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PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - TFIIS, H3K27me3, F-12 ChIP-seq

ABSTRACT: PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - TFIIS, H3K27me3, F-12 ChIP-seq

PROVIDER: PRJEB36735 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3895550.fastq.gz	Fastqsanger.gz
	ERR3895560.fastq.gz	Fastqsanger.gz
	ERR3895570.fastq.gz	Fastqsanger.gz
	ERR3895551.fastq.gz	Fastqsanger.gz
	ERR3895561.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

PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - TFIIS, H3K27me3, F-12 ChIP-seq

Project description:ChIP-seq of TFIIS, H3K27me3, and F-12 in WT, KO, and dSPOC HEK293 cells. ChIP-seq of PHF3 - GFP in WT HEK293 cells

2021-09-07 | E-MTAB-8789 | biostudies-arrayexpress

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 RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - PROseq

Project description:PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - PROseq

| PRJEB30261 | ENA

PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - RNAseq

Project description:PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - RNAseq

| PRJEB30255 | ENA

PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - SLAM - seq

Project description:PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - SLAM - seq

| PRJEB32284 | ENA

PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - Targeted SLAM-seq

Project description:PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - Targeted SLAM-seq

| PRJEB32349 | ENA

PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - PolII ChIP-seq

Project description:PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - PolII ChIP-seq

| PRJEB36717 | ENA

PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - PRO-seq Timecourse

Project description:PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - PRO-seq Timecourse

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