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Title: Teasing apart translational and transcriptional components of stochastic variations in eukaryotic gene expression
Authors: Przytycka, Teresa M.
Salari, Raheleh
Wojtowicz, Damian
Zheng, Jie
Levens, David
Pilpel, Yitzhak
Keywords: DRNTU::Engineering::Computer science and engineering
Issue Date: 2012
Source: Salari, R., Wojtowicz, D., Zheng, J., Levens, D., Pilpel, Yi., & Przytycka, T. M. (2012). Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression. PLoS Computational Biology, 8(8), e1002644.
Series/Report no.: PLoS computational biology
Abstract: The intrinsic stochasticity of gene expression leads to cell-to-cell variations, noise, in protein abundance. Several processes, including transcription, translation, and degradation of mRNA and proteins, can contribute to these variations. Recent single cell analyses of gene expression in yeast have uncovered a general trend where expression noise scales with protein abundance. This trend is consistent with a stochastic model of gene expression where mRNA copy number follows the random birth and death process. However, some deviations from this basic trend have also been observed, prompting questions about the contribution of gene-specific features to such deviations. For example, recent studies have pointed to the TATA box as a sequence feature that can influence expression noise by facilitating expression bursts. Transcription-originated noise can be potentially further amplified in translation. Therefore, we asked the question of to what extent sequence features known or postulated to accompany translation efficiency can also be associated with increase in noise strength and, on average, how such increase compares to the amplification associated with the TATA box. Untangling different components of expression noise is highly nontrivial, as they may be gene or gene-module specific. In particular, focusing on codon usage as one of the sequence features associated with efficient translation, we found that ribosomal genes display a different relationship between expression noise and codon usage as compared to other genes. Within nonribosomal genes we found that sequence high codon usage is correlated with increased noise relative to the average noise of proteins with the same abundance. Interestingly, by projecting the data on a theoretical model of gene expression, we found that the amplification of noise strength associated with codon usage is comparable to that of the TATA box, suggesting that the effect of translation on noise in eukaryotic gene expression might be more prominent than previously appreciated.
ISSN: 1553-734X
DOI: 10.1371/journal.pcbi.1002644
Rights: © This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:SCSE Journal Articles

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