Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0

Genome-wide mapping of H3K4me3 and of PHF8 and ZNF711 binding sites in SH-SY5Y cells

ABSTRACT: We analyzed the genome wide binding sites for the potential XLMR genes PHF8 and ZNF711 in the neuroblastoma cell line SH-SY5Y using antibodies specific for PHF8 and ZNF711 and correlated this with binding pattern of H3K4me3. The total number of peaks detected for PHF8 based on 9.8 million sequence reads, 9.6 million sequence reads for ZNF711 and 9.1 million sequence reads for H3K4me3 after IgG normalization were 17075, 1875 and 19534, respectively. Annotation of the peaks to genes using the hg18 genome database revealed 10039 genes positive for H3K4me3, 7682 were bound by PHF8 and 1103 genes were bound by ZNF711 within +/-1000bp from TSS. As former genome wide analysis of H3K4me3 revealed is this histone mark preferentially associated with transcription start sites. The analysis revealed that 82% of H3K4me3 positive genes are also positive for PHF8. In general, PHF8 either co-localizes or partly overlaps with regions positive for H3K4me3 and covers the putative TSS of the target genes. Examination of two different proteins and one histone modification in a human neuroblastoma cell line

ORGANISM(S): Homo sapiens

SUBMITTER: Daniela Kleine-Kohlbrecher 

PROVIDER: E-GEOD-20673 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

Json Xml
altmetric image

Publications

A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation.

Kleine-Kohlbrecher Daniela D   Christensen Jesper J   Vandamme Julien J   Abarrategui Iratxe I   Bak Mads M   Tommerup Niels N   Shi Xiaobing X   Gozani Or O   Rappsilber Juri J   Salcini Anna Elisabetta AE   Helin Kristian K  

Molecular cell 20100325 2

X-linked mental retardation (XLMR) is an inherited disorder that mostly affects males and is caused by mutations in genes located on the X chromosome. Here, we show that the XLMR protein PHF8 and a C. elegans homolog F29B9.2 catalyze demethylation of di- and monomethylated lysine 9 of histone H3 (H3K9me2/me1). The PHD domain of PHF8 binds to H3K4me3 and colocalizes with H3K4me3 at transcription initiation sites. Furthermore, PHF8 interacts with another XMLR protein, ZNF711, which binds to a subs  ...[more]

Similar Datasets

Genomics Genome-wide mapping of H3K4me3 and of PHF8 and ZNF711 binding sites in SH-SY5Y cells
2010-03-08 | GSE20673 | GEO
Genomics H3K4me3 ChIP_Seq in mouse decidua
2022-01-20 | GSE191327 | GEO
Genomics Menin and H3K4me3 ChIP_Seq in mouse decidua
2022-01-20 | GSE182539 | GEO
Transcriptomics The mental retardation gene PHF8 mediates histone H4K20/H3K9 demethylation and regulates zebrafish brain apoptosis and craniofacial development: expression analysis
2010-07-14 | E-GEOD-21555 | biostudies-arrayexpress
Genomics The mental retardation gene PHF8 mediates histone H4K20/H3K9 demethylation and regulates zebrafish brain apoptosis and craniofacial development: ChIP-Seq analysis
2010-07-14 | E-GEOD-21108 | biostudies-arrayexpress
Genomics Genome-wide Analysis of Vitamin D Receptor Binding By ChIP-Seq
2010-06-22 | GSE22484 | GEO
Genomics PHF8 targets histone methylation and RNA polymerase II to activate transcription
2010-04-26 | E-GEOD-20753 | biostudies-arrayexpress
Genomics Metabolic adaptations underlie epigenetic vulnerabilities in chemoresistant breast cancer. [ChIP-Seq]
2020-08-18 | GSE113684 | GEO
Genomics Genome-wide Analysis of Vitamin D Receptor Binding By ChIP-Seq
2010-06-22 | E-GEOD-22484 | biostudies-arrayexpress
Genomics MCPyV ST, MAX and the TRRAP complex cooperate to bind to Transcription Start Sites
2017-09-28 | GSE69877 | GEO