Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide identification of MBD2 and MBD3 binding sites by ChIP-seq

ABSTRACT: The heterogeneous collection of NuRD complexes can be grouped into the MBD2 or MBD3 containing complexes MBD2-NuRD and MBD3-NuRD. 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 a strong enrichment for MBD2 at methylated CpG sequences, whereas CpGs bound by MBD3 are devoid of methylation. Gene activity of MBD2 bound genes is four fold lower as compared to genes bound by MBD3. 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. V5 ChIP followed by high throughput sequencing in HeLa cells transiently transfected with either V5-MBD2b, V5-MBD3 or V5.

ORGANISM(S): Homo sapiens

SUBMITTER: Marek Bartkuhn 

PROVIDER: E-GEOD-41006 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Differential roles for MBD2 and MBD3 at methylated CpG islands, active promoters and binding to exon sequences.

Günther Katharina K   Rust Mareike M   Leers Joerg J   Boettger Thomas T   Scharfe Maren M   Jarek Michael M   Bartkuhn Marek M   Renkawitz Rainer R  

Nucleic acids research 20130129 5

The heterogeneous collection of nucleosome remodelling and deacetylation (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 that MBD2-NuRD, in contrast to MBD3-NuRD, converts open chromatin with euchro  ...[more]

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