 | E-MTAB-3927 | biostudies-arrayexpress

The chromatin modifiers SET-25 and SET-32 are required for initiation but not long-term maintenance of transgenerational epigenetic inheritance

Project description:Some epigenetic modifications are inherited from one generation to the next, providing a potential mechanism for the inheritance of environmentally acquired traits. Transgenerational inheritance of RNA interference phenotypes in C. elegans provides an excellent model to study this phenomenon, and whilst studies have implicated both chromatin modifications and small RNA pathways in heritable silencing their relative contributions remain unclear. Here we demonstrate that the histone methyltransferases SET-25 and SET-32 are required for the establishment of a transgenerational silencing signal, but not for long-term maintenance of this signal between subsequent generations suggesting that transgenerational epigenetic inheritance is a multi-step process, with distinct genetic requirements for establishment and maintenance of heritable silencing. Furthermore, small RNA sequencing reveals that the abundance of secondary siRNA (thought to be the effector molecules of heritable silencing) does not correlate with silencing phenotypes. Together, our results suggest that the current mechanistic models of epigenetic inheritance are incomplete.

2018-10-30 | PXD008754 | Pride

Germline inheritance of H3K9me3 and its function in constitutive heterochromatin establishment.[CUT&Tag]

Project description:Germline inheritance of H3K9me3 and its function in constitutive heterochromatin establishment.[CUT&Tag]

| PRJNA1003940 | ENA

Germline inheritance of H3K9me3 and its function in constitutive heterochromatin establishment. [GRO-seq]

Project description:Germline inheritance of H3K9me3 and its function in constitutive heterochromatin establishment. [GRO-seq]

| PRJNA1003942 | ENA

Expression data in Arabidopsis axe1-5 and met1-3 mutants.

Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis axe1-5 and met1-3 mutants.

2011-05-16 | GSE23950 | GEO

Bisulfite Methylation Profiling (BiMP) analysis of met1-3 epigenetic Recombinant Inbred Lines (epiRILs)

Project description:Epigenomic mapping of DNA methylation polymorphisms segregating within an epigenetic Recombinant Inbred Line population resultant from crossing the wild-type Col-0 and DNA maintenance methyltransferase mutant, met1-3, parental lines. Each line within the epiRIL population was self-fertilized for 7 generations, 10 individual F7 plants were then bulk harvested to create the F8 generation. Here, data files for three DNA methylation profiled epiRIL lines (epi01, epi12, epi28) are deposited. The DNA methylation polymorphisms were determined using the BiMP method with the Affymetrix Arabidopsis Tiling 1.0R array. The main objective for these samples was to create an epigenomic map to analyze the inheritance of DNA methylation polymorphisms within these three epiRIL entries. Keywords: Bisulfite Methylation Profiling (BiMP) by genome tiling array

2009-04-23 | GSE13438 | GEO

Met1 or DB7 tumor gene expression

Project description:Metastasis predictive gene signatures can result from either somatic mutation, inherited polyrmorphism or both. This experiment is designed to look at the gene expression differences due to differences in somatic mutations in the initiating oncogene, PyMT. Met1 is from a fully metastatic FVB mammary tumor cell line, DB7 contains a mutation that permits tumor formation, but suppresses metastatic ability. Keywords: Basal transcription profiles

2008-11-30 | GSE13230 | GEO

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