Identification of RING E3 pseudoligases in the TRIM protein family
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human)
SUBMITTER: 
Tania Auchynnikava
LAB HEAD: Katrin Rittinger
PROVIDER: PXD057364 | Pride | 2025-04-10
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 20K_HUMAN_1GENE_202210.fasta | Fasta | |||
| JF.7z | Other | |||
| checksum.txt | Txt | |||
| plus_intf_vs_nointf_candidates.xlsx | Xlsx | |||
| trim22.tsv | Tabular |
Items per page: 5 1 - 5 of 6 |
Similar Datasets
Project description:Deletion of the flap loop in the Rp2 subunit of human RNAPII did not alter the ability of human RNAPII to initiate transcription or elongate the initiated transcripts in vivo and in vitro, and was also dispensable for elongation factor-mediated enhancement and inhibition of transcript elongation in vitro. ChIP:chip of wild-type and flap deletion human RNAPII revealed that the mutant RNAPII was not defective for promoter binding, initiation and elongation in vivo. Eight ChIP datasets were generated as log2(IP/input) fluorescence intensities using anti-FLAG IP of wild-type RPB2-FLAG cells in biological triplicate, anti-FLAG IP of delta-FL RPB2 FLAG cells in biological triplicate, and anti-RPB1 CTD, 8WG16 of both wild-type and delta-FL cells in biological duplicate. The two 8WG16- IP datasets were combined to measure the distribution of RPB1 signal.
2011-06-24 | E-GEOD-29734 | biostudies-arrayexpress
Project description:This project sought to identify interactions of InterFeron Induced Tetratricopeptide repeat (IFIT) proteins 1 ad 5 in human cells. SILAC-labelled human HEK293T cells were transfected with FLAG-tagged human IFIT1 and IFIT5 pulldowns. After transfection, the cells were treated with human interferon 2-alpha and FLAG-immunoprecipitations performed to identify IFIT-binding proteins. Cells were then subject to LS/MS-MS analysis on a Orbitrap Fusion and data analysed in Maxquant v1.5.7.4
2018-03-16 | PXD007584 | Pride
Project description:BAF57, a component of the SWI/SNF chromatin remodeling complex conglomerate,modulates androgen receptor activity to promote prostate cancer. However the molecular consequences of tumor associated BAF57 elevation have remianed undefined in advanced disease such as castration resistant prostate cancer and/or metastasis Global gene expression analyses were performed in models mimicking tumor-associated BAF57 expression. These analyses demonstrated that BAF57 deregulation circumvented androgen mediated signaling and elicited upregulation of M-NM-12 integrin and other migration and metastasis related gene signatures. LNCaP cells were transfected to overexpress BAF57 and validated for BAF57 transcript induction. Appropriate vector control transfected cells were also used. Vector and BAF57 transfected samples were treated with 0.1% vehicle with a 1nM DHT vector control. Gene expression analyses were performed on biological duplicates.
2013-06-04 | E-GEOD-44418 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to investigate the mRNAs that bind to the FTO protein in the white fat tissue from mice. Methods: 1. White fat from CAG promoter driven transgenic Flag-tagged FTO mice were extracted with RNA protected. 2. Flag-FTO proteins were immunoprecipitated with control IP using IgG. 3. The immunoprecipitated RNAs were deep sequenced and analyzed. Results: We focused on the mRNAs which have functions related to lipid metabolism and homeostasis. Immunoprecipitated RNAs profiles from Flag-FTO IP and IgG IP were generated by deep sequencing.
2016-01-05 | E-GEOD-74255 | biostudies-arrayexpress
Project description:EndoMAP aims to systematically dissect the human endosomal protein complexes. To purify endosomes from human cells, a modified Endo-IP protocol was developed to be compatible with complexomics methodologies and evaluated by DIA-MS. Three independent biological replicates of human endosomes purified by the modified Endo-IP protocol were subjected to Blue Native PolyAcrylamide Gel Electrophoresis (BN-PAGE) co-fractionation to identify possible protein complexes based on correlation profiling.
2025-03-29 | PXD054684 | Pride
Project description:Four and a half LIM domains protein 2 (FHL2) is a co-regulator of gene transcription relevant for many signalling pathways and physiological processes. In this work, the role of FHL2 in cell differentiation has been investigated during in vitro mineralization using a Sparus aurata pre-osteoblast cell line (VSa16, [1]). A global microarray analysis was then performed to characterize the molecular pathways affected by FHL2 overexpression. [1] Pombinho, A.R., LaizM-CM-), V., Molha, D.M., Marques, S.M.P. and Cancela, M.L. (2004). Development of two bone-derived cell lines from the marine teleost Sparus aurata; evidence for extracellular matrix mineralization and cell-type specific expression of matrix Gla protein and osteocalcin. Cell Tissue Res. 315, 393-406. Sparus aurata oligo-DNA microarray (GPL6467) was used to compare gene expression profiles between Control (WT) and FHL2-transfected (F2) VSa16 cell lines. Gene expression profiles of both WT and F2 cells were assessed either at T0 (initial confluent cultures) or T4 (4 weeks of cell confluency). Four (4) pools of cells were taken from both WT and F2 groups at each time point and stored in RNA later at -20M-BM-0C until RNA extraction.
