biostudies-arrayexpressVedran FrankeHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14529Transcription 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.biostudies-arrayexpressSequencing - HiSeq 4000 platform with 75 Single end reads, performed by a commercial vendor EclipseBioSample Collection - Three biological replicates of HEK293T WT, PHF3 KO and PHF3 ∆SPOC cells grown in 15 cm dishes were harvested at ~80% confluency, pellets were resuspended in 1.5 mL TRI reagent (Sigma) and incubated for 5 min at room temperatureNucleic Acid Extraction - 300 µL chloroform (Applichem) was added and the lysate was vortexed and centrifuged at max. speed (21130xg) for 15 min at 4°C. The aqueous layer was transferred to a new tube and precipitated with 0.75 mL isopropanol. The RNA pellet was isolated by centrifugation for 30 min at 4°C, washed with 1 mL 75% ethanol, re-centrifuged for 10 min, dried and resuspended in 100 µL RNase free water. 120 µg RNA was treated with 240 U DNaseI (Roche) for 30 min at 37°C and subsequently purified by phenol-chloroform extraction and ethanol precipitation.Library Construction - m6A-eCLIP, library preparation and sequencing was performed by Eclipse Bioinnovations (San Diego, USA).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Data was mapped to the hg38 genome by Eclipse Bio, submitted are .bam files resulting from the mapping. The fastq files are derived from the BAM files. Due to processing of the data from a commercial vendor, raw fastq files were not available.UnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 4000RIP-seqHomo sapiensDea SladeVedran FrankefalsePHF3 regulates RNA stability through PHD and TLD domains - m6ATranscription 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.2025-12-03T00:00:00Z2025-12-03T02:02:04.472Z2024-10-11T15:35:31.579ZE-MTAB-14529ERP165079EFO_0002944EFO_0004170EFO_0005310EFO_0005518EFO_0003816EFO_0004184