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

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

INSTRUMENT(S): NextSeq 550

ORGANISM(S): Homo sapiens

SUBMITTER: Dea Slade

PROVIDER: E-MTAB-7899 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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 - 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

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

Project description:ChIP-seq of pSer2, and pSer5 in WT, KO, and dSPOC HEK293 cells. ChIP-seq of PHF3 - GFP in WT HEK293 cells

2021-09-07 | E-MTAB-8783 | biostudies-arrayexpress

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

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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

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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:PRO-seq data of WT, KO, and dSPOC HEK293 cells.

2021-09-07 | E-MTAB-7501 | 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

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

Project description:RNA seq of WT and PHF3 KO mouse embryonic stem cells

2021-09-07 | E-MTAB-7526 | biostudies-arrayexpress

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

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