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Transcriptional profiling of atmbd4, atmbd6 and atmbd11 mutants of Arabidopsis thaliana

ABSTRACT: Methyl CpG Binding (MBD) proteins are a class of protein that binds with methylated DNA. In the model plant Arabidopsis thaliana there are 13 MBD proteins are there. To understand the gene regulation we performed microarray analysis of mutants of three genes (atmbd4, atmbd6 and atmbd11). Ten day old seedlings of these three mutant were compared with the wild type plants grown in same condition.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE59133 | GEO | 2014/07/09

SECONDARY ACCESSION(S): PRJNA254723

REPOSITORIES: GEO

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Transcriptional profiling of atmbd4, atmbd6 and atmbd11 mutants of Arabidopsis thaliana

Project description:Methyl CpG Binding (MBD) proteins are a class of protein that binds with methylated DNA. In the model plant Arabidopsis thaliana there are 13 MBD proteins are there. To understand the gene regulation we performed microarray analysis of mutants of three genes (atmbd4, atmbd6 and atmbd11). Ten day old seedlings of these three mutant were compared with the wild type plants grown in same condition. Surface sterilized Arabidopsis seeds were grown in MS media. Ten days old seedlings were used for isolation of RNA. The wild type plants along with T-DNA mutants of atmbd4, atmbd6 and atmbd11 were used to isolate the RNA. Three biological replicates of each sample were analyzed representing wild type, atmbd4, atmbd6 and atmbd11 of Arabidopsis.

2014-07-09 | E-GEOD-59133 | biostudies-arrayexpress

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2013-04-01 | GSE39610 | GEO

Methylation-dependent and -independent genomic targeting principles of the MBD protein family

Project description:In order to gain insight into DNA methylation readout, we have established a controlled strategy for profiling genomic targeting of chromatin-interacting factors in vivo. With this approach we determined binding preferences for the methyl-CpG binding domain (MBD) family of proteins, including disease relevant mutants, deletions and isoforms. In vivo binding of MBD proteins occurs as a linear function of local methylation density, and is dependent on functional MBD domain M-bM-^@M-^S methyl-CpG interactions. This directs specificity of MBD proteins to methylated, CpG dense and inactive regulatory regions. In contrast, binding to unmethylated sites is MBD protein specific and mediated via alternative domains or protein-protein interactions. The latter is observed for NuRD complex-mediated MBD2 tethering to a subset of unmethylated, tissue-specific regulatory regions, similar to MBD3. These functional binding maps reveal methylation-dependent and -independent binding modes determined by distinct protein domains and revise current models of DNA methylation readout through MBD proteins. Comparative binding analysis for the MBD family of proteins utilizing recombinase-assisted mapping of biotin-tagged proteins (RAMBiO). This set contains maps for 29 samples including wild type MBD proteins, mutants and domain variants in mouse ES cells, derived neurons (NP and TN) and Dnmt1/3a/3b triple-KO ES cells (TKO).

2013-04-01 | E-GEOD-39610 | biostudies-arrayexpress

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Development of DNA demethylation technology in HEK293T cells

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Project description:Comparison of protein termini in Arabidopsis thaliana vpe0 quadruple mutant and wildtype seedlings shortly after germination to identify differential processed proteins.

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