Identification of sites of ubiquitination on protein TRIM52
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Cell Culture
SUBMITTER: 
WeiQiang Chen
LAB HEAD: Gijs Versteeg
PROVIDER: PXD051295 | Pride | 2025-03-25
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 20220603_E2_RSLC2_Shulkina_Versteeg_MPL_UniWien_Trim52_TryChy_100p.raw | Raw | |||
| MaxQuant_txt.zip | Other | |||
| Raw_file_experiment_list__TRIM52_Ubiquitination_PRIDE.xlsx | Xlsx | |||
| checksum.txt | Txt |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:B cells diversify and affinity-mature their antigen receptor repertoire in germinal centers (GC). GC B cells receive help signals during transient interaction with T cells, yet it remains unknown how these transient T-B interactions sustain the subsequent proliferative program of selected B cells. Here we show that the transcription factor AP4 is required for sustained GC B cell proliferation and subsequent establishment of a diverse and protective antibody repertoire. AP4 is induced by c-MYC during the T-B interactions and maintained by T cell-derived IL-21. B cell-specific deletion of AP4 resulted in reduced GC sizes and somatic hypermutation and a failure to control chronic viral infection. These results indicate that AP4 integrates T cell-mediated selection and sustained expansion of GC B cells for humoral immunity. Splenic B cells activated with anti-IgM and CD40L in vitro and germinal center B cells sorted from C57BL/6 mice eight days after immunization with sheep red blood cells (SRBCs) were obtained and genome-wide occupancy of c-MYC, AP4 and active histone marks was profiled by chromatin immunoprecipitation and high-throughput sequencing. Gene expression in MYCâAP4â LZ, MYC+AP4+ LZ, AP4+ DZ, and APâ DZ GC B cells from SRBC-immunized AP4-mCherry / c-MYC-GFP dual reporter mice was profiled by RNA-seq.
2016-08-23 | E-GEOD-80669 | biostudies-arrayexpress
Project description:Peptide fingerprinting to establish whether there is any contaminating phosphatase(s) in the purified protein.
2025-03-13 | PXD045978 | Pride
Project description:Mouse embryonic stem cells can be maintained in a naive state of pluripotency by culture conditions containing inhibitors of Mek and Gsk3. Myc activity is essential for efficient cellular reprogramming. We genetically addressed the role of c-myc and N-myc in naive ESCs cultured in 2i by inducing the deletion of both genes using CRE-mediated recombination. Our findings show that myc activity controls the biosynthetic and proliferative machines of ESCs without significantly affecting the pluripotency network.
2016-02-11 | E-MTAB-3386 | biostudies-arrayexpress
Project description:Leishmania infantum is the causative agent of visceral leishmaniasis in Latin America, a lethal disease if misdiagnosed or left untreated. The ubiquitin proteasome system (UPS) is the main regulator of intracellular proteolysis in eukaryotes and is required for parasite's to life cycle and infection. E3 ubiquitin ligases play important role in UPS and Cullin-1-RING ligases (CRL1) are the largest and most researched family of E3 in eukaryotes. CRL1 complex is made up of SKP1, Cullin1, RBX1, and F-box proteins. This complex is poorly studied in Leishmania. We investigated the interactome of CRL1 complex in L. infantum combining in vitro and in cellulo experiments to identify the interactome of Cullin1 and SKP1 through affinity purification followed by mass spectrometry analysis.
2024-07-01 | PXD051961 | Pride
Project description:The fidelity of immune responses depends on a timely controlled and selective mRNA degradation that is largely driven by RNA-binding proteins (RBPs). It remains unclear whether the selection of an individual mRNA molecule for degradation is governed by stochastic or directed processes. Here, we show that tristetraprolin (TTP, also known as ZFP36), an essential anti-inflammatory RBP, destabilizes target mRNAs via a hierarchical molecular assembly. The formation of the assembly strictly relies on the interaction of TTP with RNA. The TTP homolog ZFP36L1 exhibits similar requirements, indicating a broader relevance of this regulatory program. Unexpectedly, the assembly of the cytoplasmic mRNA-destabilization complex is licensed in the nucleus by TTP binding to pre-mRNA, while cytoplasmic mRNA does not constitute a de novo TTP target. Hence, the fate of an inflammation-induced mRNA is decided concomitantly with its synthesis. This mechanism prevents the translation of excessive and potentially harmful inflammation mediators, irrespective of transcription.
2025-01-07 | PXD051662 | Pride
Project description:As important roles of small RNA pathways, AGO proteins mediate interaction of incorporated small RNAs with their targets. The resolution of AGO associated small RNAs showed a significant landscape of AGO proteins and their binding small RNAs. To characterize small RNAs that associated with BmAGO2 protein in Bombyx mori, the small RNA population associated with BmAGO2 in BmN cells was extracted from the AGO immunoprecipitated complex and the small RNAs between 17nt to 50nt separated by a polyacrylamide gel electrophoresis were subjected to library construction and deep sequencing.The high throughput sequencing yielded a total of 11691441 reads, representing 813,702 unique reads with a abundance from 5731905 to 1. Small RNA associated with AGO2 of BmN cell infected with ie1-bacmid recombinant viruses were performed by high-throughput using Hiseq 2000.