2013-01-03 | E-GEOD-32501 | biostudies-arrayexpress
Project description:We developed a toolkit for capturing endosomes (Endo-IP) and lysosomes (Lyso-IP) in human stem cell(hESC)-derived induced neurons (iNeurons). We target a sub-population of early endosomes marked by endogenously tagged EEA1 (Early Endosome Antigen 1) protein, which represents one of the earliest populations formed after endocytic vesicle uncoating. We demonstrated its utility by revealing the endolysosomal protein landscapes for cortical-like iNeurons and stem cells. This allowed us to globally profile endocytic cargo, identifying hundreds of transmembrane proteins.
2025-01-11 | PXD055978 | Pride
Project description:Membrane contact sites between organelles are critical for transfer of biomolecules. Lipid droplets store fatty acids and form contacts with mitochondria, which regulate fatty acid oxidation and adenosine triphosphate production. Protein compartmentalization at lipid droplet-mitochondria contact sites and their effects on biological processes are poorly described. Using proximity-dependent biotinylation methods, we identify 71 proteins at lipid droplet-mitochondria contact sites, including a multimeric complex containing extended synaptotagmin (ESYT) 1, ESYT2, and VAMP Associated Protein B and C (VAPB). High resolution imaging confirms localization of this complex at the interface of lipid droplet-mitochondria-endoplasmic reticulum where it likely transfers fatty acids to enable -oxidation. Deletion of ESYT1, ESYT2 or VAPB limits lipid droplet-derived fatty acid oxidation, resulting in depletion of tricarboxylic acid cycle metabolites, remodeling of the cellular lipidome, and induction of lipotoxic stress. These findings were recapitulated in Esyt1 and Esyt2 deficient mice. Our study uncovers a fundamental mechanism that is required for lipid droplet-derived fatty acid oxidation and cellular lipid homeostasis, with implications for metabolic diseases and survival.
2025-04-28 | PXD060912 | Pride
Project description:TIA-1 related protein (TIAR) is a RNA-binding protein involved in several steps of gene expression such RNA splicing and translation. TIAR contains three RNA recognition motifs (RRMs) allowing its interaction with specific sequences localized in the untranslated regions (UTRs) of several mRNAs. In myeloid cells, TIAR has been shown to bind and regulate the translation and stability of various mRNAs encoding proteins important for the inflammatory response, such as TNFα, Cox-2 or IL-8 . Here, we generated two macrophage-like RAW 264.7 cell lines expressing either a tagged full-length TIAR protein or a RRM2-truncated mutant unable to bind RNA with high affinity . By a combination of RNA-IP and microarray analysis (RIP-chip), we identified mRNAs specifically bound by the full-length protein both in basal conditions and in response to LPS. Microarray hybridization was performed on TIAR-FLAG-associated mRNAs or TIARÎRRM2-FLAG-associated mRNAs in unstimulated and LPS-stimulated RAW264.7 cells. Enrichment of TIAR-FLAG-associated mRNAs and TIARÎRRM2-FLAG-associated mRNAS were normalized to total transcriptome of TIAR-FLAG and TIARÎRRM2-FLAG expressing-RAW264.7 cells respectively. After amplification and labelling, sample pairs were hybridized onto Mouse Exonic Evidence Based Oligonucleotide (MEEBO) arrays containing on average 38784 mouse 70mer oligonucleotide probes (Stanford University, US). Hybridizations were replicated with dye swap.
2016-02-05 | E-GEOD-77577 | biostudies-arrayexpress
Project description:The transcriptional factor Zur plays a key role in regulating zinc homeostasis in Bacillus subtilis. The genomic sites bound by Zur were mapped using a chromatine immunoprecipitation approach. This allowed the identification of 80 inter- and intragenic chromosomal sites bound by Zur. This data set contains 2 samples. Immunoprecipitated (IP) DNA from Bacillus subtilis BSAS36 strain (BSB1, a tryptophan-prototrophic derivative 168 strain expressing a SPA-tagged Zur protein) were extracted from bacterial cells in the exponential growth phase. IP and whole-cell extract DNA were hybridized on tiling array to generate ChIP-on-chip profiles. Two biological replicates were anlyzed.
2015-01-06 | E-GEOD-64671 | biostudies-arrayexpress