Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of lncRNA CALA-dependent protein interaction partners of G3BP1 in the cytoplasm

ABSTRACT: We previously identified the stimuli-responsive lncRNA CALA to impact endothelial cell function and identified G3BP1 as a main interaction partner of CALA in the cytoplasm of human umblical vein endothelial cells (HUVECs). To uncover the role of the lncRNA CALA in G3BP1-RNPs in the cytoplasm, we purified the G3BP1 interactome in control and CALA-silenced HUVECs via anti-G3BP1 immunoprecipitation followed by mass spectrometry. We thereby uncover the basal G3BP1 protein interactome in HUVECs and additionally identify lncRNA-dependent protein interactions of G3BP1 in the cytoplasm of HUVEC.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Ilka Wittig

LAB HEAD: Nicolas Jaé

PROVIDER: PXD033517 | Pride | 2022-07-04

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Data_analysis.xlsx	Xlsx
	P21_094_Luisa_A_Ctrl_01_B.raw	Raw
	P21_094_Luisa_A_Ctrl_01_C.raw	Raw
	P21_094_Luisa_A_Ctrl_01_D.raw	Raw
	P21_094_Luisa_A_Ctrl_01_E.raw	Raw

Items per page:

1 - 5 of 43

Similar Datasets

VE-cadherin associated proteins in the absence of lncRNA LASSIE

Project description:The shear stress-regulated lncRNA LASSIE interacts with junctional proteins (e.g. PECAM-1, which interacts with VE-cadherin) and influences endothelial barrier function. Here we characterize the remodeling of the VE-Cadherin complex by the lncRNA LASSIE. LASSIE silenced HUVECs were subjected to co-immunoprecipitation using an anti-VE-cadherin antibody. Differentially associated proteins were identified by Mass spectrometry. This analysis revealed a significantly decreased association of cytoskeleton-linked proteins with VE-cadherin after silencing of LASSIE. Functional assays confirmed this result and characterized LASSIE as a stabilizer of junctional complexes in endothelial cells, important for normal shear stress sensing and barrier function.

2021-09-09 | PXD018725 | Pride

Identification of VE-cadherin associated proteins regulated through the lncRNA LASSIE

Project description:The shear stress-regulated lncRNA LASSIE interacts with cytoskeletal proteins as shown by RNA-antisense purification and subsequent mass spectrometry analysis using an anti-LASSIE and a non-targeting 3’ Desthiobiotin-TEG labeled 2’ O-Me-RNA. As this analysis resulted in high protein binding to the non-targeting control oligonucleotide, the RNA antisense purification was repeated in HUVECs treated with control and anti-LASSIE siRNA. Mass spectrometry analysis confirmed binding of LASSIE to the Intermediate filament protein nestin, as nestin enrichment was decreased in the absence of LASSIE. Additional functional analyses demonstrate a role of LASSIE in shear stress sensing and barrier function in endothelial cells, by stabilizing endothelial cell junctions through connection to the cytoskeleton.

2021-09-09 | PXD018734 | Pride

Endothelial protein interaction partners of the lncRNA PCAT19

Project description:PCAT19 is an endothelial-enriched lncRNA that contributes to the proliferation-quiescence switch in a cell density-dependent manner. Here we performed an antisense-oligonucleotide pulldown of the PCAT19 lncRNA followed by mass spectrometry to identify protein interaction partners of PCAT19. Interaction partners were further analysed for their potential role with PCAT19.

2022-09-29 | PXD032669 | Pride

Antisense affinity selection of the lncRNA NTRAS in HeLa lysate

Project description:Biochemical characterization of the hypoxia-induced long non coding RNA NTRAS. NTRAS was found to regulate cell cycle progression, in vitro sprouting angiogenesis, and the paracellular permeability in human umbilical vein endothelial cells (HUVECs). Using desthiobiotinylated 2’O-Me-RNA probes, we purified endogenous NTRAS-protein-complexes and identified NTRAS interacting proteins by mass spectrometry.

2022-04-25 | PXD030620 | Pride

Identification of protein interaction partners of the lncRNA ADPGK-AS1

Project description:M2-like macrophage upregulated lncRNA ADPGK-AS1 regulates macrophage phenotype and modulates the influence of macrophages on lung tumor apoptosis and migration. Here we identified proteins that interact with ADPGK-AS1 that might give insight into how this regulation this is regulated on molecular level. We were able to identify interaction with mitochondrial ribosomal proteins, leading to regulation of mitochondrial oxidative phosphorylation.

