DARPin F10 interactome with AP-MS
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Cell Culture
SUBMITTER: 
Longlong Wang
LAB HEAD: Patrick Matthias
PROVIDER: PXD031799 | Pride | 2023-10-17
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 1547_proteinGroups.txt | Txt | |||
| 180115__wanglong_72_1547mqpar1538.xml | Xml | |||
| F1_180110_DH_1547_DarpinCtrl_1.raw | Raw | |||
| F1_180110_DH_1547_DarpinCtrl_2.raw | Raw | |||
| F1_180110_DH_1547_DarpinCtrl_3.raw | Raw |
Items per page: 5 1 - 5 of 9 |
Similar Datasets
Project description:we treated MFE cell (WT and HDAC6 KO) with different stresses, incluing MG132, CytoD and IAV infection, then use home-made HDAC6 antibody to capture HDAC6 and coimmunoprecipitate its interacting proteins.
2023-10-17 | PXD038816 | Pride
Project description:The RNA-binding protein Trim71/Lin41 is a phylogenetically conserved developmental regulator that functions in mammalian stem cell reprogramming, brain development and cancer. Trim71 recognizes target mRNAs through hairpin motifs and silences them through molecular mechanisms that await identification. Deposited data are mass spectrometry data from immunoprecipitation experiments with endogenously tagged Trim71, Ago2, and Tnrc6a. Experiments are carried out in mouse embryonic stem cells (mESCs) and uncover reciprocal interactions of Trim71, Ago2, and Tnrc6a. Trim71 protein interactions are largely independent of Ago2 levels, but strongly depend on the presence of RNA. A second set of experiments is mass spectrometry data from immunoprecipitation experiments in mESCs overexpressing a tagged peptide derived from Homo sapiens TNRC6B (‘FLAG-HA::T6BWT::Cherry’), that is known to block the Tnrc6-Ago2 interaction. We show that a wild-type version strongly binds Ago1 and Ago2, but not Trim71, while a mutant version binds neither Ago1, 2, nor Trim71.
2023-07-04 | PXD034537 | Pride
Project description:The RNA-binding protein Trim71/Lin41 is a phylogenetically conserved developmental regulator that functions in mammalian stem cell reprogramming, brain development and cancer. Trim71 recognizes target mRNAs through hairpin motifs and silences them through molecular mechanisms that await identification. Deposited data are mass spectrometry data from immunoprecipitation experiments with endogenously tagged Tnrc6a. Experiments are carried out in mouse embryonic stem cells (mESCs) in the presence and absence of RNase A.
2023-07-04 | PXD041242 | Pride
Project description:Ubn1 and Ubn2 are essential subunits of the Histone Regulator A (HiRA) complex, the H3.3 histone variant chaperone for euchromatin. We pulled-down Ubn1 and Ubn2 with a C-terminal AVI-tag in mouse embryonic stem cells and identified, besides all known components of the complex, transcription factors that may play a role in the recruitment of HiRA to chromatin.
2021-07-14 | PXD025466 | Pride
Project description:Zbtb2 is a transcription factor that plays a role in mouse embryonic stem cell (mESC) differentiation. We pulled-down endogenously tagged Zbtb2-FLAG in mESCs and found a complex interactome. We characterized the Zbtb2 complex further by co-pull-downs of overexpressed Zbtb2-AVI, after mutation of individual Zbtb2 domains or of complex subunits, as well as by taking advantage of a tagged construct displaying dominant negative activity (Zbtb2-HAF).
2021-07-14 | PXD025520 | Pride
Project description:Chromatin modifications provide additional context-dependence for DNA sequence-based gene regulation. Binding sites of the transcription factor (TF) and important tumour suppressor p53 are unusually diverse with regards to their chromatin accessibility and histone modifications, suggesting different modes of binding. Here, we show that the ability of p53 to open chromatin and activate its target genes is locally restricted by its cofactor Trim24. The histone-binding domains of Trim24 limits the role of p53 at closed chromatin but not at accessible chromatin where Trim24 is blocked by histone 3 methylation at lysine 4. In turn, p53 regulates gene expression as a function of the naïve chromatin state prior to activation. These findings establish a novel mode of gene regulation by p53 in closed chromatin and illustrate how histone modification sensing cofactors can bridge local chromatin state and TF potency.
2023-05-05 | PXD033674 | Pride
Project description:The genomic binding sites of the transcription factor (TF) and tumour suppressor p53 are unusually diverse in regards to their chromatin features, including histone modifications, opening the possibility that chromatin provides context-dependence for p53 regulation. Here, we show that the ability of p53 to open chromatin and activate its target genes is indeed locally restricted by its cofactor Trim24. Trim24 binds to both p53 and unmethylated lysine 4 of histone H3, thereby preferentially locating to those p53 sites that reside in closed chromatin, while it is deterred from accessible chromatin by lysine 4 methylation. The presence of Trim24 increases cell viability upon stress and enables p53 to impact gene expression as a function of the local chromatin state. These findings link histone methylation to p53 function and illustrate how specificity in chromatin can be achieved, not by TF-intrinsic sensitivity to histone modifications, but by employing chromatin-sensitive cofactors which locally modulate TF function.
