Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

LINC00955 Suppresses Colorectal Cancer Growth by Acting as a Molecular Scaffold of TRIM25 and Sp1 to Inhibit DNMT3B-mediated Methylation of the PHIP Promoter-nanoLCMS/MS analysis

ABSTRACT: To assess direct involvement of LINC00955 in regulation of gene expression, LINC00955 was used as an RNA probe in RNA pull-down assays and mass spectrometry analyses.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Gnglin Ren

LAB HEAD: Gnglin Ren

PROVIDER: PXD041514 | Pride | 2023-10-24

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	LINC00955.msf	Msf
	LINC00955.raw	Raw
	NC.msf	Msf
	NC.raw	Raw
	checksum.txt	Txt

Items per page:

1 - 5 of 5

Publications

LINC00955 suppresses colorectal cancer growth by acting as a molecular scaffold of TRIM25 and Sp1 to Inhibit DNMT3B-mediated methylation of the PHIP promoter.

Ren Ganglin G Li Hongyan H Hong Dan D Hu Fangyu F Jin Rongjia R Wu Shuang S Sun Wenhao W Jin Honglei H Zhao Lingling L Zhang Xiaodong X Liu Dongxiang D Huang Chuanshu C Huang Haishan H

BMC cancer 20230923 1

<h4>Background</h4>Long non-coding RNAs play an important role in the development of colorectal cancer (CRC), while many CRC-related lncRNAs have not yet been identified.<h4>Methods</h4>The relationship between the expression of LINC00955 (Long Intergenic Non-protein Coding RNA 955) and the prognosis of colorectal cancer patients was analyzed using the sequencing results of the TCGA database. LINC00955 expression levels were measured using qRT-PCR. The anti-proliferative activity of LINC00955 wa ...[more]

PMID: 37742010

Similar Datasets

Proteomic study of low-birth-weight nephropathy molecular pathogenesis in rats

Project description:We investigated the molecular pathogenesis of LBW rats obtained by intraperitoneal injection of dexamethasone into pregnant animals. Normal-birth-weight (NBW) rats were used as controls with seven animals per group. When the rats were four weeks old, the left kidneys were removed and used for comprehensive label-free proteomic studies

2022-02-15 | PXD018948 | Pride

STN7 kinase-dependent Light-harvesting complex (LHC) protein phosphorylations in the moss Physcomitrium (Physcomitrella) patens

Project description:Photosystem (PS) I and PSII enclose the reaction center subunits and cofactors responsible for the conversion of sunlight into chemical energy. In the thylakoid membrane of oxygenic photosynthetic organisms, PSII splits the water molecules and donates electrons to the electron transfer chain, and further via PSI to form NADPH. Proteins of the light-harvesting complexes (LHC) I and II are mainly associated with PSI and PSII, respectively, but also provide dynamics for the adjustments of the absorption cross-section of PSII and PSI upon changing light conditions. LHCII proteins N-terminal phosphorylation affects their interaction either with PSI or with PSII, and is a molecular mechanism present from green algae and early land plants to higher plants. The kinase STN7 is responsible for N-terminal phosphorylation of the LHCII proteins in algae and flowering plants model species, but the specific targets and role of STN7-dependent reversible phosphorylation in formation of various PS-LHC complexes in evolutionarily early land plants like mosses is poorly studied. The aim of this project was to identify the phosphorylated residues of the LHCII subunits of the moss Physcomitrium (Physcomitrella) patens (hereafter: P. patens), i.e. the LHCBM proteins, and to determine which of the phosphosites are phosphorylated by the STN7 kinase. Subsequently, the goal has been to identify which of the LHCBM subunits that are part of PSI-LHCI-LHCII complex (state complex), and of the moss-specific PSI-Large complex, are N-terminally phosphorylated in the STN7-dependent fashion.

