visualization of rna 2d structures - structure/function relationships of h/aca motifs: analysis...
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Visualization of RNA 2D Structures
Structure-Function Relationships of H/ACA MotifsFabrice Leclerc & Yann Ponty
2D models (experimental: footprinting, fluorescence, SHAPE, etc; theoretical: MFold, RNAfold, etc)
2D representations from RNA 3D structures
media to display: structural, functional, phylogenetic informations, etc
RNAplot
jViz.RNA
2D models (experimental: footprinting, fluorescence, SHAPE, etc; theoretical: MFold, RNAfold, etc)
2D representations from RNA 3D structures
media to display: structural, functional, phylogenetic informations, etc
S2S/Assemble
VARNA
2D models (experimental: footprinting, fluorescence, SHAPE, etc; theoretical: MFold, RNAfold, etc)
2D representations from RNA 3D structures
medium to display: structural, functional, phylogenetic informations, etc
PseudoViewer
R2R
C: Stockholm (RFAM)
D: Vienna (RNAfold)
E: Pseudobase
A: FASTA (aligned)B: CLUSTAL
F: BPSEQ
G: CONNECT (CT, CT2)
conformation 1 (ON)
conformation 2 (OFF)
VARNA
Arc
RIBOSWITCH
Conformational switch
graph
mutations, chemical probing data
Aalberts & Jannen, RNA, 2013
base pairing 1
base pairing 2
RNAbows
Conformational changes
Pseudoknots
PseudoViewerjViz.RNA
VARNA
Phylogenetic Data
conservation
VARNA*R2R
* post-processingPerreault et al., PLoS One, 2011 Leclerc, Molecules, 2010
2D representation
2D representation
(3D)
Conservation, covariations
RFAM: RF00065
R-Chie
Arc diagrams
Functional Data1
3’ guide sequence5’ guide sequence
Kloop
ACA box
functionalannotation
H/ACA guide RNA(Archaea)
VARNARFAM: RF00065
Functional Data2
3’ guide sequence5’ guide sequence
Kloop
ACA box
target sequence
functionalannotation
H/ACA guide RNA(Archaea)
VARNARFAM: RF00065
Functional Data3
L7Ae
Nop10
Cbf5
H/ACA guide RNA(Archaea)
VARNARFAM: RF00065
functionalannotation
Footprinting Data1
accessibilityannotation
RNAaccessibility VARNA
RFAM: RF00065
Footprinting Data2
accessibilityannotation
moreaccessibleVARNA
RFAM: RF00065
Footprinting Data3
accessibilityannotation
lessaccessibleVARNA
RFAM: RF00065
accessibilityannotation
VARNARFAM: RF00065
RNA-RNA Interactions
R2R*RILogo
VARNA
* post-processingRFAM: RF00065
H/ACA Genes
7 H/ACA genes11 H/ACA motifs
Muller et al., NAR, 2008
Pyrococcus &
Thermococcus
H/ACA folds
Muller et al., NAR, 2008
H/ACA folds & targets
Muller et al., NAR, 2008
H/ACA sub-families
R2R
H/ACA Structure-Function
+ -
Productive H/ACA
Non-productive H/ACA
Conclusions
standard and customized representations (edition, annotation)
time saving for the generation of multiple representations
time saving for the update of consensus structures
qualitatif (quantitatif) tools to evaluate structure-function models
Tools & ResourcesRFAM (VARNA), Comparative RNA Web Site & Project (RNA2DMap, CT, BPSEQ), The RNA Mapping Database - RMDB (RDAT, RNAstructure), ...
packages: Vienna Package (RNAfold, RNAalifold, etc), Boulder Alignment Editor (VARNA), SAVor (RNAfold, RNAplot), S2S/Assemble 2D & 3D, Jalview 2D & 3D (VARNA, Jmol), ...
recent tools: long RNAs: RNAfdl, pairing probabilities (alternative conformations): RNAbow, RNAllViewer, ...
Acknowledgments
Institut de Génétique & Microbiologie, Orsay
Palaiseau