Application of recombinant PHD domain instead of anti-H3K4me3 antibody
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500
ORGANISM(S): Homo sapiens
SUBMITTER: Goran Kungulovski
PROVIDER: E-MTAB-4103 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Application of recombinant PHD domain instead of anti-H3K4me3 antibody
| PRJEB11987 | ENA
Project description: Not available
| S-EPMC4802638 | biostudies-literature
Project description:Histone modifications regulate chromatin-dependent processes, yet the mechanisms by which they contribute to specific outcomes remain unclear. H3K4me3 is a prominent histone mark that is associated with active genes and promotes transcription through interactions with effector proteins that include initiation factor TFIID. We demonstrate that H3K4me3-TAF3 interactions direct global TFIID recruitment to active genes, some of which are p53 targets. Further analyses show that (i) H3K4me3 enhances p53-dependent transcription by stimulating preinitiation complex (PIC) formation; (ii) H3K4me3, through TAF3 interactions, can act either independently or cooperatively with the TATA box to direct PIC formation and transcription; and (iii) H3K4me3-TAF3/TFIID interactions regulate gene-selective functions of p53 in response to genotoxic stress. Our findings indicate a mechanism by which H3K4me3 directs PIC assembly for the rapid induction of specific p53 target genes Examination of genome wide binding sites of TAF3 full length protein vs TAF3 PHD domain alone (Full vs PHD), with or without M880A mutation (WT vs mut) in mouse MEF cells using HITseq method (PNAS 2010, 107:3135-3140, PMID: 20133638)
2013-03-02 | E-GEOD-43540 | biostudies-arrayexpress
Project description:The aim of the experiment was to determine if changes in nuclear phosphoinositides induced by depletion of PIP4K2B impacts on gene expression through a specific phosphoinositide interaction site on TAF3. TAF3 is a core promoter complex protein that contains a PHD finger that interacts with H3K4me3. We determined that The TAF3 PHD finger also interacted with phosphoinositides and generated mutants of TAF3 that were unable to interact with phosphoinositides but still were capable of interacting with H3K4me3. PIP4K2B depletion enhances C2C12 myoblast differentiation. We depleted the endogenous TAF3 from C2C12 myoblast cells and rescued the cells with either a wild type TAF3 or a mutant unable to interact with PI (KK-TAF3). These cells were then maintained as controls or depeleted of PIP4K2B. The cells were then differentiated for two days or were treated wtih a etoposide. We aimed to identify genes that were reguated by PIP4K2B that required an intact phosphoinositide binding site.
2015-02-28 | GSE66353 | GEO
Project description:The aim of the experiment was to determine if changes in nuclear phosphoinositides induced by depletion of PIP4K2B impacts on gene expression through a specific phosphoinositide interaction site on TAF3. TAF3 is a core promoter complex protein that contains a PHD finger that interacts with H3K4me3. We determined that The TAF3 PHD finger also interacted with phosphoinositides and generated mutants of TAF3 that were unable to interact with phosphoinositides but still were capable of interacting with H3K4me3. PIP4K2B depletion enhances C2C12 myoblast differentiation. We depleted the endogenous TAF3 from C2C12 myoblast cells and rescued the cells with either a wild type TAF3 or a mutant unable to interact with PI (KK-TAF3). These cells were then maintained as controls or depeleted of PIP4K2B. The cells were then differentiated for two days or were treated wtih a etoposide. We aimed to identify genes that were reguated by PIP4K2B that required an intact phosphoinositide binding site. Triplicate biological samples were analysed for each point after differentiation for three days or etoposide treatment for seven hours.
