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Proteomics analysis of tissue aging nucleic acid binding proteins

ABSTRACT: The landscape of NABPs in different mouse stage will assist in the greater understanding of the cellular and molecular mechanisms which control immune system development and aging.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Lung

SUBMITTER: Huiyu Wang

LAB HEAD: Hua Xiao

PROVIDER: PXD035412 | Pride | 2026-03-04

REPOSITORIES: Pride

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			Action	DRS
	YP202127387-GM-0-1.raw	Raw
	YP202127387-GM-0-2.raw	Raw
	YP202127387-GM-0-3.raw	Raw
	YP202127387-GM-10-1.raw	Raw
	YP202127387-GM-10-2.raw	Raw

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1 - 5 of 32

Publications

Deciphering Nucleic Acid Binding Proteome of Mouse Immune Organs Reveals Hub Proteins for Aging.

Wang Huiyu H Zhang Yan Y Wang Zeyuan Z Zhang Lu L Guo Miao M Cao Chengxi C Xiao Hua H

Molecular & cellular proteomics : MCP 20230628 8

Profiling the nucleic acid-binding proteins (NABPs) during aging process is critical to elucidate its roles in biological systems as well as transcriptional and translational regulation. Here, we developed a comprehensive strategy to survey the NABPs of mouse immune organs by using single cell preparation and selective capture technology-based proteomics. Our approach provided a global view of tissue NABPs from different organs under normal physiological conditions with extraction specificity of ...[more]

PMID: 37391046

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Proteomics analysis of tissue aging nucleic acid binding proteins

Project description:The landscape of NABPs in different mouse stage will assist in the greater understanding of the cellular and molecular mechanisms which control immune system development and aging.

2026-03-04 | PXD035405 | Pride

Proteomics analysis of cellular nucleic acid binding proteins

Project description:Organic solvents and Ti4+-IMAC capture of formaldehyde (FA) cross-linked cells followed by mass spectrometry analysis to identify nucleic acid binding proteins in human cells.

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Targeting microRNA-dependent control of X chromosome inactivation improves the Rett Syndrome phenotype

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2026-02-09 | PXD064749 | Pride

Juxtaposition of Bub1 and Cdc20 on phosphorylated Mad1 during catalytic mitotic checkpoint complex assembly (IGX-MS data)

Project description:During metaphase, in response to improper kinetochore-microtubule attachments, the spindle assembly checkpoint (SAC) activates the mitotic checkpoint complex (MCC) to inhibit the anaphase-promoting complex/cyclosome (APC/C). The Mad1-Mad2 complex provides a catalytic platform for MCC assembly. Mad1-bound Mad2 recruits open-Mad2 through asymmetric dimerization and Mad1 phosphorylation by Mps1 promotes conversion of Mad2 from an open (O-Mad2) to closed (C-Mad2) state, which binds Cdc20 to form the MCC. How Mad1 phosphorylation catalytically activates MCC formation is poorly understood. This study characterises Mad1 phosphorylation by Mps1 and provides structural and biochemical insights into a phosphorylation-specific Mad1-Cdc20 interaction, which allows for a tripartite assembly of Bub1-Mad1-Cdc20 on the C-terminal domain of Mad1. We also identify a folded state of Mad1-Mad2 complex, suggesting a model by which the Cdc20-Mad1 interaction brings the Cdc20 MIM motif near Mad2. The Cdc20 MIM motif is then entrapped by the Mad2 safety belt to form a stable complex, allowing spontaneous MCC assembly.

2023-03-11 | PXD031872 | Pride

Dynamic phosphoproteomics of BRS3 activation reveals Hippo signaling pathway for cell migration

Project description:Bombesin receptor subtype-3 (BRS3) is an orphan G-protein coupled receptor (GPCR) that involved in a range of pathological and physiological processes, while its biological functions and underlying regulatory mechanisms remain largely unknown. Quantitative phosphoproteomics approach was employed in this study to comprehensively decipher the signal transductions that occurred upon intracellular BRS3 activation. Lung cancer cell line H1299-BRS3 was treated with MK-5046, an agonist of BRS3, for different durations. Harvested cellular proteins were digested and phosphopeptides were enriched by immobilized titanium (IV) ion affinity chromatography (Ti4+-IMAC) for label-free quantification analysis. In total, 12,052 phosphopeptides were identified, corresponding to 4,015 phosphoproteins and 10,820 phosphosites. Data analysis revealed that 27 phosphopeptides corresponding to 6 proteins were involved in Hippo signaling pathway, which was significantly regulated by the activation of BRS3. Verification experiments demonstrated down-regulation of Hippo signaling pathway could induce the dephosphorylation and nucleus localization of Yes-associated protein (YAP), which further confirmed its association with cell migration through kinase inhibition. Our data collectively demonstrate that BRS3 activation contributes to cell migration through down-regulating Hippo signaling pathway.

2023-07-12 | PXD035666 | Pride

Detecting differential peaks in ChIP-seq signals with ODIN

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Structural basis for the assembly of Mis18a/b core modules

Project description:The centromere, defined by the enrichment of CENP-A (a Histone H3 variant) containing nucleosomes, is a specialised chromosomal locus that acts as a microtubule attachment site. To preserve centromere identity, CENP-A levels must be maintained through active CENP-A loading during the cell cycle. A central player mediating this process is the Mis18 complex (Mis18a, Mis18b and Mis18BP1), which recruits the CENP-A specific chaperone HJURP to centromeres for CENP-A deposition. Here, using a multi-pronged approach, we characterise the structure of the Mis18 complex and show that multiple hetero- and homo-oligomeric interfaces facilitate the hetero-octameric Mis18 complex assembly composed of 4 Mis18a, 2 Mis18b and 2 Mis18BP1. Evaluation of structure-guided/separation-of-function mutants reveals structural determinants essential for Mis18 complex assembly and centromere maintenance. Our results provide new mechanistic insights on centromere maintenance, highlighting that while Mis18a can associate with centromeres and deposit CENP-A independently of Mis18b, the latter is indispensable for the optimal level of CENP-A loading required for preserving the centromere identity.

2024-05-15 | PXD047345 | Pride

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RNxQuest: an extension to the xQuest pipeline enabling analysis of protein-RNA cross-linking/mass spectrometry data

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Integrative Structural Characterization of the Human Canonical and Non-canonical Cop9 Signalosome Complexes

Project description:The COP9 signalosome (CSN) is an evolutionarily conserved protein complex that functions as a deneddylase to inactivate Cullin-RING E3 ligases for controlling protein ubiquitination. CSN possesses structural flexibility that is important for its activation upon binding to a diverse array of CRLs. The canonical and non-canonical CSN complexes consist of 8 (CSN1-8) and 9 (CSN1-9) subunits, respectively. Although CSN9 is not essential for CSN assembly and function, it appears to be important in non-catalytic regulation of CRLs by CSN. Here we employed a combinatory cross-linking mass spectrometry (XL-MS) approach to generate the largest PPI maps of human CSN complexes, which significantly enhanced the precision of integrative structural modeling. The resulting integrative structures allowed us not only to elucidate architectures of both complexes, but also to assess CSN structural dynamics that was not described in the crystal structure. In addition, we have determined CSN9 docking sites and its impact on the CSN structure. While CSN9 binding did not induce global conformational changes, it triggered subunit local reorientations that may be associated with CSN9 involvement in CSN-mediated steric regulation of CRLs.

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