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A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes [ChIP-seq]

ABSTRACT: We found SUVH-SDJ complex occupies promoter methylated genes and promotes the expression of these genes.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE124377 | GEO | 2018/12/27

REPOSITORIES: GEO

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A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes [RNA-seq]

Project description:We found SUVH-SDJ complex occupies promoter methylated genes and promotes the expression of these genes.

2018-12-30 | GSE124485 | GEO

A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes [Bisulfite-seq]

Project description:We found SUVH-SDJ complex occupies promoter methylated genes and promotes the expression of these genes.

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A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes

Project description:A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes

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A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes

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

2018-12-30 | GSE124486 | GEO

A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes [ChIP-seq]

Project description:A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes [ChIP-seq]

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A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes [Bisulfite-seq]

Project description:A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes [Bisulfite-seq]

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A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes [RNA-seq]

Project description:A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes [RNA-seq]

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MBD2a-NuRD Binds to the Methylated γ-Globin Gene Promoter and Uniquely Forms a Complex Required for Silencing of HbF Expression

Project description:During human development, there is a switch in the erythroid compartment at birth that results in silencing of expression of fetal hemoglobin (HbF). Reversal of this silencing has been shown to be effective in overcoming the pathophysiologic defect in sickle cell anemia. Among the many transcription factors and epigenetic effectors that are known to mediate HbF silencing, two of the most potent are BCL11A and MBD2-NuRD. In this report we present direct evidence that MBD2- NuRD occupies the γ-globin gene promoter in adult erythroid cells and positions a nucleosome there that results in a closed chromatin conformation that prevents binding of the transcriptional activator, NF-Y. We show that the specific isoform, MBD2a, is required for the formation and stable occupancy of this repressor complex that includes BCL11A, MBD2a-NuRD and the arginine methyltransferase, PRMT5. The methyl cytosine binding preference and the arginine rich (GR) domain of MBD2a are required for high affinity binding to methylated γ-globin gene proximal promoter DNA sequences. Mutation of the methyl cytosine binding domain of MBD2 results in a variable but consistent loss of γ-globin gene silencing, in support of the importance of promoter methylation. The GR domain of MBD2a is also required for recruitment of PRMT5, which in turn results in placement of the repressive chromatin mark H3K8me2s at the promoter. These findings 2 support a unified model that integrates the respective roles of BCL11A, MBD2a-NuRD, PRMT5 and DNA methylation in HbF silencing.

2023-06-28 | GSE224834 | GEO

A DNA methylation reader complex that enhances gene transcription

Project description:DNA methylation generally functions as a repressive transcriptional signal, but it is also known to activate gene expression. In either case, the downstream factors remain largely unknown. By using comparative interactomics, we isolated proteins in Arabidopsis thaliana that associate with methylated DNA. Two SU(VAR)3-9 homologs, the transcriptional antisilencing factor SUVH1, and SUVH3, were among the methyl reader candidates. SUVH1 and SUVH3 bound methylated DNA in vitro, were associated with euchromatic methylation in vivo, and formed a complex with two DNAJ domain-containing homologs, DNAJ1 and DNAJ2. Ectopic recruitment of DNAJ1 enhanced gene transcription in plants, yeast, and mammals. Thus, the SUVH proteins bind to methylated DNA and recruit the DNAJ proteins to enhance proximal gene expression, thereby counteracting the repressive effects of transposon insertion near genes.

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Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation

Project description:DNA methylation functions in gene silencing and the maintenance of genome integrity. In plants, non-CG DNA methylation is linked through a self-reinforcing loop with histone 3 lysine 9 dimethylation (H3K9me2). The plant-specific SUPPRESSOR OF VARIEGATION 3–9 HOMOLOG (SUVH) family H3K9 methyltransferases (MTases) bind to DNA methylation marks and catalyze H3K9 methylation. Here, we analyzed the structure and function of Arabidopsis thaliana SUVH6 to understand how this class of enzyme maintains methylation patterns in the genome. We reveal that SUVH6 has a distinct 5mC base-flipping mechanism involving a thumb loop element. Autoinhibition of H3 substrate entry is regulated by a SET domain loop, and a conformational transition in the postSET domain upon cofactor binding may control catalysis. In vitro DNA binding and in vivo ChIP-seq data reveal that the different SUVH family H3K9 MTases have distinct DNA binding preferences, targeting H3K9 methylation to sites with different methylated DNA sequences, explaining the context biased non-CG DNA methylation in plants.

2018-08-17 | GSE114009 | GEO

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