2022-06-24 | PXD026183 | Pride

PPARgamma ubiquitination sites in HEK293T cells

Project description:Peroxisome proliferator–activated receptor γ (PPARγ) is the central regulator of adipogenesis, and its dysregulation is linked to obesity and metabolic diseases. Identification of the factors that regulate PPARγ expression and activity is therefore crucial for combating obesity. Aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor with a known role in xenobiotic detoxification. Recent studies have suggested that AhR also plays essential roles in energy metabolism. However, the detailed mechanisms remain unclear. We previously reported that experiments with adipocyte-specific Cullin 4b (Cul4b)-knockout mice showed that CUL4B suppresses adipogenesis by targeting PPARγ. Here, using immunoprecipitation, ubiquitination, real-time PCR and Gst-pulldown assays, we report that AhR functions as the substrate receptor in CUL4B–RING E3 ubiquitin ligase (CRL4B) complex and is required for recruiting PPARγ. AhR overexpression reduced PPARγ stability and suppressed adipocyte differentiation, and AhR knockdown stimulated adipocyte differentiation in 3T3-L1 cells. Furthermore, we found that two lysine sites on residues 268 and 293 in PPARγ are targeted for CRL4B-mediated ubiquitination, indicating cross-talk between acetylation and ubiquitination. Our findings establish a critical role of AhR in regulating PPARγ stability and suggest that the AhR–PPARγ interaction may represent a potential therapeutic target for managing metabolic diseases arising from PPARγ dysfunction.

2019-11-01 | PXD015830 | Pride

Characterisation of the free and membrane-associated fractions of the thylakoid lumen proteome in Arabidopsis thaliana

Project description:In plants chloroplasts, the lumen of the thylakoid membrane houses proteins that are vital for photosynthetic electron transport, including water-splitting at photosystem (PS) II and shuttling of electrons from cytochrome b6f to PSI. Other lumen proteins maintain photosynthetic activity through biogenesis and turnover of PSII complexes. Although all lumen proteins are soluble, these known details have highlighted interactions of some lumen proteins with thylakoid membranes or thylakoid-intrinsic proteins. Meanwhile, the functional details of most lumen proteins, as well as their distribution between the soluble and membrane-associated lumen fractions, remain unknown. The current study isolated the soluble free lumen (FL) and membrane-associated lumen (MAL) fractions from Arabidopsis thaliana, and used gel- and mass spectrometry-based proteomics methods to analyse the contents of each proteome. These results identified lumenal proteins, and clearly distinguished the difference between the FL and MAL proteomes. The most abundant proteins in the FL fraction were involved in PSII assembly and repair, while the MAL proteome was enriched in proteins that support of the oxygen-evolving complex (OEC). Novel proteins, including a new PsbP domain-containing isoform, as well as several novel post-translational modifications and N-termini, are reported, and bi-dimensional separation of the lumen proteome identified several potential multi-protein oligomers in the thylakoid lumen.

2021-07-30 | PXD027229 | Pride

Drosophila SWR1 and NuA4 complexes are defined by DOMINO isoform

Project description:Histone acetylation and deposition of H2A.Z variant are integral aspects of active transcrip-tion. In Drosophila, the single DOMINO chromatin regulator complex is thought to combine both activities via an unknown mechanism. Here we show that alternative isoforms of the DOMINO nucleosome remodeling ATPase, DOM-A and DOM-B, directly specify two distinct multi-subunit complexes. Both complexes are necessary for transcriptional regulation but through different mechanisms. The DOM-B complex incorporates H2A.V (the fly ortholog of H2A.Z) genome-wide in an ATP-dependent manner, like the yeast SWR1 complex. The DOM-A complex, instead, functions as an ATP-independent histone acetyltransferase com-plex similar to the yeast NuA4, targeting lysine 12 of histone H4. Our work provides an in-structive example of how different evolutionary strategies lead to similar functional separation. In yeast and humans, nucleosome remodeling and histone acetyltransferase complexes orig-inate from gene duplication and paralog specification. Drosophila generates the same diversi-ty by alternative splicing of a single gene.

