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Whole genome bisulfite sequencing of hdp1-1 and hdp2-1 mutants (both with 35S-SUC2 transgene)

ABSTRACT: Using whole genome bisulfite sequencing to provide single-base resolution of DNA methylation status in hdp1-1 and hdp2-1 mutants

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE78846 | GEO | 2024/10/11

REPOSITORIES: GEO

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Whole genome bisulfite sequencing of hdp1-1 and hdp2-1and other relative mutants (all with 35S-SUC2 transgene)

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Whole genome bisulfite sequencing of hdp1-1 and hdp2-1and other relative mutants (Col-0 background)

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MethlyC-Seq of wild type (with 35S-SUC2 transgene) and idm3-1, mbd7-1 mutants (same 35S-SUC2 background)

Project description:In eukaryotes, heterochromatin is characterized by numerous epigenetic marks, including DNA methylation. Spreading of these marks into nearby active genes must be avoided in order to maintain appropriate gene expression. Here, we uncover Arabidopsis Methyl-CpG-Binding Domain 7 (MBD7) and Increased DNA Methylation 3 (IDM3) as anti-silencing factors that prevent transgene repression and genome-wide DNA hypermethylation. MBD7 preferentially binds to highly methylated, CG-dense regions associated with non-CG methylation and physically associates with other anti-silencing factors, including the histone acetyltransferase IDM1, IDM2, and IDM3. IDM1 and IDM2 were previously shown to facilitate active DNA demethylation by the 5-methylcytosine DNA glycosylase/lyase ROS1. Thus, MBD7 tethers the IDM proteins to methylated DNA, which enables the function of DNA demethylases that in turn establish chromatin boundaries and limit DNA methylation Using MethylC-Seq to provide single-base resolution of DNA methylation status in WT and idm3-1, mbd7-1 mutants

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MethlyC-Seq of wild type (with 35S-SUC2 transgene) and idm3-1, mbd7-1 mutants (same 35S-SUC2 background)

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35S-SUC2 WT and antisilencing mutants

Project description:This SuperSeries is composed of the SubSeries listed below.

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ChIP-seq data for HDP2 transgenic line

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ChIP-seq of WT(with 35S-SUC2 transgene) and proMBD7::gMBD7:4xMYC transgenic plants

Project description:In eukaryotes, heterochromatin is characterized by numerous epigenetic marks, including DNA methylation. Spreading of these marks into nearby active genes must be avoided in order to maintain appropriate gene expression. Here, we uncover Arabidopsis Methyl-CpG-Binding Domain 7 (MBD7) and Increased DNA Methylation 3 (IDM3) as anti-silencing factors that prevent transgene repression and genome-wide DNA hypermethylation. MBD7 preferentially binds to highly methylated, CG-dense regions associated with non-CG methylation and physically associates with other anti-silencing factors, including the histone acetyltransferase IDM1, IDM2, and IDM3. IDM1 and IDM2 were previously shown to facilitate active DNA demethylation by the 5-methylcytosine DNA glycosylase/lyase ROS1. Thus, MBD7 tethers the IDM proteins to methylated DNA, which enables the function of DNA demethylases that in turn establish chromatin boundaries and limit DNA methylation Using ChIP-seq to study the genomic targeting principle of MBD7 protein

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Arabidopsis SUC1 loads the phloem in suc2 mutants when expressed from the SUC2 promoter.

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| S-EPMC3254675 | biostudies-literature

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