characteristics.text: SAMN00008869
characteristics.characteristic: External Id
characteristics.text: Center for Genomic Regulation
characteristics.characteristic: INSDC center name
characteristics.text: 2010-04-26T00:00:00Z
characteristics.characteristic: INSDC first public
characteristics.text: 2013-06-12T08:46:53.963Z
characteristics.characteristic: INSDC last update
characteristics.text: SRS004362
characteristics.characteristic: INSDC secondary accession
characteristics.text: live
characteristics.characteristic: INSDC status
characteristics.text: Generic
characteristics.characteristic: NCBI submission model
characteristics.text: Generic.1.0
characteristics.characteristic: NCBI submission package
characteristics.text: SRS004362
characteristics.characteristic: SRA accession
characteristics.text: 2
characteristics.characteristic: antibody ab35471
characteristics.text: Hs68
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0006441
characteristics.characteristic: cell line
characteristics.text: serum-starved for 4 days; re-stimulated for 4 hours
characteristics.characteristic: condition
characteristics.text: Mutations in PHF8 are associated with X-linked mental retardation and cleft lip/cleft palate. PHF8 contains a plant homeodomain (PHD) in its N-terminus and is member of a family of JmjC-domain containing proteins. While PHDs can act as methyl lysine recognition motifs, JmjC-domains can catalyze lysine demethylation. Here, we show that PHF8 is a histone demethylase that removes repressive histone H3 dimethyl lysine 9 marks. Our biochemical analysis revealed specific association of the PHF8 PHD domain with histone H3 trimethylated at lysine 4 (H3K4me3). Chromatin-immunoprecipitation followed by high throughput sequencing indicated that PHF8 is enriched at transcription start sites of many active or poised genes, mirroring the presence of RNA polymerase II (RNAPII) and of H3K4me3-bearing nucleosomes. We show that PHF8 can act as a transcriptional co-activator and its activation function largely depends on binding of the PHD to H3K4me3. Furthermore, we present evidence for direct interaction of PHF8 with the C-terminal domain of RNAPII. Importantly, a PHF8 disease mutant is defective in demethylation and in co-activation. This is the first demonstration of a chromatin-modifying enzyme, which associates with promoters via the H3K4me3 modification and RNAPII.
characteristics.characteristic: description
characteristics.text: 10
characteristics.characteristic: fixed sonicated chromatin
characteristics.text: 135 +/- 25
characteristics.characteristic: fragment size
characteristics.text: Homo sapiens
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: organism
characteristics.text: 35
characteristics.characteristic: read length
characteristics.text: Generic sample from Homo sapiens
characteristics.characteristic: title