Translational efficiency across healthy and tumor tissues is proliferation‐related
Abstract Different tissues express genes with particular codon usage and anticodon tRNA repertoires. However, the codon–anticodon co‐adaptation in humans is not completely understood, nor is its effect on tissue‐specific protein levels. Here, we first validated the accuracy of small RNA‐seq for tRNA...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2020-03-01
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| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.15252/msb.20199275 |
| _version_ | 1797284711885701120 |
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| author | Xavier Hernandez‐Alias Hannah Benisty Martin H Schaefer Luis Serrano |
| author_facet | Xavier Hernandez‐Alias Hannah Benisty Martin H Schaefer Luis Serrano |
| author_sort | Xavier Hernandez‐Alias |
| collection | DOAJ |
| description | Abstract Different tissues express genes with particular codon usage and anticodon tRNA repertoires. However, the codon–anticodon co‐adaptation in humans is not completely understood, nor is its effect on tissue‐specific protein levels. Here, we first validated the accuracy of small RNA‐seq for tRNA quantification across five human cell lines. We then analyzed the tRNA abundance of more than 8,000 tumor samples from TCGA, together with their paired mRNA‐seq and proteomics data, to determine the Supply‐to‐Demand Adaptation. We thereby elucidate that the dynamic adaptation of the tRNA pool is largely related to the proliferative state across tissues. The distribution of such tRNA pools over the whole cellular translatome affects the subsequent translational efficiency, which functionally determines a condition‐specific expression program both in healthy and tumor states. Furthermore, the aberrant translational efficiency of some codons in cancer, exemplified by ArgAGA, is associated with poor patient survival†. The regulation of these tRNA profiles is partly explained by the tRNA gene copy numbers and their promoter DNA methylation. |
| first_indexed | 2024-03-07T17:52:42Z |
| format | Article |
| id | doaj.art-5328167fdb934cf4bd1d3f8b3a425a36 |
| institution | Directory Open Access Journal |
| issn | 1744-4292 |
| language | English |
| last_indexed | 2024-03-07T17:52:42Z |
| publishDate | 2020-03-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj.art-5328167fdb934cf4bd1d3f8b3a425a362024-03-02T13:36:04ZengSpringer NatureMolecular Systems Biology1744-42922020-03-01163n/an/a10.15252/msb.20199275Translational efficiency across healthy and tumor tissues is proliferation‐relatedXavier Hernandez‐Alias0Hannah Benisty1Martin H Schaefer2Luis Serrano3Centre for Genomic Regulation (CRG) The Barcelona Institute of Science and Technology Barcelona SpainCentre for Genomic Regulation (CRG) The Barcelona Institute of Science and Technology Barcelona SpainCentre for Genomic Regulation (CRG) The Barcelona Institute of Science and Technology Barcelona SpainCentre for Genomic Regulation (CRG) The Barcelona Institute of Science and Technology Barcelona SpainAbstract Different tissues express genes with particular codon usage and anticodon tRNA repertoires. However, the codon–anticodon co‐adaptation in humans is not completely understood, nor is its effect on tissue‐specific protein levels. Here, we first validated the accuracy of small RNA‐seq for tRNA quantification across five human cell lines. We then analyzed the tRNA abundance of more than 8,000 tumor samples from TCGA, together with their paired mRNA‐seq and proteomics data, to determine the Supply‐to‐Demand Adaptation. We thereby elucidate that the dynamic adaptation of the tRNA pool is largely related to the proliferative state across tissues. The distribution of such tRNA pools over the whole cellular translatome affects the subsequent translational efficiency, which functionally determines a condition‐specific expression program both in healthy and tumor states. Furthermore, the aberrant translational efficiency of some codons in cancer, exemplified by ArgAGA, is associated with poor patient survival†. The regulation of these tRNA profiles is partly explained by the tRNA gene copy numbers and their promoter DNA methylation.https://doi.org/10.15252/msb.20199275codon usageThe Cancer Genome AtlastissuetranslationtRNA |
| spellingShingle | Xavier Hernandez‐Alias Hannah Benisty Martin H Schaefer Luis Serrano Translational efficiency across healthy and tumor tissues is proliferation‐related Molecular Systems Biology codon usage The Cancer Genome Atlas tissue translation tRNA |
| title | Translational efficiency across healthy and tumor tissues is proliferation‐related |
| title_full | Translational efficiency across healthy and tumor tissues is proliferation‐related |
| title_fullStr | Translational efficiency across healthy and tumor tissues is proliferation‐related |
| title_full_unstemmed | Translational efficiency across healthy and tumor tissues is proliferation‐related |
| title_short | Translational efficiency across healthy and tumor tissues is proliferation‐related |
| title_sort | translational efficiency across healthy and tumor tissues is proliferation related |
| topic | codon usage The Cancer Genome Atlas tissue translation tRNA |
| url | https://doi.org/10.15252/msb.20199275 |
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