Transcriptomics

Dataset Information

121

Expression data from HeLa cells after MBD2 and MBD3 knock down


ABSTRACT: 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.

ORGANISM(S): Homo sapiens  

SUBMITTER: Katharina Guenther   Marek Bartkuhn  Rainer Renkawitz 

PROVIDER: E-GEOD-41003 | ArrayExpress | 2013-02-08

SECONDARY ACCESSION(S): GSE41003PRJNA175532

REPOSITORIES: GEO, 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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