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Translation of 5' leaders is pervasive in genes resistant to eIF2 repression.

Andreev DE, O'Connor PB, Fahey C, Kenny EM, Terenin IM, Dmitriev SE, Cormican P, Morris DW, Shatsky IN, Baranov PV - Elife (2015)

Bottom Line: However, the persistent translation of certain mRNAs is required for deployment of an adequate stress response.Although this led to a 5.4-fold general translational repression, the protein coding open reading frames (ORFs) of certain individual mRNAs exhibited resistance to the inhibition.Phylogenetic analysis suggests that at least two regulatory uORFs (namely, in SLC35A4 and MIEF1) encode functional protein products.

View Article: PubMed Central - PubMed

Affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.

ABSTRACT
Eukaryotic cells rapidly reduce protein synthesis in response to various stress conditions. This can be achieved by the phosphorylation-mediated inactivation of a key translation initiation factor, eukaryotic initiation factor 2 (eIF2). However, the persistent translation of certain mRNAs is required for deployment of an adequate stress response. We carried out ribosome profiling of cultured human cells under conditions of severe stress induced with sodium arsenite. Although this led to a 5.4-fold general translational repression, the protein coding open reading frames (ORFs) of certain individual mRNAs exhibited resistance to the inhibition. Nearly all resistant transcripts possess at least one efficiently translated upstream open reading frame (uORF) that represses translation of the main coding ORF under normal conditions. Site-specific mutagenesis of two identified stress resistant mRNAs (PPP1R15B and IFRD1) demonstrated that a single uORF is sufficient for eIF2-mediated translation control in both cases. Phylogenetic analysis suggests that at least two regulatory uORFs (namely, in SLC35A4 and MIEF1) encode functional protein products.

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Related in: MedlinePlus

Analysis of differential gene expression.(A) The Z-score based normalization approach for theidentification of differentially expressed genes. Z-score is used tomitigate expression variance for the genes expressed at different levels.(B) and (C) Left panels: correlation ofZ-scores between replicas calculated for the changes in RNA levels(B) and translation efficiencies (C). Rightpanels: the most significantly regulated genes.DOI:http://dx.doi.org/10.7554/eLife.03971.006
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fig1s2: Analysis of differential gene expression.(A) The Z-score based normalization approach for theidentification of differentially expressed genes. Z-score is used tomitigate expression variance for the genes expressed at different levels.(B) and (C) Left panels: correlation ofZ-scores between replicas calculated for the changes in RNA levels(B) and translation efficiencies (C). Rightpanels: the most significantly regulated genes.DOI:http://dx.doi.org/10.7554/eLife.03971.006

Mentions: Owing to the stochastic nature of massively parallel sequencing, the accuracy of anestimate of the level of expression of a gene is dependent on its sequencing depth.Therefore the estimated expression levels of weakly expressed genes have greatervariability than highly expressed genes. To mitigate this effect we used a Z-scoretransformation (see review by Quackenbush,2002). Genes were first ordered based on their lowest read depth (minimumexpression). The parameters of the distribution of expression changes for the geneswith similar expression levels were used to calculate Z-scores of differentialexpression for individual genes (see ‘Materials and methods’ and Figure 1—figure supplement 2). We used aZ-score of 4 as an arbitrary threshold of statistical significance for differentiallyregulated genes to minimize the false discovery rate.


Translation of 5' leaders is pervasive in genes resistant to eIF2 repression.

Andreev DE, O'Connor PB, Fahey C, Kenny EM, Terenin IM, Dmitriev SE, Cormican P, Morris DW, Shatsky IN, Baranov PV - Elife (2015)

Analysis of differential gene expression.(A) The Z-score based normalization approach for theidentification of differentially expressed genes. Z-score is used tomitigate expression variance for the genes expressed at different levels.(B) and (C) Left panels: correlation ofZ-scores between replicas calculated for the changes in RNA levels(B) and translation efficiencies (C). Rightpanels: the most significantly regulated genes.DOI:http://dx.doi.org/10.7554/eLife.03971.006
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383229&req=5

fig1s2: Analysis of differential gene expression.(A) The Z-score based normalization approach for theidentification of differentially expressed genes. Z-score is used tomitigate expression variance for the genes expressed at different levels.(B) and (C) Left panels: correlation ofZ-scores between replicas calculated for the changes in RNA levels(B) and translation efficiencies (C). Rightpanels: the most significantly regulated genes.DOI:http://dx.doi.org/10.7554/eLife.03971.006
Mentions: Owing to the stochastic nature of massively parallel sequencing, the accuracy of anestimate of the level of expression of a gene is dependent on its sequencing depth.Therefore the estimated expression levels of weakly expressed genes have greatervariability than highly expressed genes. To mitigate this effect we used a Z-scoretransformation (see review by Quackenbush,2002). Genes were first ordered based on their lowest read depth (minimumexpression). The parameters of the distribution of expression changes for the geneswith similar expression levels were used to calculate Z-scores of differentialexpression for individual genes (see ‘Materials and methods’ and Figure 1—figure supplement 2). We used aZ-score of 4 as an arbitrary threshold of statistical significance for differentiallyregulated genes to minimize the false discovery rate.

Bottom Line: However, the persistent translation of certain mRNAs is required for deployment of an adequate stress response.Although this led to a 5.4-fold general translational repression, the protein coding open reading frames (ORFs) of certain individual mRNAs exhibited resistance to the inhibition.Phylogenetic analysis suggests that at least two regulatory uORFs (namely, in SLC35A4 and MIEF1) encode functional protein products.

View Article: PubMed Central - PubMed

Affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.

ABSTRACT
Eukaryotic cells rapidly reduce protein synthesis in response to various stress conditions. This can be achieved by the phosphorylation-mediated inactivation of a key translation initiation factor, eukaryotic initiation factor 2 (eIF2). However, the persistent translation of certain mRNAs is required for deployment of an adequate stress response. We carried out ribosome profiling of cultured human cells under conditions of severe stress induced with sodium arsenite. Although this led to a 5.4-fold general translational repression, the protein coding open reading frames (ORFs) of certain individual mRNAs exhibited resistance to the inhibition. Nearly all resistant transcripts possess at least one efficiently translated upstream open reading frame (uORF) that represses translation of the main coding ORF under normal conditions. Site-specific mutagenesis of two identified stress resistant mRNAs (PPP1R15B and IFRD1) demonstrated that a single uORF is sufficient for eIF2-mediated translation control in both cases. Phylogenetic analysis suggests that at least two regulatory uORFs (namely, in SLC35A4 and MIEF1) encode functional protein products.

Show MeSH
Related in: MedlinePlus