Estimating accuracy of RNA-Seq and microarrays with proteomics

Fu, Xing; Fu, Ning; Guo, Songlin; Zheng, Yan; Xu, Ying; Hu, Hao; Menzel, Corinna; Chen, Wei; Li, Yixue; Zeng, Rong; Khaitovich, Philipp

doi:10.1186/1471-2164-10-161

Cited by 269 publications

(233 citation statements)

References 34 publications

(38 reference statements)

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“…In eukaryotic systems, mRNA transcript levels often do not correspond with protein quantities (Lian et al 2001;Griffin et al 2002;Cox et al 2005;Kislinger et al 2006;Wilhelm et al 2006;Schmidt et al 2007;Fu et al 2009). For example, in human medulloblastoma cells, there is a relatively poor correlation between steady-state protein and mRNA levels (R = 0.29) (Vogel et al 2010).…”

Section: Discussionmentioning

confidence: 99%

“…In eukaryotic systems, there is a poor correlation between steady-state mRNA and protein levels (Lian et al 2001;Griffin et al 2002;Cox et al 2005;Kislinger et al 2006;Wilhelm et al 2006;Schmidt et al 2007;Fu et al 2009). Although some of this discrepancy can be attributed to mRNA stability and the efficiency of translation initiation, the contribution of alternative splicing (AS) to this problem is largely ignored.…”

Section: [Supplemental Materials Is Available For This Article]mentioning

confidence: 99%

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Frac-seq reveals isoform-specific recruitment to polyribosomes

et al. 2013

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Pre-mRNA splicing is required for the accurate expression of virtually all human protein coding genes. However, splicing also plays important roles in coordinating subsequent steps of pre-mRNA processing such as polyadenylation and mRNA export. Here, we test the hypothesis that nuclear pre-mRNA processing influences the polyribosome association of alternative mRNA isoforms. By comparing isoform ratios in cytoplasmic and polyribosomal extracts, we determined that the alternative products of ∼30% (597/1954) of mRNA processing events are differentially partitioned between these subcellular fractions. Many of the events exhibiting isoform-specific polyribosome association are highly conserved across mammalian genomes, underscoring their possible biological importance. We find that differences in polyribosome association may be explained, at least in part by the observation that alternative splicing alters the cis-regulatory landscape of mRNAs isoforms. For example, inclusion or exclusion of upstream open reading frames (uORFs) in the 5′UTR as well as Alu-elements and microRNA target sites in the 3′UTR have a strong influence on polyribosome association of alternative mRNA isoforms. Taken together, our data demonstrate for the first time the potential link between alternative splicing and translational control of the resultant mRNA isoforms.

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Section: Discussionmentioning

confidence: 99%

Section: [Supplemental Materials Is Available For This Article]mentioning

confidence: 99%

Frac-seq reveals isoform-specific recruitment to polyribosomes

et al. 2013

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“…This study represents the first large scale quantitative analysis of the plant plasma membrane proteome upon activation of an immune receptor. Because of the often observed disparities when comparing gene expression data and protein levels, quantitative proteomics represents a valuable means to more accurately assess (sub)cellular dynamics in response to diverse stimuli (78). Furthermore, we demonstrate that combining transgenic plant lines with inducible effector expression and quantitative MS/MS is a powerful tool for identifying proteins and processes that are targeted by individual effectors during infection.…”

Section: Down-regulated Proteins Andmentioning

confidence: 99%

Quantitative Proteomics Reveals Dynamic Changes in the Plasma Membrane During Arabidopsis Immune Signaling

Elmore

Smith

et al. 2012

Molecular & Cellular Proteomics

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The plant plasma membrane is a crucial mediator of the interaction between plants and microbes. Understanding how the plasma membrane proteome responds to diverse immune signaling events will lead to a greater understanding of plant immunity and uncover novel targets for crop improvement. Here we report the results from a large scale quantitative proteomics study of plasma membraneenriched fractions upon activation of the Arabidopsis thaliana immune receptor RPS2. More than 2300 proteins were identified in total, with 1353 proteins reproducibly identified across multiple replications. Label-free spectral counting was employed to quantify the relative protein abundance between different treatment samples. Over 20% of up-regulated proteins have known roles in plant immune responses. Significantly changing proteins include those involved in calcium and lipid signaling, membrane transport, primary and secondary metabolism, protein phosphorylation, redox homeostasis, and vesicle trafficking.

