The methyl binding domain 3 (MBD3) family proteins promote Tet2 enzymatic activity for mediating 5mC conversion
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ABSTRACT:
PROVIDER: PRJNA301898 | ENA |
REPOSITORIES: ENA
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Project description:Ten-eleven translocation (TET) proteins are key players involved in the dynamic regulation of cytosine methylation and demethylation. Inactivating mutations of TET2 are frequently found in human malignancies, highlighting the essential role of TET2 in cellular transformation. However, the factors that control TET enzymatic activity remain largely unknown. Here we found that MBD3 and its analogue MBD3L2 can specifically modulate the enzymatic activity of Tet2 protein, but not Tet1 and Tet3 proteins, in converting 5mC into 5hmC. Moreover, MBD3L2 is more effective than MDB3 in promoting Tet2 enzymatic activity via strengthening the binding affinity between Tet2 and the methylated DNA target. Further analysis revealed pronounced decreases in 5mC levels at MBD3L2 and Tet2 co-occupied genomic regions, most of which are promoter elements associated with either cancer-related genes or genes involved in the regulation of cellular metabolic processes. Our data add new insights into the regulation of Tet2 activity by MBD3 and MBD3L2 in modulating its target gene activities in cancer development and have important applications in understanding how dysregulation of TET2 may contribute to human malignancy.
2016-03-03 | GSE74914 | GEO
Project description:Ten-eleven translocation (TET) proteins are key players involved in the dynamic regulation of cytosine methylation and demethylation. Inactivating mutations of TET2 are frequently found in human malignancies, highlighting the essential role of TET2 in cellular transformation. However, the factors that control TET enzymatic activity remain largely unknown. Here we found that MBD3 and its analogue MBD3L2 can specifically modulate the enzymatic activity of Tet2 protein, but not Tet1 and Tet3 proteins, in converting 5mC into 5hmC. Moreover, MBD3L2 is more effective than MDB3 in promoting Tet2 enzymatic activity via strengthening the binding affinity between Tet2 and the methylated DNA target. Further analysis revealed pronounced decreases in 5mC levels at MBD3L2 and Tet2 co-occupied genomic regions, most of which are promoter elements associated with either cancer-related genes or genes involved in the regulation of cellular metabolic processes. Our data add new insights into the regulation of Tet2 activity by MBD3 and MBD3L2 in modulating its target gene activities in cancer development and have important applications in understanding how dysregulation of TET2 may contribute to human malignancy.
2016-03-03 | GSE74794 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2016-03-03 | GSE74915 | GEO
Project description:Methyl CpG binding domain 3 (Mbd3) protein belongs to the MBD family of proteins, responsible for reading the DNA methylation pattern. MBD family proteins bind the methyl-CpG domain and are also involved in heterochromatin formation. Mbd3 protein does not have the ability to selectively recognize methyl-CpG islands, however, its characteristic feature is the ability to bind to 5-hydroxymethylcytosine and unmethylated DNA. Little is known about the role of Mbd3 in epilepsy and epileptogenesis. Our previous study (Bednarczyk et al., 2016) showed an increase in levels of NuRD complex proteins, including Mbd3 protein, in the brain of epileptic animals in a rat model of temporal epilepsy induced by electrical stimulation of the amygdala. Amygdala stimulation induced the binding of NuRD complex containing MBD3 to larger number of regions of DNA. In the present study, we investigated whether the Mbd3 protein is involved in the determination of the seizure threshold. An increase in Mbd3 protein levels was demonstrated in the entorhinal cortex/amygdala in the rat’s brain 4 hours after pentylenetetrazole (PTZ)-induced seizures. No alterations in MBD3 protein levels were detected in hippocampus and somatosensory cortex. No alterations in MBD3 mRNA expression were observed at any time point in any studied brain area. Reduction of Mbd3 level using AAV vector coding shRNA against Mbd3 injected to the amygdala prolonged the latency time to the onset of an acute seizure in PTZ challenge test indicating increase in seizure threshold. This was accompanied by increased anxiety in the open field test. In the contrast, an overexpression of Mbd3 using AAV decreased anxiety and increased their excitability in the open field test. Moreover Mbd3 overexpression in the amygdala accelerated epileptogenesis in the PTZ-kindling model. In order to identify the role of Mbd3 protein in the regulation of gene expression, mRNA profiling with RNA-seq was performed in a model of magnesium deficiency-induced epileptiform discharges in vitro. Mbd3 overexpression in vitro induced changes in gene expression in a time- and state-specific manner. Our data indicate the pro-epileptic properties of the Mbd3 protein in vivo and in vitro.
