Inclusion of 5' UTR and the coding region for folding an eukaryotic mRNA |
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In eukaryotic organisms, the complete mature mRNA is transported from
nucleus into cytoplasm where many translation-regulation processes take
place. Thus, the eukaryotic mRNA is very likely to have time to fold as
an entity (perhaps in the presence of mRNA binding proteins that are
beyond our means for computational modeling). Because long-range
base-pairing interactions are common in RNA secondary structures, the
3' UTR region of the eukaryotic mRNA is unlikely to be folded as a
separate domain independent of the rest of the mRNA. This implies that
the secondary structure of the 3' UTR region can be influenced by other
regions of the mRNA molecule. Therefore, it would be prudent to include
bases of the 5' UTR region and the coding region (CD), especially
the part of coding region adjacent to the 3' UTR, even if the primary
interest is to predict the structure of the 3' UTR. We have observed
that, in some cases, this practice can substantially increase the
accuracy of the predictions. Here we give a specific example.
In the case of pMV19, a lin-41 3' UTR reporter with two wild-type binding sites for let-7 (Vella et al. Genes Dev. 18, 132-137, 2004), the inclusion of the lin-41 5' UTR region and coding region for RNA folding makes a drastic difference on the predictions. Since pMV19 is not repressed by let-7, there should be no effective let-7 binding sites in the 3' UTR region. When we include the 5' UTR and the coding region for RNA folding, the energetic results agree with the experimental observation. However, if we fold the 3' UTR alone without including the 5' UTR and the coding region, we identify several good binding sites, which disagree with the testing data. The results from STarMir are given below. |
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Energetic results for including 5' UTR and the coding region for folding the target
Target name = pMV19
microRNA name = let7
Site 1
dG_{total} = -6.079
dG_{disruption} = -9.021
dG_{hybrid} = -15.1
dG_{N}+dG_{initiation} = -0.455
5'->3' U UUUU UUUAAGUC U
Target 284 UUGU UAGCUU CU ACCUC 314
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miRNA 22 GAUA GUUGGA GA UGGAG 1
3'->5' UU U U U
Site 2
dG_{total} = -2.231
dG_{disruption} = -12.869
dG_{hybrid} = -15.1
dG_{N}+dG_{initiation} = -0.108
5'->3' U CCCAC AUG C G U
Target 128 ACU CAACC GC GCU UCA 155
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miRNA 22 UGA GUUGG UG UGG AGU 1
3'->5' U UAU A A
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Energetic results for using only the 3' UTR
for RNA folding
Target name = pMV19
microRNA name = let7
Site 1
dG_{total} = -22.342
dG_{disruption} = -6.658
dG_{hybrid} = -29.0
dG_{N}+dG_{initiation} = -2.335
5'->3' U AUU U
Target 84 UUAUACAACC CUGCCUC 105
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miRNA 22 GAUAUGUUGG GAUGGAG 1
3'->5' UU AU U
Site 2
dG_{total} = -18.667
dG_{disruption} = -9.333
dG_{hybrid} = -28.0
dG_{N}+dG_{initiation} = -0.171
5'->3' U GUU A A
Target 35 UUAUACAACC CUAC CUCA 58
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miRNA 22 GAUAUGUUGG GAUG GAGU 1
3'->5' UU AU
Site 3
dG_{total} = -14.182
dG_{disruption} = -3.118
dG_{hybrid} = -17.3
dG_{N}+dG_{initiation} = -0.771
5'->3' C UG U C
Target 215 UACA CU CU UCUC 231
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miRNA 22 AUGU GA GA GGAG 1
3'->5' UUGAU UG U U U
Site 4
dG_{total} = -11.447
dG_{disruption} = -4.353
dG_{hybrid} = -15.8
dG_{N}+dG_{initiation} = -2.074
5'->3' G C UG A U C G
Target 106 AAC AU A ACCU CU CC 127
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miRNA 22 UUG UA U UGGA GA GG 1
3'->5' A UG U U AGU
Site 5
dG_{total} = -9.793
dG_{disruption} = -5.307
dG_{hybrid} = -15.1
dG_{N}+dG_{initiation} = -2.747
5'->3' U UUUU UUUAAGUC U
Target 284 UUGU UAGCUU CU ACCUC 314
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miRNA 22 GAUA GUUGGA GA UGGAG 1
3'->5' UU U U U
Site 6
dG_{total} = -9.457
dG_{disruption} = -10.143
dG_{hybrid} = -19.6
dG_{N}+dG_{initiation} = -0.3
5'->3' A AG G
Target 2 GGCCUACU ACC 16
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miRNA 22 UUGGAUGA UGG 1
3'->5' UUGAUAUG AGU
Site 7
dG_{total} = -2.908
dG_{disruption} = -12.592
dG_{hybrid} = -15.5
dG_{N}+dG_{initiation} = -1.012
5'->3' U CCCAC AUG C G U
Target 128 ACU CAACC GC GCU UCA 155
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miRNA 22 UGA GUUGG UG UGG AGU 1
3'->5' U UAU A A
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