Browse
Submit Data
Databases
API
Help

Dataset Information

142 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Novel QconCAT-Based Proteomics Method for Determining Allele-Specific Protein Expression (ASPE)

ABSTRACT: In the present study, we developed a novel targeted proteomics approach for quantification of allele-specific protein expression (ASPE) based on scheduled high resolution multiple reaction monitoring (sMRM-HR) with a heavy stable isotope-labeled quantitative concatamer (QconCAT) internal protein standard. This strategy was applied to the determination of the ASPE of UGT2B15 in human livers using the common UGT2B15 nonsynonymous variant rs1902023 (i.e. Y85D) as the marker to differentiate expressions from the two alleles. This novel ASPE approach has the potential to be widely utilized for the identification of cis-genetic variants capable of regulating gene expression at the protein level.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Liver

SUBMITTER: Jian Shi

LAB HEAD: Hao-Jie Zhu, Ph.D.

PROVIDER: PXD008788 | Pride | 2018-08-28

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Determining Allele-Specific Protein Expression (ASPE) Using a Novel Quantitative Concatamer Based Proteomics Method.

Shi Jian J Wang Xinwen X Zhu Huaijun H Jiang Hui H Wang Danxin D Nesvizhskii Alexey A Zhu Hao-Jie HJ

Journal of proteome research 20180904 10

Measuring allele-specific expression (ASE) is a powerful approach for identifying cis-regulatory genetic variants. Here, we developed a novel targeted proteomics method for the quantification of allele-specific protein expression (ASPE) based on scheduled parallel reaction monitoring (PRM) with a heavy stable isotope-labeled quantitative concatamer (QconCAT) internal protein standard. This strategy was applied to the determination of the ASPE of UGT2B15 in human livers using the common UGT2B15 n ...[more]

PMID: 30141943

Similar Datasets

Comparison of Protein Expressions of Drug-Metabolizing Enzymes between Human Liver and the Hepatic Cell Lines HepG2, Hep3B and Huh7 using SWATH and MRM-HR Proteomics

Project description:Human hepatic cell lines have been widely used as an in vitro model for the study of drug metabolism and liver toxicity. However, the validity of this model is still a subject of debate because the expressions of various proteins including drug-metabolizing enzymes (DMEs) in the cell lines can differ significantly from that of human livers. In the present study, we first conducted an untargeted proteomics of the microsomes of the cell lines HepG2, Hep3B, and Huh7 in comparison with human livers using a SWATH method. Furthermore, a targeted proteomic approach, named high-resolution multiple reaction monitoring (MRM-HR), was utilized to compare the expressions of pre-selected DMEs between human livers and the cell lines.

2018-04-18 | PXD008190 | Pride

Transcriptome analysis of Escherichia coli O157:H7 EDL933 inside Acanthamoeba using microarrays

Project description:The transcriptome of Escherichia coli K-12 has been widely studied over a variety of conditions for the past decade while such studies involving E. coli O157:H7, its pathogenic cousin, are just now being conducted. To better understand the impact of intracellular life within a ruminant and environmental protozoan on E. coli O157:H7, global transcript levels of strain EDL933 cells inside Acanthamoeba were compared to cell grown in the protozoan media (ATCC PYG712) by microarray. Nine independent RNA samples from cell from within Acanthamoeba were paired with seven independent RNA samples from control cultures for hybridization to nine two-color microarrays. For four arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other five arrays to overcome dye bias.

2010-12-01 | E-GEOD-16762 | biostudies-arrayexpress

Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock using microarrays

Project description:The transcriptome of Escherichia coli K-12 has been widely studied over a variety of conditions for the past decade while such studies involving E. coli O157:H7, its pathogenic cousin, are just now being conducted. To better understand the impact of heat shock on E. coli O157:H7, global transcript levels of strain EDL933 cells shifted from 37°C to 50°C for 15 min were compared to cells left at 37°C using microarrays. Keywords: Stress Response Twelve independent RNA samples from heat shocked cultures were paired with twelve independent RNA samples from control cultures for hybridization to twelve two-color microarrays. For six arrays, the control RNA sample was labeled with Cy3 dye and the experimental RNA sample was labeled with Cy5 dye, the dyes were reversed for the other six arrays to overcome dye bias.