2013-03-05 | E-GEOD-41841 | biostudies-arrayexpress
Project description:Transcriptome remodeling in heart disease occurs through the coordinated actions of transcription factors, histone modifications and other chromatin features at pathology-associated genes. It remains unknown the extent to which genome-wide chromatin reorganization also contributes to the pathologic gene expression. We examined the roles of two chromatin structural proteins, CTCF (CCCTC-binding factor) and HMGB2 (high mobility group protein B2), in regulating pathologic transcription and chromatin remodeling. Our data demonstrate a reciprocal relationship between HMGB2 and CTCF in controlling aspects of chromatin structure and gene expression. Both proteins regulate each otherâs expression as well as transcription in cardiac myocytes: however, only HMGB2 does so in a manner that involves global reprogramming of chromatin accessibility. We demonstrate that the actions of HMGB2 on local chromatin accessibility are conserved across genomic loci, whereas the effects on transcription are loci-dependent and emerge in concert with histone modification and other chromatin features. Lastly, while both proteins share gene targets, HMGB2 and CTCF neither bind these genes simultaneously nor do they physically co-localize in myocyte nuclei. Our study uncovers a previously unknown relationship between these two ubiquitous chromatin proteins and provides a mechanistic explanation for how HMGB2 regulates gene expression and cellular phenotype. Furthermore, we demonstrate direct evidence for hierarchical remodeling of chromatin on a genome-wide scale in the setting of cardiac disease. Examination of a chromatin structural protein, HMGB2 in basal and agonist-treated cells.
2016-06-15 | E-GEOD-80453 | biostudies-arrayexpress
Project description:All constructs were expressed in RKO cells (human rectal carcinoma cell line). A fusion construct of TurboID (mutated BirA* from E. Coli) and green fluorescent protein (GFP) or human TRIM52. Cells were stimulated with Epoxomicin (proteasome inhibitor) or left untreated. Biotinylated proteins were extracted from the cell lysate through pull-down and quantified using label-free MS to identify the proteins in close proximity to TRIM52 using GFP as a specificity control.
2025-03-25 | PXD051272 | Pride
Project description:The centromere-specific Histone H3-variant CENH3 (also known as CENP-A) is considered to be an epigenetic mark for establishment and propagation of centromere identity. Pulse-induction of CENH3 (Drosophila CID) in Schneider S2 cells incorporates into noncentromeric regions and generates CID islands that resist clearing from chromosome arms for multiple cell generations. We demonstrate that CID islands represent functional ectopic kinetochores, which are non-randomly distributed on the chromosome and display a preferential localization near telomeres and pericentric heterochromatin in transcriptionally silent, intergenic chromatin domains. Although overexpression of heterochromatin protein 1 (HP1) or increasing Histone acetylation interferes with CID islands formation on a global scale, induction of a locally defined region of synthetic heterochromatin by targeting HP1-LacI fusions to stably integrated Lac Operator arrays produces a proximal hotspot for CID islands formation. These data suggest that the characteristics of regions bordering heterochromatin promote de novo kinetochore assembly and thereby contribute to centromere identity.
2011-07-15 | E-MTAB-652 | biostudies-arrayexpress
Project description:UFMylation mediates the covalent modification of substrate proteins with UFM1 (Ubiquitin- fold modifier 1) and regulates the selective degradation of endoplasmic reticulum (ER) via autophagy (ER-phagy) to maintain ER homeostasis. Specifically, collisions of the ER-bound ribosomes trigger ribosome UFMylation, which in turn activates C53-mediated autophagy that clears the toxic incomplete polypeptides. C53 has evolved non-canonical shuffled ATG8 interacting motifs (sAIMs) that are essential for ATG8 interaction and autophagy initiation. Why these non-canonical motifs were selected during evolution, instead of canonical ATG8 interacting motifs remains unknown. Here, using a phylogenomics approach, we show that UFMylation is conserved across the eukaryotes and secondarily lost in fungi and some other species. Further biochemical assays have confirmed those results and showed that the unicellular algae, Chlamydomonas reinhardtii has a functional UFMylation machinery, overturning the assumption that this process is linked to multicellularity. Our conservation analysis also revealed that UFM1 co-evolves with the sAIMs in C53, reflecting a functional link between UFM1 and the sAIMs. Using biochemical and structural approaches, we confirmed the interaction of UFM1 with the C53 sAIMs and found that UFM1 and ATG8 bound to the sAIMs in a different mode. Conversion of sAIMs into canonical AIMs prevented binding of UFM1 to C53, while strengthening ATG8 interaction. This led to the autoactivation of the C53 pathway and sensitized Arabidopsis thaliana to ER stress. Altogether, our findings reveal an ancestral toggle switch embodied in the sAIMs that regulates C53- mediated autophagy to maintain ER homeostasis.
2022-11-22 | PXD038157 | Pride