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

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

PROVIDER: PRJEB32349 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3299640.fastq.gz	Fastqsanger.gz
	ERR3299650.fastq.gz	Fastqsanger.gz
	ERR3299660.fastq.gz	Fastqsanger.gz
	ERR3299670.fastq.gz	Fastqsanger.gz
	ERR3299680.fastq.gz	Fastqsanger.gz

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

Project description:Tergeted SLAM seq of WT, PHF3 KO and dSPOC, HEK293 cells

2021-09-07 | E-MTAB-7899 | biostudies-arrayexpress

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 - 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 - SLAM - seq

Project description:Pulse-chase experiment using SLAM-seq in WT, PHF3KO, and dSPOC, HEK293 cells

2021-09-07 | E-MTAB-7898 | 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 - RNAseq

Project description:Total RNA sequencing of WT, PHF3 KO and dSPOC, HEK293 cells

2021-09-07 | E-MTAB-7498 | biostudies-arrayexpress

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

| PRJEB34179 | 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:PRO-seq timecourse sampled at 0m, 10m, 25m, 40m after DRB inhibition WT, PHF3 KO and dSPOC, HEK293 cells

2021-09-07 | E-MTAB-8278 | biostudies-arrayexpress

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