Strong association between mRNA folding strength and protein abundance in <i>S. cerevisiae</i>

Zur, Hadas; Tuller, Tamir

doi:10.1038/embor.2011.262

Cited by 91 publications

(134 citation statements)

References 36 publications

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“…11 that segment GC Sim (referring to HindIII restriction fragments in the Hi-C experiment) is less correlated with 3D distances than the GC content. In addition, the very high correlation reported here cannot be explained by the phenomena reported in the papers mentioned above 12,47,48 , and is probably related to additional explanations such as various aspects of gene expression regulation that are related to mRNA folding and GC content 28,50,51 .…”

Section: Resultscontrasting

confidence: 64%

“…1, CUFS is strongly related to various gene features, among them gene expression level, protein-protein interaction (PPI) graph distance and GO terminology distance, as can be expected from a measure of functional similarity (technical details regarding how these measures were computed appear in the Methods section). Finally, it is clear that codon bias is related to various aspects of gene expression regulation [25][26][27][28][29] , which should be related, at least partially, to gene function in various ways 30 . For example, recently it was shown that non-optimal codon bias, in terms of adaptation to the tRNA pool, is a mechanism to achieve circadian clock 31,32 .…”

Section: Resultsmentioning

confidence: 99%

“…First, we show that CUFS can serve as a proxy for gene function and expression patterns, and strongly correlates with 3DGD. CUB is known to be related to gene expression optimization 29 , mRNA folding stability, amino acid content and gene function [25][26][27][28]30 and may also be related to yet unknown molecular mechanisms in the eukaryotic cell. Thus, our analyses demonstrate that CUFS is a robust measure, insensitive to a particular experimental protocol, which can be used for computing functional similarity among genes in future systems biology and genomic studies.…”

Section: Discussionmentioning

confidence: 99%

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Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

2014

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It has been shown that the distribution of genes in eukaryotic genomes is not random; however, formerly reported relations between gene function and genomic organization were relatively weak. Previous studies have demonstrated that codon usage bias is related to all stages of gene expression and to protein function. Here we apply a novel tool for assessing functional relatedness, codon usage frequency similarity (CUFS), which measures similarity between genes in terms of codon and amino acid usage. By analyzing chromosome conformation capture data, describing the three-dimensional (3D) conformation of the DNA, we show that the functional similarity between genes captured by CUFS is directly and very strongly correlated with their 3D distance in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, mouse and human. This emphasizes the importance of threedimensional genomic localization in eukaryotes and indicates that codon usage is tightly linked to genome architecture.

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Section: Resultscontrasting

confidence: 64%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

2014

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“…1 Several studies have explored correlations between protein abundance and a multitude of transcript features, including molecular weight, codon adaption (also tRNA adaptation), half-life, folding energy, and various sequence features (6,(13)(14)(15).…”

mentioning

confidence: 99%

“…It is used to capture the effects of tRNA abundance and mRNA sequence on the translation rate (6,16). The folding of the mRNA transcript can influence protein translation (14). For instance, it has been noted that the mRNA folding energy influences the rate of viral protein translation (17).…”

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confidence: 99%

Predicting the Dynamics of Protein Abundance

Mehdi

Patrick

Bailey

et al. 2014

Molecular & Cellular Proteomics

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Protein synthesis is finely regulated across all organisms, from bacteria to humans, and its integrity underpins many important processes. Emerging evidence suggests that the dynamic range of protein abundance is greater than that observed at the transcript level. Technological breakthroughs now mean that sequencing-based measurement of mRNA levels is routine, but protocols for measuring protein abundance remain both complex and expensive. This paper introduces a Bayesian network that integrates transcriptomic and proteomic data to predict protein abundance and to model the effects of its determinants. We aim to use this model to follow a molecular response over time, from condition-specific data, in order to understand adaptation during processes such as the cell cycle. With microarray data now available for many conditions, the general utility of a protein abundance predictor is broad.Whereas most quantitative proteomics studies have focused on higher organisms, we developed a predictive model of protein abundance for both Saccharomyces cerevisiae and Schizosaccharomyces pombe to explore the latitude at the protein level. Our predictor primarily relies on mRNA level, mRNA-protein interaction, mRNA folding energy and half-life, and tRNA adaptation. The combination of key features, allowing for the low certainty and uneven coverage of experimental observations, gives comparatively minor but robust prediction accuracy. The model substantially improved the analysis of protein regulation during the cell cycle: predicted protein abundance identified twice as many cell-cycle-associated proteins as experimental mRNA levels. Predicted protein abundance was more dynamic than observed mRNA expression, agreeing with experimental protein abundance from a human cell line. We illustrate how the same model can be used to predict the folding energy of mRNA when protein abundance is available, lending credence to the emerging view that mRNA folding affects translation efficiency. The software and data used in this research are available at http://bioinf.scmb. uq.edu.au/proteinabundance/. Molecular & Cellular Proteomics 13:

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Agglomeration behaviour of magnetic microparticles during separation and recycling processes in mRNA purification

Wommer

Soerjawinata

Ulber

et al. 2021

Engineering in Life Sciences

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Purification of mRNA with oligo(dT)‐functionalized magnetic particles involves a series of magnetic separations for buffer exchange and washing. Magnetic particles interact and agglomerate with each other when a magnetic field is applied, which can result in a decreased total surface area and thus a decreased yield of mRNA. In addition, agglomeration may also be caused by mRNA loading on the magnetic particles. Therefore, it is of interest how the individual steps of magnetic separation and subsequent redispersion in the buffers used affect the particle size distribution. The lysis/binding buffer is the most important buffer for the separation of mRNA from the multicomponent suspension of cell lysate. Therefore, monodisperse magnetic particles loaded with mRNA were dispersed in the lysis/binding buffer and in the reference system deionized water, and the particle size distributions were measured. A concentration‐dependent agglomeration tendency was observed in deionized water. In contrast, no significant agglomeration was detected in the lysis/binding buffer. With regard to magnetic particle recycling, the influence of different storage and drying processes on particle size distribution was investigated. Agglomeration occurred in all process alternatives. For de‐agglomeration, ultrasonic treatment was examined. It represents a suitable method for reproducible restoration of the original particle size distribution.

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Strong association between mRNA folding strength and protein abundance in S. cerevisiae

Cited by 91 publications

References 36 publications

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function

Predicting the Dynamics of Protein Abundance

Agglomeration behaviour of magnetic microparticles during separation and recycling processes in mRNA purification

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