Differentially expressed genes in Gdown1 KO liver [array]
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE144209 | GEO | 2021/01/06
REPOSITORIES: GEO
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Project description:Differentially expressed genes in Gdown1 KO liver [array]
| PRJNA603067 | ENA
Project description:To investigate the biological role of Gdown1, differentially expressed genes in Gdown1 knockout and p53/Gdown1 double-knockout mouse liver were analyzed by RNA-seq.
2021-01-06 | GSE144210 | GEO
Project description:Differentially expressed genes in Gdown1 knockout and Gdown1/p53 double-knockout mouse liver [RNA-seq]
| PRJNA603066 | ENA
Project description:Approximately half of purified mammalian RNA polymerase II (Pol II) is associated with a tightly interacting sub-stoichiometric subunit called Gdown1, encoded by the POLR2M gene. Previous in vitro and structural studies have established that Gdown1 potently inhibits transcription initiation through competitive interactions with general transcription factors and blocks the Pol II termination activity of transcription termination factor 2 (TTF2). However, the biological functions of Gdown1 remain poorly understood. Here, we utilized genetic, microscopic, and multi-omics approaches to functionally characterize Gdown1 in multiple human cell lines. Remarkably, acute depletion of Gdown1 led to minimal direct effects on gene expression and transcription. We show that Gdown1 resides predominantly in the cytoplasm of interphase cells, shuttles between the cytoplasm and nucleus, and is directly regulated by nuclear export. Gdown1 enters the nucleus at the onset of mitosis prior to complete breakdown of the nuclear envelope, whereupon association with Pol II becomes possible. Consistently, genetic ablation of Gdown1 is associated with partial de-repression of mitotic transcription, and Gdown1 KO cells present with a growth defect and evidence of aberrant mitoses coupled to p53 pathway activation. Evidence is presented demonstrating that Gdown1 association with Pol II elongation complexes in vitro modulates the combined functions of purified productive elongation factors PAF1C, RTF1, SPT6, DSIF, and P-TEFb. Collectively, our findings support a model wherein the Pol II-regulatory function of Gdown1 occurs during mitosis and is required for genome integrity.
2022-01-03 | GSE186133 | GEO
Project description:Approximately half of purified mammalian RNA polymerase II (Pol II) is associated with a tightly interacting sub-stoichiometric subunit, Gdown1. Previous studies have established that Gdown1 inhibits transcription initiation through competitive interactions with general transcription factors and blocks the Pol II termination activity of transcription termination factor 2 (TTF2). However, the biological functions of Gdown1 remain poorly understood. Here, we utilized genetic, microscopic, and multi-omics approaches to functionally characterize Gdown1 in three human cell lines. Acute depletion of Gdown1 caused minimal direct effects on transcription. We show that Gdown1 resides predominantly in the cytoplasm of interphase cells, shuttles between the cytoplasm and nucleus, and is regulated by nuclear export. Gdown1 enters the nucleus at the onset of mitosis. Consistently, genetic ablation of Gdown1 is associated with partial de-repression of mitotic transcription, and Gdown1 KO cells present with evidence of aberrant mitoses coupled to p53 pathway activation. Evidence is presented demonstrating that Gdown1 modulates the combined functions of purified productive elongation factors PAF1C, RTF1, SPT6, DSIF, and P-TEFb in vitro. Collectively, our findings support a model wherein the Pol II-regulatory function of Gdown1 occurs during mitosis and is required for stably maintaining a pattern of gene expression across cell divisions. To characterize potential interactors of Gdown1 in the cytoplasm, an eGFP-TEV-Gdown1 HAP1 cell line was developed. Cytosolic extracts were prepared, GFP-Trap Agarose (Chromotek) was utilized to pull down Gdown1 and associated factors, and associated proteins were characterized by LC-MS/MS.
2022-02-14 | PXD029425 | Pride
Project description:Most human genes are loaded with promoter proximally paused RNA polymerase II (RNAP II) molecules that are poised for release into productive elongation by P-TEFb. Gdown1, a protein that renders RNAP II responsive to mediator, is involved in RNAP II elongation control. During in vitro transcription assays Gdown1 specifically blocked elongation stimulation by TFIIF, inhibited the termination activity of TTF2, and influenced pausing factors NELF and DSIF, but did not affect the function of TFIIS or the mRNA capping enzyme. Without P-TEFb, Gdown1 led to the production of stably paused polymerases in the presence of nuclear extract. ChIP-Seq data demonstrated that Gdown1 mapped over essentially all poised polymerases across the human genome. Gdown1 increases the stability of poised polymerases while maintaining their responsiveness to P-TEFb, and mediator overcomes a Gdown1-mediated block of initiation by allowing TFIIF function. 7 ChIP-Seq data for Pol II and Gdown1 in human HeLa cell. See associated publication.
2012-01-13 | E-GEOD-32442 | biostudies-arrayexpress
Project description:Most human genes are loaded with promoter proximally paused RNA polymerase II (RNAP II) molecules that are poised for release into productive elongation by P-TEFb. Gdown1, a protein that renders RNAP II responsive to mediator, is involved in RNAP II elongation control. During in vitro transcription assays Gdown1 specifically blocked elongation stimulation by TFIIF, inhibited the termination activity of TTF2, and influenced pausing factors NELF and DSIF, but did not affect the function of TFIIS or the mRNA capping enzyme. Without P-TEFb, Gdown1 led to the production of stably paused polymerases in the presence of nuclear extract. ChIP-Seq data demonstrated that Gdown1 mapped over essentially all poised polymerases across the human genome. Gdown1 increases the stability of poised polymerases while maintaining their responsiveness to P-TEFb, and mediator overcomes a Gdown1-mediated block of initiation by allowing TFIIF function.
2012-01-13 | GSE32442 | GEO
Project description:Nuclear export restricts Gdown1 to a mitotic function
| PRJNA772715 | ENA
Project description:We applied DIA Proteomic Analysis to explore Differentially expressed proteins between WT sperms and Cfap77-KO sperms. In this DIA Proteomic Analysis project, there were 6 Mus_musculus samples named W1,W2,W3,C1,C2,C3 and we did 1 technical duplicate experiments. Totally 94339 peptides and 6525 proteins were identified with 1% FDR. Proteins with 2 fold change (mean value of all comparision groups) and P-value (t-test of all comparision groups) less than 0.05 were defined as differentially expressed proteins.
2024-09-18 | PXD056128 |
Project description:We applied iTRAQ Quantification Proteomics to explore Differentially expressed proteins between WT testis and Cfap70-KO testis. In this iTRAQ quantification project,there were 6 Mus_musculus samples named C_1, C_2, C_3, K_1, K_2, K_3 and we did 1 technical duplicate experiments. Totally 480850 spectrums were generated, 38748 peptides and 6734 proteins were identified with 1% FDR. proteins with 1.2 fold change(mean value of all comparison groups) and P-value(t-test of all comparision groups) less than 0.05 were defined as differentially expressed proteins.
2022-04-11 | PXD033133 |