2015-02-28 | E-GEOD-66353 | biostudies-arrayexpress
Project description:PHF3 regulates RNA stability through PHD and TLD domains - RNAseq PHD - TLD
| PRJEB81153 | ENA
Project description:Transcription and RNA processing are tightly coupled and precisely coordinated to ensure appropriate levels of mature transcripts. The C-terminal domain (CTD) of RNA polymerase II (Pol II) is phosphorylated differentially during the transcription cycle and serves as a landing pad for a variety of transcriptional regulators and RNA processing proteins. PHD finger protein 3 (PHF3) binds to the serine-2 phosphorylated Pol II CTD with its Spen Paralogue and Orthologue C-terminal (SPOC) domain and regulates transcription elongation and mRNA stability. Here we show that PHF3 is an RNA-binding protein that recognizes a G-rich motif prone to form G-quadruplexes (G4s) within RNAs required for neurogenesis. We identify PHF3 TFIIS-like domain (TLD) as an RNA-binding domain, which shows nanomolar affinity for G-rich RNAs. TLD recruits PHF3 onto target RNAs and acts in concert with the plant homeodomain (PHD) to promote target RNA destabilization. PHF3 SPOC and PHD-TLD domains mediate interactions with various RNA-binding proteins (RBPs) that regulate mRNA stability. While PHF3 SPOC-dependent interactions with the m6A writer complex, splicing and elongation factors do not impact m6A RNA modification, alternative splicing or polyadenylation, PHF3 PHD-TLD domains interact with the PAF1 complex as a positive regulator of mRNA stability and interfere with its binding to Pol II. Our results establish PHF3 as an RNA-binding protein that binds G-rich RNAs through its TLD domain and destabilizes RNAs through PHD-TLD domains.
2025-09-26 | GSE278179 | GEO
Project description:The lysine-specific demethylase 2A gene (KDM2A) is ubiquitously expressed and its transcripts consist of several alternatively spliced forms, including KDM2A and the shorter form N782 that lacks the 3’ end encoding F-box and LRR. KDM2A binds to numerous CpG-rich genomic loci and regulates various cellular activities; however, the mechanism of the pleiotropic function is unknown. Here, we identify the mechanism of KDM2A played by its CXXC-PHD domain. KDM2A is necessary for a rapid proliferation of post-natal keratinocytes while its 3’ end eclipses the stimulatory effect. EGFP-N782 binds to chromatin together with the XRCC5/6 complex, and the CXXC-PHD domain regulates the CpG-rich IGFBPL1 promoter. In vitro, CXXC-PHD enhances binding of nuclear extract ORC3 to the CpG-rich promoter, but not to the AT-rich DIP2B promoter to which ORC3 binds constitutively. Furthermore, CXXC-PHD recruits 94 nuclear factors involved in replication, ribosome synthesis, and mitosis, including POLR1A to the IGFBPL1 promoter. This recruitment is unprecedented; however, the result suggests that these nuclear factors bind to their cognate loci, as substantiated by the result that CXXC-PHD recruits POLR1A to the rDNA promoter. We propose that CXXC-PHD promotes permissiveness for nuclear factors to interact, but involvement of the XRCC5/6 complex in the recruitment is undetermined.
2019-06-28 | PXD012941 | Pride
Project description:Transcription and RNA processing are tightly coupled and precisely coordinated to ensure appropriate levels of mature transcripts. The C-terminal domain (CTD) of RNA polymerase II (Pol II) is phosphorylated differentially during the transcription cycle and serves as a landing pad for a variety of transcriptional regulators and RNA processing proteins. PHD finger protein 3 (PHF3) binds to the serine-2 phosphorylated Pol II CTD with its Spen Paralogue and Orthologue C-terminal (SPOC) domain and regulates transcription elongation and mRNA stability. Here we show that PHF3 binds target RNAs by recognizing a G-rich motif prone to form G-quadruplexes (G4s). Two PHF3 zinc finger domains, PHD (plant homeo domain) and TLD (TFIIS-like domain) act in concert to bind and destabilize target RNAs and their deletion in HEK293T cells causes massive deregulation of gene expression. Together these results establish PHF3 as a Pol II and an RNA-binding protein that coordinates transcription elongation with RNA decay to regulate neuronal gene expression.
2025-12-04 | E-MTAB-14530 | biostudies-arrayexpress
Project description:Nucleosomes must be deacetylated behind elongating RNA polymerase II to prevent cryptic initiation of transcription within the coding region. RNA polymerase II signals for deacetylation through methylation of histone H3 lysine 36 (H3K36) which provides the recruitment signal for the Rpd3S deacetylase complex. Recognition of methyl-H3K36 by Rpd3S requires the chromodomain of its Eaf3 subunit. Paradoxically, Eaf3 is also a subunit of the NuA4 acetyltransferase complex yet NuA4 does not recognize methyl H3K36 nucleosomes. We found that methyl H3K36 nucleosome recognition by Rpd3S also requires the PHD domain of its Rco1 subunit. Thus, the coupled chromo and PHD domains of Rpd3S specifies recognition of the methyl H3K36 mark; demonstrating the first combinatorial domain requirement within a protein complex to read a specific histone code.
2007-05-16 | E-TABM-260 | biostudies-arrayexpress