2023-05-05 | PXD039553 | Pride
Project description:Catalytic activity of the ISWI family of remodelers is critical for nucleosomal organization and transcription factor binding, including the insulator protein CTCF. To define which subcomplex mediates these diverse functions we phenotyped a panel of isogenic mouse stem cell lines each lacking one of six ISWI accessory subunits. Individual deletions of either CERF, RSF1, ACF, WICH or NoRC subcomplexes only moderately affect the chromatin landscape, while removal of the NURF-specific subunit BPTF leads to drastic reduction in chromatin accessibility and Snf2h ATPase localization around CTCF sites. While this reduces distances to the adjacent nucleosomes it only modestly impacts CTCF binding itself. In absence of accessibility, the insulator function of CTCF is nevertheless impaired resulting in lower occupancy of cohesin and cohesin-loading factors, and reduced insulation at these sites, highlighting the need of NURF-mediated remodeling for open chromatin and proper CTCF function. Our comprehensive analysis reveals a specific role for NURF in mediating Snf2h localization and chromatin opening at bound CTCF sites showing that local accessibility is critical for cohesin binding and insulator function.
2024-03-13 | PXD042945 | Pride
Project description:Cerebral organoids â three-dimensional cultures of human cerebral tissue derived from pluripotent stem cells â have emerged as models of human cortical development. However, the extent to which in vitro organoid systems recapitulate neural progenitor cell proliferation and neuronal differentiation programs observed in vivo remains unclear. Here we use single-cell RNA sequencing (scRNA-seq) to dissect and compare cell composition and progenitor-to-neuron lineage relationships in human cerebral organoids and fetal neocortex. Covariation network analysis using the fetal neocortex data reveals known and novel interactions among genes central to neural progenitor proliferation and neuronal differentiation. In the organoid, we detect diverse progenitors and differentiated cell types of neuronal and mesenchymal lineages, and identify cells that derived from regions resembling the fetal neocortex. We find that these organoid cortical cells use gene expression programs remarkably similar to those of the fetal tissue in order to organize into cerebral cortex-like regions. Our comparison of in vivo and in vitro cortical single cell transcriptomes illuminates the genetic features underlying human cortical development that can be studied in organoid cultures. 734 single-cell transcriptomes from human fetal neocortex or human cerebral organoids from multiple time points were analyzed in this study. All single cell samples were processed on the microfluidic Fluidigm C1 platform and contain 92 external RNA spike-ins. Fetal neocortex data were generated at 12 weeks post conception (chip 1: 81 cells; chip 2: 83 cells) and 13 weeks post conception (62 cells). Cerebral organoid data were generated from dissociated whole organoids derived from induced pluripotent stem cell line 409B2 (iPSC 409B2) at 33 days (40 cells), 35 days (68 cells), 37 days (71 cells), 41 days (74 cells), and 65 days (80 cells) after the start of embryoid body culture. Cerebral organoid data were also generated from microdissected cortical-like regions from H9 embryonic stem cell derived organoids at 53 days (region 1, 48 cells; region 2, 48 cells) or from iPSC 409B2 organoids at 58 days (region 3, 43 cells; region 4, 36 cells).
2015-12-07 | E-GEOD-75140 | biostudies-arrayexpress
Project description:Nup133 belongs to the Y-complex, a key component of the nuclear pore complex (NPC) scaffold. Studies on a null mutation in mice previously revealed that Nup133 is essential for embryonic development but not for mouse embryonic stem cells (mESCs) proliferation. Using single pore detection and average NE-fluorescence intensity, we find that Nup133 is dispensable for interphase and postmitotic NPC scaffold assembly in pluripotent mESCs. However, loss of Nup133 specifically perturbs the formation of the nuclear basket as manifested by the absence of Tpr in about half of the NPCs combined with altered dynamics of Nup153. Nup153 is a large multifunctional protein that interacts with both the Y-complex and Tpr through its N-terminal NPC-targeting domain (NTD, [aa 1-339]) (Hase and Cordes, 2003; Vasu et al., 2001). To explore the possibility that the interaction between Nup153-NTD and the Y-complex or Tpr requires Nup133, we performed pull down assays on whole protein extracts from WT and Nup133-/- mESCs using recombinant Nup153-NTD [aa 1-339] as bait. Nup153 [aa 1-245], lacking the binding domains for the Y-complex and Tpr served as control. Western blot and quantitative mass spectrometry analyses detected Nup133 only in WT samples and documented its specific enrichment, along with other tested Y-Nups and Tpr, in the Nup153-NTD [aa 1-339] bound fraction. These analyses also revealed a similar enrichment of Tpr and Y-complex proteins in Nup153-NTD [aa 1-339]-purified extracts from either WT or Nup133-/- mESCs. These data show that in the context of whole cell lysates containing NPCs as dissociated subcomplexes, the lack of Nup133 neither precludes nor appreciably affects the biochemical interaction between Nup153-NTD and the Y-complex or Tpr. This differs from the in vivo situation that revealed a measurable impact of Nup133 on Nup153 dynamics and Tpr localization in the context of assembled NPCs. This apparent discrepancy between our in vitro and in vivo data indicates that the structural integrity of the NPC is likely required to visualize the contribution of Nup133 to the binding of Nup153 to Tpr or to the Y-complex. Hase, M.E., and Cordes, V.C. (2003). Direct interaction with nup153 mediates binding of Tpr to the periphery of the nuclear pore complex. Mol Biol Cell 14, 1923-1940. Vasu, S., Shah, S., Orjalo, A., Park, M., Fischer, W.H., and Forbes, D.J. (2001). Novel vertebrate nucleoporins Nup133 and Nup160 play a role in mRNA export. J Cell Biol 155, 339-354.
2018-05-28 | PXD009466 | Pride