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Quantitative prediction of miRNA-mRNA interaction based on equilibrium concentrations.

Ragan C, Zuker M, Ragan MA - PLoS Comput. Biol. (2011)

Bottom Line: Computational approaches have proven valuable for predicting which mRNAs can be targeted by a given miRNA, but currently available prediction methods do not address the extent of duplex formation under physiological conditions.Although our method does not predict whether the targeted mRNA is degraded and/or its translation to protein inhibited, our quantitative estimates generally track experimentally supported results, indicating that this approach can be used to predict whether an interaction occurs at specified concentrations.Our approach offers a more-quantitative understanding of post-translational regulation in different cell types, tissues, and developmental conditions.

View Article: PubMed Central - PubMed

Affiliation: ARC Centre of Excellence in Bioinformatics, and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.

ABSTRACT
MicroRNAs (miRNAs) suppress gene expression by forming a duplex with a target messenger RNA (mRNA), blocking translation or initiating cleavage. Computational approaches have proven valuable for predicting which mRNAs can be targeted by a given miRNA, but currently available prediction methods do not address the extent of duplex formation under physiological conditions. Some miRNAs can at low concentrations bind to target mRNAs, whereas others are unlikely to bind within a physiologically relevant concentration range. Here we present a novel approach in which we find potential target sites on mRNA that minimize the calculated free energy of duplex formation, compute the free energy change involved in unfolding these sites, and use these energies to estimate the extent of duplex formation at specified initial concentrations of both species. We compare our predictions to experimentally confirmed miRNA-mRNA interactions (and non-interactions) in Drosophila melanogaster and in human. Although our method does not predict whether the targeted mRNA is degraded and/or its translation to protein inhibited, our quantitative estimates generally track experimentally supported results, indicating that this approach can be used to predict whether an interaction occurs at specified concentrations. Our approach offers a more-quantitative understanding of post-translational regulation in different cell types, tissues, and developmental conditions.

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Our method applied to experimentally confirmed target sites in human with specified initial concentration.(a) Predicted proportion of mRNA reduction is estimated from the proportion of mRNA remaining unbound for 42 experimentally supported interactions at the same initial concentrations as in the confirmation experiment. The x-axis shows each miRNA target site, and the y-axis shows the predicted proportion of mRNA remaining unbound after each interaction; i.e. if no mRNA has bound to miRNA (no interaction has occurred) the remaining proportion of mRNA is 1 (100%), and if all mRNA has bound to miRNA the remaining proportion is 0 (0%). (b) Predicted proportion of mRNA reduction compared with 36 experimentally supported interactions at the same initial concentrations as in the confirmation experiment. The x-axis shows the experimentally confirmed and the y-axis show these predicted proportion of mRNA remaining unbound after each interaction. The red and orange dots show successfully predicted target mRNAs, and light blue and dark blue show these unsuccessfully predicted with the initial concentrations specified in the experiment and at 1 M, respectively.
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pcbi-1001090-g003: Our method applied to experimentally confirmed target sites in human with specified initial concentration.(a) Predicted proportion of mRNA reduction is estimated from the proportion of mRNA remaining unbound for 42 experimentally supported interactions at the same initial concentrations as in the confirmation experiment. The x-axis shows each miRNA target site, and the y-axis shows the predicted proportion of mRNA remaining unbound after each interaction; i.e. if no mRNA has bound to miRNA (no interaction has occurred) the remaining proportion of mRNA is 1 (100%), and if all mRNA has bound to miRNA the remaining proportion is 0 (0%). (b) Predicted proportion of mRNA reduction compared with 36 experimentally supported interactions at the same initial concentrations as in the confirmation experiment. The x-axis shows the experimentally confirmed and the y-axis show these predicted proportion of mRNA remaining unbound after each interaction. The red and orange dots show successfully predicted target mRNAs, and light blue and dark blue show these unsuccessfully predicted with the initial concentrations specified in the experiment and at 1 M, respectively.

Mentions: Among the experimentally supported targets described above in human, miRNA concentrations used for experimental confirmation were reported for 41; one target was confirmed using two different miRNA concentrations (Table S3). These concentrations ranged between 2.5 nM and 300 nM. We tested our model on these 42 interactions, using the reported miRNA concentration and setting the mRNA concentration to be the same. The 41 experimentally supported targets include six sites that we did not recover in our initial search, and four that were recovered but were not predicted to be bound at 1 miRNA (above) and are therefore not expected to bind miRNA at lower experimental concentrations. These ten are shown in dark blue in Figure 3A.