2023-08-13 | PXD030605 | Pride

Identification of protein interaction partners of the lncRNA Lassie

Project description:The shear stress-regulated lncRNA LASSIE interferes with endothelial cell function as knockdown of Lassie affects apoptosis, proliferation and angiogenic sprouting in vitro. RNA-antisense purification and subsequent mass spectrometry analysis identifed junctional proteins (such as PECAM-1) as interactors of LASSIE . Additional functional analyses demonstrate a role of LASSIE in shear stress sensing and barrier function in endothelial cells, by stabilizing endothelial cell junctions through connection to the cytoskeleton.

2021-07-22 | PXD018724 | Pride

Identification of protein interaction partners of the lncRNA CALA

Project description:The stimuli-responsive lncRNA CALA impacts endothelial cell function as silencing impairs angiogenic capacity in vitro. To uncover the molecular mechanism of CALA, we here combined antisense affinity selection of CALA-RNPs with mass spectrometry to identify the protein interactome of CALA. We therefore specifically enrich CALA-RNPs using two distinct antisense probes targeting CALA (LFN – probe#1, LF – probe #2) over a scrambled, non-target control (Scr/NTC) and thereby uncover CALA to interact with components of ribonucleoprotein complexes.

2022-07-04 | PXD033516 | Pride

Identification of interacting proteins of lncRNA HIF1α-AS1

Project description:LncRNA Hypoxia-inducible factor 1α-antisense 1 (HIF1α-AS1) is located on the antisense strand of the important Hypoxia-inducible factor 1α (HIF1α) gene, but being transcribed in antisense direction along the HIF1α promoter. Here we used the 3’end biotinylated HIF1a-AS1 RNA and a control RNA for RNA Pulldown and searched for interacting proteins in nuclear extracts of human umbilical vein endothelial cells (HUVEC).

2022-09-23 | PXD023512 | Pride

Protein expression and oxidation in the hippocampus of neuronal nucleoredoxin knockout (Nestin-NXN-/-) versus floxed control mice (NXN-flfl)

Project description:Nucleoredoxin (NXN) is a thioredoxin-like member of the large group of redoxins which maintain redox balances in the cell. Its primary localization is the cytoplasm, and it is highly expressed in neurons. It has been described as a redox regulator of WNT signaling via maintenance of the redox balance of Disheveled (Dvl). Previous proteomic analyses in NXN-knockdown SH-SY5Y cells found a high fraction of reduced proteins involved in development and cell differentiation. The results suggested NXN mainly acted as oxidase under the culture conditions. The functions in vivo are not known, but full deletion of NXN is embryonically lethal owing to cranial deformities. We have generated mice with a pan-neuronal Nestin-Cre driven deletion of NXN (Nestin-NXN-/-) to study its functions in neurons. Nestin-NXN-/- develop normally and are healthy up to old age. They show a loss of exploratory and playful behavior but have no deficits of cognitive functions, social behavior or readouts of anxiety. Using a Yeast-2-Hybrid screen, calcium calmodulin kinase 2a was identified as interaction partner. Camk2a is crucial for long-term potentiation and thereby learning and memory but is also associated with psychiatric diseases, and it is regulated via redox modification of cysteines that impact on the autophosphorylation status of a critical threonine. Camk2a colocalized and co-precipitated with NXN and its activity depended on the presence of NXN. To further study the functions of NXN in neurons we performed a proteomic screen of the hippocampal proteome and the redox proteome using the BIAM switch method.

2021-09-10 | PXD024624 | Pride

Enrichment of m6A and G3BP1 on mRNA of bursa of Fabricius of Muscovy ducklings infected by HN10 NDRV

Project description:one-day-old healthy Muscovy ducklings were collected and randomly separated into groups (n = 10 for each group). Ducklings were administered 500 μl of the HN10 strain at a titer of 106.4 TCID50/ml for NDRV infection, whereas sterile DMEM was used as a negative control (NC). The bursa of Fabricius specimens was harvested at 72 hours postinfection (hpi). RNA was isolated, and IP was performed to enrich m6A modified RNA and G3BP1 bound RNA respectively.

2024-11-15 | E-MTAB-14565 | biostudies-arrayexpress