Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators - RNAseq

ABSTRACT: RNAseq of HEK cell lines created by making KO or removing the SPOC domain of PHF3, DIDO1, SHARP, and RBM15 proteins

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Vedran Franke

PROVIDER: E-MTAB-12358 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators - ChIP-seq

Project description:The heptarepeats of the C-terminal domain of Pol II are extensively modified throughout the transcription cycle. The CTD coordinates RNA synthesis and processing by recruiting transcription regulation factors as well as RNA capping, splicing and 3’end processing factors. The SPOC domain of PHF3 was recently identified as a new CTD reader domain specifically binding to phosphorylated Serine-2 residues in adjacent CTD repeats. Here, we establish the SPOC domains of the human proteins DIDO, SHARP and RBM15 as phosphoserine binding modules that can act as CTD readers but also recognize other phosphorylated binding partners. We report the crystal structure of SHARP (SPEN) SPOC-CTD and identify the molecular determinants for its specific binding to phosphorylated Serine-5. PHF3 and DIDO SPOC domains preferentially interact with the Pol II elongation complex, while RBM15 and SHARP SPOC domains engage with the m6A writer and reader proteins. Our findings establish the SPOC domain as a major interface between the transcription machinery and regulators of transcription and co-transcriptional processes. Here we include ChIP seq data from SHARP and PHF3 with and without the SPOC domain.

2023-02-22 | E-MTAB-11506 | 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 domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators - TTseq

Project description:TTseq of HEK cell lines created by making KO or removing the SPOC domain of PHF3, DIDO1, SHARP, and RBM15 proteins

2023-06-19 | E-MTAB-12359 | 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

Whole Transcriptome Sequencing of Cervical Adenocarcinoma

Project description:The raw data consists of Transcriptome sequencing of 24 tumor samples and 5 normal samples of cervical adenocarcinoma samples

2022-02-11 | E-MTAB-9281 | biostudies-arrayexpress

Generation of zero-valent sulfur from dissimilatory sulfate reduction in sulfate-reducing bacteria

Project description:We report a new DSR pathway that directly generates zero-valent sulfur (ZVS) in phylogenetically diverse SRB.

2023-04-27 | E-MTAB-12239 | biostudies-arrayexpress

RNA-seq of primary aortic human endothelial cells before and after TNFα stimulation

Project description:To characterize the transcriptome of primary vascular endothelial cells (ECs) during TNFα-response, we performed total RNA-seq on primary human aortic ECs (HAEC), before and after TNFα (45 min. 10 ng/mL).

2020-06-01 | E-MTAB-7896 | biostudies-arrayexpress

Investigating the effects of Ceylon cinnamon water extract and metformin on HepG2 cells for type 2 diabetes therapy

Project description:performing high-throughput RNA sequencing (RNA-Seq) transcriptomic analysis of hepatic cells after metformin or CWE treatment to identify changes in diabetes-related gene expression. Outcomes of this project provide evidence for the effectiveness of Ceylon cinnamon water extract compared to the current standard therapy for type 2 diabetes, metformin.

2022-02-14 | E-MTAB-11418 | biostudies-arrayexpress

RNA-seq of shControl and shRUNX1-ETO Kasumi-1 cells

Project description:RUNX1-ETO knockdown was performed in Kasumi-1 cells and transcriptomic analyses by RNA-sequencing were performed at two different time points (day2 and day9). Control cells (Kasumi-1 shControl) were also analysed at day2 and day9. All samples were analysed in triplicates.

2022-02-01 | E-MTAB-9016 | biostudies-arrayexpress

A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-01-19 | E-GEOD-70149 | biostudies-arrayexpress