Public Library of Science 2005-12 2005-12-09 Genre/Form: Text Material Type: Internet resource Document Type: Archival Material, Internet Resource All Authors / Contributors: Ringnér, Markus; Krogh, Morten OCLC Number: 841551483 Language Note: English 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.
Read Online Folding Free Energies of 5′-UTRs Impact Post-Transcriptional Regulation on a Genomic Scale in Yeast - Ringnér, Markus; Krogh, Morten | ePub
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The transition rate corresponds to the free energy maximum on the pathway from one stable state (the free energy.
Mrna, since the 5'utrs of several eucaryotic mrnas have recently in a cell- free system, and of a heterologous gene product in cultured energy (ag) of - 114 kcal/mol.
This list of rna structure prediction software is a compilation of software tools and web portals rnaalifold, folds precomputed alignments using mix of free- energy and covariation measures.
For the folding it makes use of a very realistic energy model for rnas as it is by algorithms: calculating a partition function, predicting a maximum free energy in mrna 5'-untranslated region (5'-utr) and 3'-utr; (ii).
Oct 26, 2012 while rna folding energies are difficult to predict computationally because we and others have hypothesized that the 5′utr immediately proximal these genes are significantly enriched for high membrane-to-free (mfi.
In foldit terms, the lower the free energy, the higher the score.
Where, n is the native (folded) state, and d is the denatured (unfolded) state. The following diagram rates of folding and unfolding and the free energy diagram. The folding most experiments collect 5-10 half-lives worth of data.
Mrnas with favorable 5 utr features that may help efficient translation. Top, 5 utr length, the number of stable free energies, stable folds within first.
13 multiple sequence analysis, and free energy analysis using maximum expected accuracy (mea).
Sep 1, 2005 the major 5′-utr splice variants of the mrna transcripts of each sp-a lowest free energy and other relevant parameters of mrna folding,.
Download table correlations between secondary structure in 5′-utrs and transcript features from publication: folding free energies of 5′-utrs impact.
Topographic features of the conformational energy landscape determine the proficiency with which proteins fold to their native conformation.
The journey from a highly energetic unfolded chain of amino acids to the relatively stable folded protein can be straightforward, or it can involve numerous parallel.
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