2009-04-01 | E-GEOD-11463 | biostudies-arrayexpress

Integrated phosphoproteome and transcriptome analysis reveals Chlamydia-induced epithelial-to-mesenchymal transition in host cells

Project description:Chlamydia trachomatis are the etiological agents of a range of diseases and are epidemiologically associated with cervical and ovarian cancers. The interplay between host and chlamydia is highly complex, and to obtain panoramic view of the functional interplay, we performed combinatorial global phosphoproteomic and transcriptomic analyses of C. trachomatis-induced signaling. We identified numerous previously unknown C. trachomatis phosphoproteins and C. trachomatis-regulated host phosphoproteins that are substrates of kinases involved in various cellular processes. Interestingly, several host transcription factors (TFs) that are phosphorylated in C. trachomatis infections, including ETS2 repressor factor (ERF), proto-oncogenic transcription factor ETS1 are targets of ERK MAPK signaling. While these TFs were found to be essential for Chlamydia development, we demonstrated their involvement in inducing epithelial-to-mesenchymal transition in C. trachomatis infected cells by transcriptional regulation of genes involved in cellular motility and invasion. Our data reveals substantially unexplored complexity of C. trachomatis-induced signaling and provides broader insights into pro-carcinogenic potential of C. trachomatis.

2018-12-07 | PXD011960 | Pride

DDX54 regulates transcriptome dynamics during DNA damage response, DDX54 co-IP

Project description:The cellular response to genotoxic stress is a well-characterized network of DNA surveillance pathways. The contribution of posttranscriptional gene regulatory networks to the DNA damage response (DDR) has not been extensively studied. Here, we systematically identified RNA-binding proteins differentially interacting with polyadenylated transcripts upon exposure of human breast carcinoma cells to ionizing irradiation (IR). Interestingly, more than 260 proteins showed increased binding to poly(A) RNA in IR-exposed cells and were comprised of many nucleolar proteins. The functional analysis of DDX54, a candidate genotoxic stress responsive RNA helicase, revealed that DDX54 is an immediate-to-early DDR regulator required for the splicing efficacy of its target IR-induced pre-mRNAs. Upon IR exposure, DDX54 acts by increased interaction with a well defined class of pre-mRNAs which harbor introns with weak acceptor splice sites, as well as by protein-protein contacts within components of U2 snRNP and spliceosomal B complex, resulting in lower intron retention and higher processing rates of its target transcripts. Since DDX54 promotes survival after exposure to IR its expression and/or mutation rate may impact DDR-related pathologies. Our work indicates the relevance of many uncharacterized RBPs potentially involved in the DDR.

2018-06-06 | PXD005190 | Pride

DDX54 regulates transcriptome dynamics during DNA damage response, RBPome

2017-06-12 | PXD005189 | Pride

DDX54 regulates transcriptome dynamics during DNA damage response, whole proteome

2017-06-12 | PXD005188 | Pride

DDX54 regulates transcriptome dynamics during DNA damage response, DDX54 BioID

2017-06-12 | PXD005191 | Pride

Inosine induces context-dependent recoding and translational stalling

Project description:To test how inosine in a codon is translated, we synthesized short reporter-transcripts coding for an N-terminal Flag-tag and a test-peptide containing inosine in one defined codon. All codons containing inosines in at least one position were tested. Codons that would lead to ambiguous translation products were omitted. The transcripts were generated using in vitro transcription with ITP instead of GTP and subsequently in vitro translated using rabbit reticulocyte lysate and resulting peptides were analyzed by LC-MS/MS. The templates for in vitro transcription were generated using linearized DNA plasmids.

2018-11-06 | PXD010329 | Pride

RPL12 phosphorylation regulates translation during mitosis - pSILAC B cell -

Project description:Emerging evidence indicates that heterogeneity in ribosome composition can give rise to specialized functions. Until now, research mainly focused on differences in core ribosomal proteins and associated factors. The impact of posttranslational modifications has not yet been studied systematically. Analyzing ribosome heterogeneity is challenging since individual proteins can be part of different subcomplexes (40S, 60S, 80S and polysomes). Here, we develop polysome proteome profiling (3P) to obtain unbiased proteomic maps across ribosomal subcomplexes. 3P combines extensive fractionation by sucrose gradient centrifugation with quantitative mass spectrometry. The high resolution of the profiles allows us to assign proteins to specific subcomplexes. Phosphoproteomics on 3P fractions reveals that phosphorylation of serine 38 in RPL12 -- a known mitotic CDK1 substrate -- is strongly depleted in polysomes. Follow-up experiments confirm that RPL12 phosphorylation regulates translation of specific subsets of mRNAs during mitosis. Together, our results show that posttranslational modification of ribosomal proteins can regulate translation.

2018-08-31 | PXD009276 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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