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Transcriptome analysis of A549 cells expressing a SUMOylation-deficient TRIM28 mutant in the context of influenza A virus infection

ABSTRACT: Aim: Identify differentially expressed genes in human lung epithelial cells expressing a SUMOylation-deficient TRIM28 mutant (TRIM28 6KR) compared to TRIM28 wt.

ORGANISM(S): Homo sapiens

PROVIDER: GSE133329 | GEO | 2019/08/05

REPOSITORIES: GEO

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Transcriptome analysis of A549 cells expressing a SUMOylation-deficient TRIM28 mutant in the context of influenza A virus infection

Project description:Transcriptome analysis of A549 cells expressing a SUMOylation-deficient TRIM28 mutant in the context of influenza A virus infection

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TRIM28-dependent SUMOylation protects the adult ovary from the male pathway (ChIP-Seq 2)

Project description:We study the role of the protein Trim28 in the maintenance of sexual identity of the adult ovary. With the help of conditional knock out (cKO) of Trim28 using the Nr5a1:Cre, we observed that deletion of the Trim28 gene in granulosa cells of the adult ovary induces their transdifferentiation into Sertoli cells, the supporting cell lineage of the testicular seminiferous tubules. FOXL2 expression has disappeared and follicles were completely remodeled into tubular structures with cells that expressed the Sertoli cell markers SOX8, SOX9 and DMRT1. Histological analysis confirmed the progressive reorganization of ovarian follicles into tubular structures and the and the transdifferentiation of granulosa cells by cells with a Sertoli cell morphology. TRIM28 acts as a SUMO-E3 ligase by interacting with the SUMO-E2 conjugating enzyme UBC9 (encoded by the Ube2i gene) via the Plant homeodomain (PHD), and can self-SUMOylate. To study in vivo the role of TRIM28-dependent SUMOylation, we generated a point mutation in exon 13 of mouse Trim28 within the PHD domain of the TRIM28 protein (C651F) that abrogates its SUMO-E3 ligase activity. We generated Trim28Phd/cKO mice (termed PHD mutant). Like in cKO ovaries, FOXL2 expression was undetectable, whereas we observed expression of the Sertoli cell markers SOX9, SOX8 and DMRT1 within structures organized in pseudo-tubules in PHD ovaries. Our results indicate that maintenance of the female pathway in the adult ovary depends on the E3-SUMO ligase activity of TRIM28.

2022-05-24 | GSE166384 | GEO

TRIM28-dependent SUMOylation protects the adult ovary from the male pathway

Project description:TRIM28-dependent SUMOylation protects the adult ovary from the male pathway

| PRJNA700643 | ENA

TRIM28-dependent SUMOylation protects the adult ovary from the male pathway (RNA-Seq)

Project description:TRIM28-dependent SUMOylation protects the adult ovary from the male pathway (RNA-Seq)

| PRJNA700646 | ENA

TRIM28-dependent SUMOylation protects the adult ovary from the male pathway (RNA-Seq)

2022-05-24 | GSE166382 | GEO

Changes to SUMO2 conjugation during Influenza virus infection of cultured cells

Project description:Dynamic SUMO modifications of diverse cellular protein groups are critical to orchestrate resolution of stresses such as genome damage, hypoxia or proteotoxicity. Defense against pathogen insult (usually reliant upon host recognition of ‘non-self’ nucleic acids), is also modulated by SUMO, but the underlying mechanisms are incompletely understood. Here, we used quantitative SILAC-based proteomics to survey pan-viral host SUMOylation responses, creating a resource of almost 600 common and unique SUMO remodeling events that are mounted during influenza A and B virus infections, as well as during viral immune stimulation. By integrating knock-out/reconstitution models and transcriptomics, we provide evidence that influenza virus triggered loss of SUMO-modified TRIM28 leads to derepression of endogenous retroviral elements, unmasking this cellular pool of ‘self’ double-stranded (ds) RNA. Consequently, loss of SUMO-modified TRIM28 potentiates canonical cytosolic dsRNA-activated interferon-mediated defenses. Our data suggest that a key nuclear mechanism that prevents expression of endogenous retroviruses has been functionally co-opted via a stress-induced SUMO switch to augment antiviral immunity.

2019-08-12 | PXD014136 | Pride

TRIM28-dependent SUMOylation protects the adult ovary from the male pathway (ChIP-Seq 1)

Project description:TRIM28-dependent SUMOylation protects the adult ovary from the male pathway (ChIP-Seq 1)

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TRIM28-dependent SUMOylation protects the adult ovary from the male pathway (ChIP-Seq 2)

Project description:TRIM28-dependent SUMOylation protects the adult ovary from the male pathway (ChIP-Seq 2)

| PRJNA700645 | ENA

TRIM28-dependent SUMOylation protects the adult ovary from the male pathway (ChIP-Seq 1)

2022-05-24 | GSE166383 | GEO

Transcriptome analysis in sumoylation deficient (ubc9-6) budding yeast and in a strain with a sumoylation-impairing mutation in the TFIIF subunit, Tfg1

Project description:Transcription related proteins are among the most frequently identified targets of SUMO post-translational modification, but the gene-specific and genome-wide effects of transcription machinery sumoylation are not well-understood. To explore this, we examined whether dramatically reducing cellular sumoylation levels affects the levels of mRNAs in budding yeast. RNA-seq was performed using polyadenylate (polyA)-enriched RNAs from the sumoylation-deficient ubc9-6 strain and its wild-type parent. Indeed, the abundance of hundreds of mRNAs were upregulated or downregulated in the mutant strain, implying that sumoylation has a widespread influence on RNA polymerase II (RNAPII) transcription or mRNA stability. Interestingly, about one third of mRNAs that were significantly upregulated in the ubc9-6 strain encode proteins that are involved in small molecule metabolic processes, suggesting that sumoylation is normally involved in restricting these pathways. As part of our analysis of transcription-related sumoylation, we determined that the large subunit of TFIIF, Tfg1, is a major target of sumoylation among the general transcription factors (GTFs) of RNAPII. To determine whether sumoylation of Tfg1 specifically is involved in regulating mRNA levels, we performed RNA-seq on polyA-enriched RNAs derived from strains expressing wild-type (Tfg1-HA) or sumoylation-deficient (Tfg1-K60,61R-HA) forms of Tfg1. However, with few exceptions, impairing Tfg1 sumoylation had no effect on the mRNA transcriptome. Together, our data demonstrate that gene expression is extensively regulated by sumoylation, but this likely involves the coordinated modification of multiple proteins at multiple levels.

2021-09-21 | GSE167427 | GEO

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