Genomics

Dataset Information

17

Mapping of NIPP1-WT and NIPP-RATA binding sites to ENCODE regions


ABSTRACT: To gain unbiased insight into the association of NIPP1 with regulatory, coding and intergenic regions of the human genome, DamID experiments and subsequent analysis by ENCODE arrays were performed. The DamID method uses fusions of the bacterial Dam DNA methylase and the protein of interest, to direct the enzymatic activity to the protein’s genomic binding sites, where the DNA is methylated. Methylated DNA is then extracted, enriched and further analysed by microarray. The PP1 (Protein Phosphatase 1) interacting protein NIPP1 has been implicated to play a role in regulation of gene expression through PRC2 function, but also has a function in splicing. The array analysis was performed to obtain a general picture of the sites of chromatin association of NIPP1 and specifically their spatial relation to coding regions as well as to identify target regions to be analysed in more detail. In addition, a PP1 binding deficient mutant (NIPP1-RATA) was analysed, thus allowing to distinguish PP1 dependent and independent sites of association with the genome by microarray analysis. NIPP1-WT is referred to as FDN and the mutant referred to as RATA in the following descriptions. Overall design: DamID for FDN (NIPP1-WT) (2 replicates) and DamID for RATA (NIPP1 mutant) (2 replicates) vs. control (DamID without fused protein) (2 replicates)

INSTRUMENT(S): GeneChip ENCODEver2.0R Array - NCBI build 36

SUBMITTER: Wouter Van Delm   

PROVIDER: GSE22123 | GEO | 2010-07-19

SECONDARY ACCESSION(S): PRJNA127589

REPOSITORIES: GEO

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Publications

The phosphatase interactor NIPP1 regulates the occupancy of the histone methyltransferase EZH2 at Polycomb targets.

Van Dessel Nele N   Beke Lijs L   Görnemann Janina J   Minnebo Nikki N   Beullens Monique M   Tanuma Nobuhiro N   Shima Hiroshi H   Van Eynde Aleyde A   Bollen Mathieu M  

Nucleic acids research 20100729 21


Polycomb group (PcG) proteins are key regulators of stem-cell and cancer biology. They mainly act as repressors of differentiation and tumor-suppressor genes. One key silencing step involves the trimethylation of histone H3 on Lys27 (H3K27) by EZH2, a core component of the Polycomb Repressive Complex 2 (PRC2). The mechanism underlying the initial recruitment of mammalian PRC2 complexes is not well understood. Here, we show that NIPP1, a regulator of protein Ser/Thr phosphatase-1 (PP1), forms a c  ...[more]

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