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PHF3 regulates RNA stability through PHD and TLD domains - ChIPseq CNOT

ABSTRACT: PHF3 regulates RNA stability through PHD and TLD domains - ChIPseq CNOT

PROVIDER: PRJEB63536 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR11605604.fastq.gz	Fastqsanger.gz
	ERR11605605.fastq.gz	Fastqsanger.gz
	ERR11605606.fastq.gz	Fastqsanger.gz
	ERR11605607.fastq.gz	Fastqsanger.gz
	ERR11605608.fastq.gz	Fastqsanger.gz

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PHF3 binds G-rich RNAs and regulates RNA stability through its TFIIS-like domain (TLD) and plant homeodomain (PHD)

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

The SPOC proteins DIDO3 and PHF3 co-regulate gene expression and neuronal differentiation - RNAseq

Project description:Transcription is regulated by a multitude of activators and repressors, which bind to the RNA polymerase II (Pol II) machinery and modulate its progression. Death-inducer obliterator (DIDO) and PHD finger protein 3 (PHF3) are paralogue proteins that regulate transcription elongation by docking onto phosphorylated serine-2 in the C-terminal domain (CTD) of Pol II through their SPOC domains. Here we show that DIDO3 and PHF3 form a complex that bridges the Pol II elongation machinery with chromatin and RNA processing factors, and tethers Pol II in a phase-separated microenvironment. Their SPOC domains and C-terminal intrinsically disordered regions are critical for transcription regulation. PHF3 and DIDO exert cooperative and antagonistic effects on the expression of neuronal genes and are both essential for neuronal differentiation. The dataset contains RNAseq of HEK293 cells with various perturbations of PHF3 and DIDO1 genes.

2023-11-16 | E-MTAB-12782 | biostudies-arrayexpress

The SPOC proteins DIDO3 and PHF3 co-regulate gene expression and neuronal differentiation - 3' RNA-seq

Project description:Transcription is regulated by a multitude of activators and repressors, which bind to the RNA polymerase II (Pol II) machinery and modulate its progression. Death-inducer obliterator (DIDO) and PHD finger protein 3 (PHF3) are paralogue proteins that regulate transcription elongation by docking onto phosphorylated serine-2 in the C-terminal domain (CTD) of Pol II through their SPOC domains. Here we show that DIDO3 and PHF3 form a complex that bridges the Pol II elongation machinery with chromatin and RNA processing factors, and tethers Pol II in a phase-separated microenvironment. Their SPOC domains and C-terminal intrinsically disordered regions are critical for transcription regulation. The dataset contains 3' Sequencing of WT, PHF3 KO, and PHF3 dSPOC mutant HEK293 cell line. Cytoplasmic and nuclear fractions were profiled separately.

2023-10-31 | E-MTAB-12757 | biostudies-arrayexpress

PHF3 binds G-rich RNAs and regulates RNA stability through its TFIIS-like domain (TLD) and plant homeodomain (PHD)

Project description:PHF3 binds G-rich RNAs and regulates RNA stability through its TFIIS-like domain (TLD) and plant homeodomain (PHD)

| PRJNA1165812 | ENA

SET-9 and SET-26 impact transgenerational epigenetic inheritance and germline mortality through their PHD finger and SET domains [RNA-Seq ]

Project description:Transgenerational epigenetic inheritance (TEI), the transmission of epigenetic states between generations, has been observed in complex organisms ranging from plants to nematode worms, insects and mammals. One form of TEI that has been robustly studied is the inheritance of gene silencing. In Caenorhabditis elegans transgenerational gene silencing can be partitioned into three phases: the initiation of silencing, establishment of a heritable silencing signal within the parent individuals, and maintenance of this silencing signal within subsequent generations. Silencing involves nuclear and cytoplasmic components, and most genes involved in the process are linked to small RNA processing pathways. To date, two predicted histone methyltransferases have been implicated in the establishment of TEI, set-25 and set-32. Here, we demonstrate that the closely related paralogues set-9 and set-26 function in establishment and maintenance of TEI. We also identify a third related gene that lacks any predicted ordered domains; we name this gene intrinsically disordered protein-1 (idp-1). Strikingly, idp-1 also plays a role in establishment of TEI. SET-9 and SET-26 each contain a PHD finger and a SET domain. We show that the SET domains of SET-9 and SET-26 likely have no histone lysine methyltransferase activity, but that the PHD fingers bind trimethylated histone 3 lysine 4 (H3K4me3) in the absence of adjacent histone marks. We demonstrate that despite modelling data that suggests that set-9 and set-26 lack histone lysine methyltransferase activity, the function of both genes in TEI requires their PHD finger and SET domains. Our data confirm that the SET domain is functional and identifies three new chromatin factors required for epigenetic inheritance.

2024-12-31 | GSE245980 | GEO

SET-9 and SET-26 impact transgenerational epigenetic inheritance and germline mortality through their PHD finger and SET domains [small RNA-seq]

2024-12-31 | GSE245981 | GEO

Deficiency of myeloid PHD proteins aggravates atherogenesis via macrophage apoptosis and paracrine fibrotic signaling [bulk RNA-seq]

Project description:Atherosclerotic plaque hypoxia is detrimental for macrophage function. Prolyl hydroxylases (PHDs) initiate cellular responses to hypoxia and may therefore govern macrophage function in plaque hypoxia. PHD inhibitors are clinically investigated to treat anemia in patients with chronic kidney disease, but the consequences for cardiovascular disease are not clear. Hence, we studied the influence of myeloid specific PHD deficiency on atherosclerotic plaque development and stability.

2022-03-30 | GSE150088 | GEO

Deficiency of myeloid PHD proteins aggravates atherogenesis via macrophage apoptosis and paracrine fibrotic signaling [single-cell RNA-seq]

2022-03-30 | GSE150089 | GEO

Anti-Pol II pS5 co-immunoprecipitation in PHF3 WT, KO and ΔSPOC HEK293T cells

Project description:The analysis of differential interactome of Pol II pS5 in PHF3 WT, KO and ΔSPOC HEK293T cells using Pol II pS5 (4H8) antibody coupled to Protein G beads.

2023-10-25 | PXD039537 | Pride

chipseq

Project description:chipseq data

| PRJEB39779 | ENA