2020-05-27 | PXD017729 | Pride

A core proliferative program induced by B-cell receptor stimulation in chronic lymphocytic leukemia cells

Project description:The B-cell receptor (BCR) signaling is crucial for the pathophysiology of chronic lymphocytic leukemia (CLL). Although the BCR has recently emerged as a new therapeutic target the precise mechanisms by which BCR signaling controls neoplastic B-cell proliferation are still ill characterized. Here, by comparing proliferating vs. non-proliferating cells from aggressive CLL patients, we longitudinally characterized the transcriptional and proteomic response of CLL cells after BCR engagement ex vivo. Of the 5,733 genes and/or proteins which expression was modulated after BCR activation, we identified a CLL proliferative signature including 430 genes and 374 proteins. Mathematical modelling of this signature revealed a nested sub-regulatory network comprising transcription factors activated within hours after cell activation linked to proteins involved in cell proliferation days after stimulation. The mining of this core cellular program sustaining primary human cancer cells proliferation provides an evidence based-resource for innovative therapeutic perspectives.

2021-03-29 | PXD013573 | Pride

A core proliferative program induced by B-cell receptor stimulation in chronic lymphocytic leukemia cells

2021-09-08 | PXD013696 | Pride

Protective cellular mechanism of estrogen against kidney stone formation: A proteomics approach and functional validation

Project description:Kidney stone disease is influenced by multiple factors, including but not limited to age, gender, genetic background, hydration status, diet and drug. Regarding the gender, epidemiologic data across the world has shown that females at the reproductive age (15-49 years) have lower incidence/prevalence of kidney stone disease approximately 1.5-2.5 folds as compared to males at the same age. However, this gap is narrower in the postmenopausal age, whereas the postmenopausal females with higher serum estrogen levels are less likely to have kidney stones. Furthermore, female stone formers (patients with kidney stones) are associated with lower estrogen levels. Therefore, estrogen has been proposed to serve as the protective hormone against kidney stone disease. However, the precise mechanisms underlying such protective effects of estrogen remain unclear and require further investigations. This study thus investigated the effects of estradiol (which is the most prevalent and potent form of estrogen in females at the reproductive age) on cellular proteome of renal tubular cells using a proteomics approach.

2019-09-09 | PXD014768 | Pride

Systematic Evaluation of Protein Reduction and Alkylation reveals Massive Unspecific Side Effects by Iodine-containing Reagents

Project description:In this study, we systematically evaluated reduction and alkylation of proteins using three reducing agents (DTT, TCEP, and BME) in combination with four alkylation agents (IAA, IAC, AA, and CAA). We tested these conditions using strong anion exchange (SAX) fractionated in-solution digests and in-gel digested fractions of samples enriched for cytosolic proteins of HeLa cells. We analyzed the data using Proteome Discoverer 2 in combination with the MASCOT search engine with different combinations of variable and fixed modifications as well as error tolerant and mass tolerant searches. Furthermore, we compared IAA and AA alkylated samples by dimethyl labeling and performed multi stage activation triggered by the neutral loss of alkylated methionine side chains. This led to the identification of prominent offside alkylation due to iodine containing reagents at tyrosine, serine, threonine, histidine, lysine, methionine, aspartic and glutamic acid as well as the peptide N-terminus with varying abundances based on the reduction and alkylation reagents used.

2017-05-30 | PXD005183 | Pride

Multiplexed complexome profiling using tandem mass tags

Project description:Complexome profiling is a rapidly spreading, powerful approach to gain insight into the nature of protein complexes. It identifies and quantifies protein complexes separated into multiple fractions of increasing molecular mass using mass spectrometry-based, label-free bottom-up proteomics. Complexome profiling enables a sophisticated and thorough characterization of the composition, molecular mass, assembly and interactions of protein complexes. However, in practice, its application is limited by the large number of samples it generates and the related time and costs of mass spectrometry analyses. Here we implemented tandem mass tags for multiplexing complexome profiling.

2021-08-20 | PXD023211 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data