2024-02-09 | GSE227084 | GEO
Project description:The methyl binding domain 3 (MBD3) family proteins promote Tet2 enzymatic activity for mediating 5mC conversion [microarray]
| PRJNA301557 | ENA
Project description:The methyl binding domain 3 (MBD3) family proteins promote Tet2 enzymatic activity for mediating 5mC conversion [HTS]
| PRJNA301900 | ENA
Project description:Maintenance of chromatin structure is essential to eukaryotic life; dysregulation is known to be causal for aberrant development and disease. The Mi-2/nucleosome remodeling and histone deacetylase (NuRD) complex is a multiprotein machine proposed to regulate chromatin structure by nucleosome remodeling and histone deacetylation activities. We identified the localization of MBD3, a component of Mi-2/NuRD complex, in two breast cancer cell lines (MCF7 and MDA-MB-231) using ChIP-Seq. MBD3 showed cell-type specific localization with overlap across cell lines being less than 50%. MBD3 localized across gene bodies, peaking around the transcription start site (TSS). Contrary to existing models, MBD3 preferentially associated with CpG rich promoters marked by H3K4me3. These data suggest that MBD3, and by extension the Mi-2/NuRD complex, may have roles in fine tuning expression for active genes. These data represent an important first step in defining regulatory mechanisms by which Mi-2/NuRD complex controls chromatin structure and gene expression. Identification of MBD3 localization in human breast cancer cell lines
2013-10-31 | E-GEOD-44737 | biostudies-arrayexpress
Project description:To obtain a comprehensive and quantitative view on MBD2 vs MBD3-NuRD complex stoichiometry, we performed biotin co-immunoprecipitations in Mbd3 KO ES cells expressing either biotin-tagged MBD2a or MBD3a and identified known NuRD complex members using label-free mass spectrometry (Supplementary Fig. 8b-c). We then calculated the intensity-based absolute quantification (iBAQ) values of the most predominant and statistically significant MBD-interacting proteins in both cell lines, which can be used to estimate the relative abundance. While we observe very similar complex composition between MBD2a-NuRD and MBD3a-NuRD, peptides shared between SALL1-4 proteins show a preferred interaction with the MBD2a-NuRD complex.
2023-06-30 | PXD042407 | Pride
Project description:Maintenance of chromatin structure is essential to eukaryotic life; dysregulation is known to be causal for aberrant development and disease. The Mi-2/nucleosome remodeling and histone deacetylase (NuRD) complex is a multiprotein machine proposed to regulate chromatin structure by nucleosome remodeling and histone deacetylation activities. We identified the localization of MBD3, a component of Mi-2/NuRD complex, in two breast cancer cell lines (MCF7 and MDA-MB-231) using ChIP-Seq. MBD3 showed cell-type specific localization with overlap across cell lines being less than 50%. MBD3 localized across gene bodies, peaking around the transcription start site (TSS). Contrary to existing models, MBD3 preferentially associated with CpG rich promoters marked by H3K4me3. These data suggest that MBD3, and by extension the Mi-2/NuRD complex, may have roles in fine tuning expression for active genes. These data represent an important first step in defining regulatory mechanisms by which Mi-2/NuRD complex controls chromatin structure and gene expression.
2013-10-31 | GSE44737 | GEO
Project description:The heterogeneous collection of NuRD complexes can be grouped into the MBD2 or MBD3 containing complexes MBD2-NuRD and MBD3-NuRD. MBD2 is known to bind to methylated CpG sequences in vitro in contrast to MBD3. Although functional differences have been described, a direct comparison of MBD2 and MBD3 in respect to genome-wide binding and function has been lacking. Here we show when depleting cells for MBD2, the MBD2 bound genes increase their activity, whereas MBD2 plus MBD3 bound genes reduce their activity. Most strikingly, MBD3 is enriched at active promoters, whereas MBD2 is bound at methylated promoters and enriched at exon sequences of active genes. This suggests a functional connection between MBD2 binding to chromatin and splicing. 9 Total samples were analysed. Three individual replicates for HeLa cells treated with siRNA against MBD2, MBD3 or scrambled siRNA were performed. We calculated the fold change of gene expression of cells treated with MBD2- or MBD3-siRNA over cells treated with scrambled siRNA.
2013-02-08 | E-GEOD-41003 | biostudies-arrayexpress