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“…All sample replicates were processed in a completely randomized order to minimize any possible batch effects. For protein data, proteins were extracted from 100 mg tissue, using label-free quantitative mass spectrometry according to a previously published method (41). Analysis was performed on an LTQ mass spectrometer equipped with a metal needle electrospray interface mass spectrometer (ThermoFinnigan) in a data-dependent collection model (each full scan followed by 10 MS/MS scans of the most intense ions).…”

Section: Methodsmentioning

confidence: 99%

Rapid metabolic evolution in human prefrontal cortex

Giavalisco

Liu

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Human evolution is characterized by the rapid expansion of brain size and drastic increase in cognitive capabilities. It has long been suggested that these changes were accompanied by modifications of brain metabolism. Indeed, human-specific changes on gene expression or amino acid sequence were reported for a number of metabolic genes, but actual metabolite measurements in humans and apes have remained scarce. Here, we investigate concentrations of more than 100 metabolites in the prefrontal and cerebellar cortex in 49 humans, 11 chimpanzees, and 45 rhesus macaques of different ages using gas chromatography-mass spectrometry (GC-MS). We show that the brain metabolome undergoes substantial changes, both ontogenetically and evolutionarily: 88% of detected metabolites show significant concentration changes with age, whereas 77% of these metabolic changes differ significantly among species. Although overall metabolic divergence reflects phylogenetic relationships among species, we found a fourfold acceleration of metabolic changes in prefrontal cortex compared with cerebellum in the human lineage. These human-specific metabolic changes are paralleled by changes in expression patterns of the corresponding enzymes, and affect pathways involved in synaptic transmission, memory, and learning.H uman evolution is characterized by rapid expansion of brain size and increase in cognitive capabilities, leading to the emergence of unique and complex cognitive skills. These changes have long been associated with changes in brain metabolism, in particular with respect to increased energy demand (1). Large brains are metabolically costly. Thus, humans allocate approximately 20% of their total energy to the brain, compared with 11-13% for apes and 2-8% for other mammalian species (2). This increased metabolic demand has been associated with elevated expression of genes involved in neuronal functions and energy metabolism (3, 4). These changes may have been evolutionary advantageous, as indicated by signatures of positive selection reported for the amino acid changes, which occur in the mitochondrial electron-transport chain proteins, in anthropoid primates and humans, as well as elevated expression of the energy metabolism pathways in the human brain (5, 6). On the histological level, human brains show the largest density of glia cells relative to neurons in the prefrontal cortex, which provides an indirect indication of increased neuronal metabolic demand (7).Changes in brain metabolism are also implicated in neuropsychiatric disorders, such as schizophrenia, which affect some of the human-specific cognitive abilities (8, 9). Furthermore, direct measurements of 21 metabolites in the prefrontal cortex of adult human controls compared with human schizophrenia patients, chimpanzees, and rhesus macaques, carried out using proton NMR spectroscopy have shown significant overlap between human-specific evolutionary changes and metabolic differences between controls and schizophrenia patients (10). Notably, this study has identified not ...

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Estimating accuracy of RNA-Seq and microarrays with proteomics

Cited by 269 publications

References 34 publications

Frac-seq reveals isoform-specific recruitment to polyribosomes

Frac-seq reveals isoform-specific recruitment to polyribosomes

Quantitative Proteomics Reveals Dynamic Changes in the Plasma Membrane During Arabidopsis Immune Signaling

Rapid metabolic evolution in human prefrontal cortex

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