visualization of rna 2d structures - structure/function relationships of h/aca motifs: analysis...

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

Rougier, JDEV2013

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