Quantitative prediction of miRNA-mRNA interaction based on equilibrium concentrations.

Ragan C, Zuker M, Ragan MA - PLoS Comput. Biol. (2011)

Our method applied to experimentally confirmed target sites in human with specified initial concentration.(a) Predicted proportion of mRNA reduction is estimated from the proportion of mRNA remaining unbound for 42 experimentally supported interactions at the same initial concentrations as in the confirmation experiment. The x-axis shows each miRNA target site, and the y-axis shows the predicted proportion of mRNA remaining unbound after each interaction; i.e. if no mRNA has bound to miRNA (no interaction has occurred) the remaining proportion of mRNA is 1 (100%), and if all mRNA has bound to miRNA the remaining proportion is 0 (0%). (b) Predicted proportion of mRNA reduction compared with 36 experimentally supported interactions at the same initial concentrations as in the confirmation experiment. The x-axis shows the experimentally confirmed and the y-axis show these predicted proportion of mRNA remaining unbound after each interaction. The red and orange dots show successfully predicted target mRNAs, and light blue and dark blue show these unsuccessfully predicted with the initial concentrations specified in the experiment and at 1 M, respectively.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3044769&req=5

pcbi-1001090-g003: Our method applied to experimentally confirmed target sites in human with specified initial concentration.(a) Predicted proportion of mRNA reduction is estimated from the proportion of mRNA remaining unbound for 42 experimentally supported interactions at the same initial concentrations as in the confirmation experiment. The x-axis shows each miRNA target site, and the y-axis shows the predicted proportion of mRNA remaining unbound after each interaction; i.e. if no mRNA has bound to miRNA (no interaction has occurred) the remaining proportion of mRNA is 1 (100%), and if all mRNA has bound to miRNA the remaining proportion is 0 (0%). (b) Predicted proportion of mRNA reduction compared with 36 experimentally supported interactions at the same initial concentrations as in the confirmation experiment. The x-axis shows the experimentally confirmed and the y-axis show these predicted proportion of mRNA remaining unbound after each interaction. The red and orange dots show successfully predicted target mRNAs, and light blue and dark blue show these unsuccessfully predicted with the initial concentrations specified in the experiment and at 1 M, respectively.
Mentions: Among the experimentally supported targets described above in human, miRNA concentrations used for experimental confirmation were reported for 41; one target was confirmed using two different miRNA concentrations (Table S3). These concentrations ranged between 2.5 nM and 300 nM. We tested our model on these 42 interactions, using the reported miRNA concentration and setting the mRNA concentration to be the same. The 41 experimentally supported targets include six sites that we did not recover in our initial search, and four that were recovered but were not predicted to be bound at 1 miRNA (above) and are therefore not expected to bind miRNA at lower experimental concentrations. These ten are shown in dark blue in Figure 3A.

Bottom Line: Computational approaches have proven valuable for predicting which mRNAs can be targeted by a given miRNA, but currently available prediction methods do not address the extent of duplex formation under physiological conditions.Although our method does not predict whether the targeted mRNA is degraded and/or its translation to protein inhibited, our quantitative estimates generally track experimentally supported results, indicating that this approach can be used to predict whether an interaction occurs at specified concentrations.Our approach offers a more-quantitative understanding of post-translational regulation in different cell types, tissues, and developmental conditions.

View Article: PubMed Central - PubMed

Affiliation: ARC Centre of Excellence in Bioinformatics, and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.

ABSTRACT
MicroRNAs (miRNAs) suppress gene expression by forming a duplex with a target messenger RNA (mRNA), blocking translation or initiating cleavage. Computational approaches have proven valuable for predicting which mRNAs can be targeted by a given miRNA, but currently available prediction methods do not address the extent of duplex formation under physiological conditions. Some miRNAs can at low concentrations bind to target mRNAs, whereas others are unlikely to bind within a physiologically relevant concentration range. Here we present a novel approach in which we find potential target sites on mRNA that minimize the calculated free energy of duplex formation, compute the free energy change involved in unfolding these sites, and use these energies to estimate the extent of duplex formation at specified initial concentrations of both species. We compare our predictions to experimentally confirmed miRNA-mRNA interactions (and non-interactions) in Drosophila melanogaster and in human. Although our method does not predict whether the targeted mRNA is degraded and/or its translation to protein inhibited, our quantitative estimates generally track experimentally supported results, indicating that this approach can be used to predict whether an interaction occurs at specified concentrations. Our approach offers a more-quantitative understanding of post-translational regulation in different cell types, tissues, and developmental conditions.

Show MeSH
Related in: MedlinePlus