Folding free energies of 5'-UTRs impact post-transcriptional regulation on a genomic scale in yeast
Ringnér, Markus LU
and Krogh, Morten
LU
(2005)
In PLoS Computational Biology
1(7).
p.585-592
- Abstract
- Using high-throughput technologies, abundances and other features of genes and proteins have been measured on a genome-wide scale in Saccharomyces cerevisiae. In contrast, secondary structure in 5'-untranslated regions ( UTRs) of mRNA has only been investigated for a limited number of genes. Here, the aim is to study genome-wide regulatory effects of mRNA 5'-UTR folding free energies. We performed computations of secondary structures in 5'-UTRs and their folding free energies for all verified genes in S. cerevisiae. We found significant correlations between folding free energies of 5'-UTRs and various transcript features measured in genome-wide studies of yeast. In particular, mRNAs with weakly folded 5'-UTRs have higher translation rates,... (More)
- Using high-throughput technologies, abundances and other features of genes and proteins have been measured on a genome-wide scale in Saccharomyces cerevisiae. In contrast, secondary structure in 5'-untranslated regions ( UTRs) of mRNA has only been investigated for a limited number of genes. Here, the aim is to study genome-wide regulatory effects of mRNA 5'-UTR folding free energies. We performed computations of secondary structures in 5'-UTRs and their folding free energies for all verified genes in S. cerevisiae. We found significant correlations between folding free energies of 5'-UTRs and various transcript features measured in genome-wide studies of yeast. In particular, mRNAs with weakly folded 5'-UTRs have higher translation rates, higher abundances of the corresponding proteins, longer half-lives, and higher numbers of transcripts, and are upregulated after heat shock. Furthermore, 5'-UTRs have significantly higher folding free energies than other genomic regions and randomized sequences. We also found a positive correlation between transcript half- life and ribosome occupancy that is more pronounced for short-lived transcripts, which supports a picture of competition between translation and degradation. Among the genes with strongly folded 5'-UTRs, there is a huge overrepresentation of uncharacterized open reading frames. Based on our analysis, we conclude that (i) there is a widespread bias for 5'-UTRs to be weakly folded, (ii) folding free energies of 5'-UTRs are correlated with mRNA translation and turnover on a genomic scale, and (iii) transcripts with strongly folded 5'-UTRs are often rare and hard to find experimentally. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/398648
- author
- Ringnér, Markus
LU
and Krogh, Morten
LU
- organization
- publishing date
- 2005-12-09
- type
- Contribution to journal
- publication status
- published
- subject
- in
- PLoS Computational Biology
- volume
- 1
- issue
- 7
- pages
- 585 - 592
- publisher
- Public Library of Science (PLoS)
- external identifiers
-
- wos:000239480500007
- scopus:55449088127
- ISSN
- 1553-7358
- DOI
- 10.1371/journal.pcbi.0010072
- language
- English
- LU publication?
- yes
- id
- 0e60ade5-938f-4dc4-bcba-dc85722ead4b (old id 398648)
- date added to LUP
- 2016-04-01 12:04:52
- date last changed
- 2024-04-23 04:17:30
@article{0e60ade5-938f-4dc4-bcba-dc85722ead4b,
abstract = {{Using high-throughput technologies, abundances and other features of genes and proteins have been measured on a genome-wide scale in Saccharomyces cerevisiae. In contrast, secondary structure in 5'-untranslated regions ( UTRs) of mRNA has only been investigated for a limited number of genes. Here, the aim is to study genome-wide regulatory effects of mRNA 5'-UTR folding free energies. We performed computations of secondary structures in 5'-UTRs and their folding free energies for all verified genes in S. cerevisiae. We found significant correlations between folding free energies of 5'-UTRs and various transcript features measured in genome-wide studies of yeast. In particular, mRNAs with weakly folded 5'-UTRs have higher translation rates, higher abundances of the corresponding proteins, longer half-lives, and higher numbers of transcripts, and are upregulated after heat shock. Furthermore, 5'-UTRs have significantly higher folding free energies than other genomic regions and randomized sequences. We also found a positive correlation between transcript half- life and ribosome occupancy that is more pronounced for short-lived transcripts, which supports a picture of competition between translation and degradation. Among the genes with strongly folded 5'-UTRs, there is a huge overrepresentation of uncharacterized open reading frames. Based on our analysis, we conclude that (i) there is a widespread bias for 5'-UTRs to be weakly folded, (ii) folding free energies of 5'-UTRs are correlated with mRNA translation and turnover on a genomic scale, and (iii) transcripts with strongly folded 5'-UTRs are often rare and hard to find experimentally.}},
author = {{Ringnér, Markus and Krogh, Morten}},
issn = {{1553-7358}},
language = {{eng}},
month = {{12}},
number = {{7}},
pages = {{585--592}},
publisher = {{Public Library of Science (PLoS)}},
series = {{PLoS Computational Biology}},
title = {{Folding free energies of 5'-UTRs impact post-transcriptional regulation on a genomic scale in yeast}},
url = {{http://dx.doi.org/10.1371/journal.pcbi.0010072}},
doi = {{10.1371/journal.pcbi.0010072}},
volume = {{1}},
year = {{2005}},
}