Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation.
To understand the complex relationship governing transcript abundance and the level of the encoded protein, we integrate genome-wide experimental data of ribosomal density on mRNAs with a novel stochastic model describing ribosome traffic dynamics during translation elongation. This analysis reveals...
Saved in:
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2013-01-01
|
| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002866&type=printable |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849726926377189376 |
|---|---|
| author | Luca Ciandrini Ian Stansfield M Carmen Romano |
| author_facet | Luca Ciandrini Ian Stansfield M Carmen Romano |
| author_sort | Luca Ciandrini |
| collection | DOAJ |
| description | To understand the complex relationship governing transcript abundance and the level of the encoded protein, we integrate genome-wide experimental data of ribosomal density on mRNAs with a novel stochastic model describing ribosome traffic dynamics during translation elongation. This analysis reveals that codon arrangement, rather than simply codon bias, has a key role in determining translational efficiency. It also reveals that translation output is governed both by initiation efficiency and elongation dynamics. By integrating genome-wide experimental data sets with simulation of ribosome traffic on all Saccharomyces cerevisiae ORFs, mRNA-specific translation initiation rates are for the first time estimated across the entire transcriptome. Our analysis identifies different classes of mRNAs characterised by their initiation rates, their ribosome traffic dynamics, and by their response to ribosome availability. Strikingly, this classification based on translational dynamics maps onto key gene ontological classifications, revealing evolutionary optimisation of translation responses to be strongly influenced by gene function. |
| format | Article |
| id | doaj-art-d9d0f10823684ce6a9ac28480eb6f4e7 |
| institution | DOAJ |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-d9d0f10823684ce6a9ac28480eb6f4e72025-08-20T03:10:02ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582013-01-0191e100286610.1371/journal.pcbi.1002866Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation.Luca CiandriniIan StansfieldM Carmen RomanoTo understand the complex relationship governing transcript abundance and the level of the encoded protein, we integrate genome-wide experimental data of ribosomal density on mRNAs with a novel stochastic model describing ribosome traffic dynamics during translation elongation. This analysis reveals that codon arrangement, rather than simply codon bias, has a key role in determining translational efficiency. It also reveals that translation output is governed both by initiation efficiency and elongation dynamics. By integrating genome-wide experimental data sets with simulation of ribosome traffic on all Saccharomyces cerevisiae ORFs, mRNA-specific translation initiation rates are for the first time estimated across the entire transcriptome. Our analysis identifies different classes of mRNAs characterised by their initiation rates, their ribosome traffic dynamics, and by their response to ribosome availability. Strikingly, this classification based on translational dynamics maps onto key gene ontological classifications, revealing evolutionary optimisation of translation responses to be strongly influenced by gene function.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002866&type=printable |
| spellingShingle | Luca Ciandrini Ian Stansfield M Carmen Romano Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation. PLoS Computational Biology |
| title | Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation. |
| title_full | Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation. |
| title_fullStr | Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation. |
| title_full_unstemmed | Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation. |
| title_short | Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation. |
| title_sort | ribosome traffic on mrnas maps to gene ontology genome wide quantification of translation initiation rates and polysome size regulation |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002866&type=printable |
| work_keys_str_mv | AT lucaciandrini ribosometrafficonmrnasmapstogeneontologygenomewidequantificationoftranslationinitiationratesandpolysomesizeregulation AT ianstansfield ribosometrafficonmrnasmapstogeneontologygenomewidequantificationoftranslationinitiationratesandpolysomesizeregulation AT mcarmenromano ribosometrafficonmrnasmapstogeneontologygenomewidequantificationoftranslationinitiationratesandpolysomesizeregulation |