Reliable Prediction of Viral RNA Structures
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1 Reliable Prediction of Viral RNA Structures Winterseminar 2016, Bled Roman Ochsenreiter TBI Wien Bled, Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
2 Viruses Figure: Crystal Structure and Schematic of Rhinovirus A 1 Genome size (nt): Human: Rhinovirus: Zhao et al Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
3 Viruses and RNA Structure Viruses have little space (small genomes) for information storage Specific Functions are often provided by RNA Structures Figure: Pestivirus IRES 1, Rhinovirus CRE-Element 1 Rfam IDs: RF00209, RF00220 Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
4 Our Arsenal Tools for prediction of RNA Secondary Structure: Structure Prediction Tools RNAfold Prediction of MFE structures/structure Ensembles RNAalifold RNA folding with evolutionary constraints RNAplfold Local structure Prediction AliDot Heuristic - predicts plausible Structures from alignments RNAz Uses machine learning for conserved structure detection How do they perform on Viruses? Can we use our tools to find annotated structures? What is the optimal approach? Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
5 HIV1 Structure - The Gold Standard Figure: HIV1 genome, folded with SHAPE-Data 1 1 Watts et al Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
6 Local vs. Global Folding How far reaching are base-pairings in HIV1? Basepair Spans in HIV1 Counts Basepair Span Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
7 Local vs. Global Folding How many HIV1-MFE basepairs do we miss by folding locally? Missed MFE basepairs in local Structures % RNAplfold Window Size Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
8 Global vs. Local Folding RNAfold vs RNAplfold - Shared Basepairs RNAfold - with SHAPE constraints Winsize Winsize Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
9 Local vs. Global Folding Missed MFE basepairs > Window size % RNAplfold Window Size Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
10 Annotated viral RNA Structures Name Hits Length RRE HIV GSL HIV POL-1 SL HIV FE HIV-1 SL HIV-1 DIS mir-tar HIV-1 SL HIV-1 SD HIV PBS astro FSE 3 51 mir Table: Rfam - Annotated RNA structures in 200 Reference HIV1 genomes Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
11 Reproduction of Rfam-annotated Structures Element 1: HIV-1 DIS (Retroviral Psi packaging element) Figure: HIV Retroviral Psi packaging Element Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
12 Reproduction of Rfam-annotated Structures Reference (Rfam)...((((.(((((((...)))))))...))))... RNAfold (global) ))..)))(((((((((.(((((...((...) RNAfold (local)..((((.(((((((.(...).)))))))...))))... Table: HIV1 Psi Packaging Element, Alignment Size: 200, MPI = Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
13 Reproduction of Rfam-annotated Structures Reference (Rfam)...((((.(((((((...)))))))...))))... RNAfold (global) ))..)))(((((((((.(((((...((...) RNAfold (local)..((((.(((((((.(...).)))))))...))))... Alifold (local, clustal)..((((.(((((.((...)))))))...))))... Alifold (local, mlocarna)...(((((((...)))))))... Alifold (global) )).((((.(((((((...)))))))...))))... Table: HIV1 Psi Packaging Element, Alignment Size: 200, MPI = Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
14 Reproduction of Rfam-annotated Structures Reference (Rfam)...((((.(((((((...)))))))...))))... RNAfold (global) ))..)))(((((((((.(((((...((...) RNAfold (local)..((((.(((((((.(...).)))))))...))))... Alifold (local, clustal)..((((.(((((.((...)))))))...))))... Alifold (local, mlocarna)...(((((((...)))))))... Alifold (global) )).((((.(((((((...)))))))...))))... mlocarna..((((.(((((((...(...).)))))))...))).).. AliDot..((((...(((...)))...)))).. RNAz..((((.(((((.((...)))))))...))))... Table: HIV1 Psi Packaging Element, Alignment Size: 200, MPI = Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
15 Reproduction of Rfam-annotated Structures Element 2: HIV POL-1 SL (HIV pol-1 Stem Loop) Figure: HIV pol-1 stem loop Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
16 Reproducibility of HIV POL-1 SL Reference (Rfam)...(((((((((((((((((((...(((((((((...)))))))))...((((((...)))))).)))))))))))))))))))... RNAfold (global) )))(((((...((((.((((...(((((((((.((...)).)))))))))...)))).))))...((((((((((.(((((((...((((...))) RNAfold (local)...((((((((.((((((((((...(((((((((.((...)).)))))))))...((((((...)))))).)))))))))).)))))))).. Table: HIV1 Polymerase 1 stem loop, Alignment Size: 200, MPI=87.99 Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
17 Reproducibility of HIV POL-1 SL Reference (Rfam)...(((((((((((((((((((...(((((((((...)))))))))...((((((...)))))).)))))))))))))))))))... RNAfold (global) )))(((((...((((.((((...(((((((((.((...)).)))))))))...)))).))))...((((((((((.(((((((...((((...))) RNAfold (local)...((((((((.((((((((((...(((((((((.((...)).)))))))))...((((((...)))))).)))))))))).)))))))).. Alifold (local, clustal)...((((...))))... Alifold (local, mlocarna)..((((((((.((((((((((...(((((((...((...))...)))))))...((...))...)))))))))).))))))))... Alifold (global)..((((((((.((((((((((...(((((((..(((...))).)))))))...(((.((...)).))).)))))))))).))))))))... Table: HIV1 Polymerase 1 stem loop, Alignment Size: 200, MPI=87.99 Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
18 Reproducibility of HIV POL-1 SL Reference (Rfam)...(((((((((((((((((((...(((((((((...)))))))))...((((((...)))))).)))))))))))))))))))... RNAfold (global) )))(((((...((((.((((...(((((((((.((...)).)))))))))...)))).))))...((((((((((.(((((((...((((...))) RNAfold (local)...((((((((.((((((((((...(((((((((.((...)).)))))))))...((((((...)))))).)))))))))).)))))))).. Alifold (local, clustal)...((((...))))... Alifold (local, mlocarna)..((((((((.((((((((((...(((((((...((...))...)))))))...((...))...)))))))))).))))))))... Alifold (global)..((((((((.((((((((((...(((((((..(((...))).)))))))...(((.((...)).))).)))))))))).))))))))... mlocarna..((((((((.((((((((((...(((((((...((...))...)))))))...((...))...)))))))))).))))))))... AliDot... RNAz...((((...))))... Table: HIV1 Polymerase 1 stem loop, Alignment Size: 200, MPI=87.99 Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
19 Summary Even though long range interactions are found, the HIV1 genome is dominated by short-range base pairings Unconstrained, global Folding fails to reproduce known structures Sequence - based alignments can bias consensus-structure based folding of viral structures Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
20 Acknowledgements Ivo Hofacker Christoph Flamm TBI collegues..and you! Roman Ochsenreiter TBI Wien Reliable Prediction of Viral RNA Structures Bled, / 20
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