Structure and topology of RNA in living systems

30 Jan 2023, 08:00 → 2 Feb 2023, 12:30 Europe/Rome

Aula Renzo Leonardi (ECT*)

Anze Božič (Jožef Stefan Institute), Luca Tubiana (University of Trento, Italy), Samuela Pasquali (University Paris Cité, Paris, France)

Description

RNA is an incredibly versatile biological macromolecule whose function is carried out not only on the level of its primary sequence of nucleotides, but also by the local and global structures that are created when the constituent nucleotides form base pairs. Many RNA structures are thus involved in translational control, RNA localization, gene regulation, RNA stability, and more. Furthermore, in a large number of bacterial, plant, animal, and human viruses, positive-strand RNA takes on the role of their genomes. Far from simply coding for the protein products, both local structural elements as well as long-range structural interactions in the genomes of RNA viruses are involved in many fundamental viral processes such as virus disassembly, translation, genome replication, and packaging, and are thus in general important for viral fitness.

Aim

The aim of the workshop is to bring together researchers working on various aspects of RNA structure, topology, and function from both theoretical and experimental point of view, with a special focus on the genomes of RNA viruses.

Invited speakers

• R. Amit, Technion
• G. Bussi, SISSA
• M. Comas-García, Universidad Autonóma de San Luis Potosi
• M. Hagan, Brandeis University
• M. Marz, Friedrich-Schiller-University Jena
• C. Micheletti, SISSA
• K. Roeder, University of Cambridge
• B. Sargueil, Université Paris Cité
• R. Smyth, Helmholtz Institute for RNA-based Infection Research
• G. Stirnemann, Université de Paris
• M. Szachniuk, Poznan University of Technology
• J. Trylska, University of Warsaw
• R. Twarock, University of York

Book of abstracts.pdf

Monday 30 January

08:30 → 09:00 REGISTRATION

09:00 → 09:15 Introduction

Speaker: Luca Tubiana

09:00 → 10:30 Session I

Luca Tubiana: Introduction
Mauricio Comas-Garcia: Selective packaging of HIV-1 genomic RNA

09:15 → 10:30 Selective packaging of HIV-1 genomic RNA

Speaker: Mauricio Comas-Garcia

Comas-Garcia.pdf

10:30 → 11:00 Coffee break

11:00 → 12:30 Session II

11:00 → 11:45 Using synthetic biology to unravel RNA tertiary interactions

Speaker: Roee Amit

11:45 → 12:30 Computational modeling of icosahedral shell assembly and encapsulation of flexible polymers

Speaker: Michael Hagan

Trento2023 (1).pdf

12:30 → 14:30 Lunch break

14:30 → 16:00 Session III

14:30 → 15:15 Spiders, entanglements, and RNA structure prediction

Speaker: Marta Szachniuk

Slides-Trento-Szachniuk.pptx

15:15 → 16:00 Probing the structure and function of long viral RNAs

Speaker: Redmond Smyth

16:00 → 16:30 Coffee break

16:30 → 17:00 Molecular Dynamics to investigate Impact of RNA modifications on RNA structural dynamics and recognition

Speaker: Valerio Piomponi

Piomponi_slides_Trento2023.pdf

16:30 → 17:30 Short talks I

17:00 → 17:30 WebTetrado, your assistant in the G4 space

Speaker: Michal Zurkowski

WebTetrado.pdf

Tuesday 31 January

09:00 → 09:45 Physical models for the degradation resistance of xrRNAs

Speaker: Christian Micheletti

09:00 → 10:30 Session IV

09:45 → 10:30 RNA as a randomly branched polymer

Speaker: Anže Božič

Trento2022-ABozic.pdf

10:30 → 11:00 Coffee break

11:00 → 11:45 RNA secondary structures in RNA viruses

Speaker: Manja Marz

2301trento (1).pdf

11:00 → 12:30 Session V

11:45 → 12:30 Dissecting RNA dynamics combining molecular simulations and solution experiments

Speaker: Giovanni Bussi

Trento2023.pdf

12:30 → 14:30 Lunch break

14:30 → 15:15 Conformational space exploration of minimal ribozymes for autocatalytic networks

Speaker: Guillaume Stirnemann

14:30 → 16:00 Session VI

15:15 → 16:00 Simulations of RNA structural dynamics and ligand association paths: the case of an aminoglycoside-sensing riboswitch

Speaker: Joanna Trylska

Wednesday 1 February

09:00 → 09:45 RNA structural ensembles from energy landscape explorations

Speaker: Konstantin Roeder

TalkTrento230201.pdf

09:00 → 10:30 Session VII

09:45 → 10:30 Quantitative electrostatic force tomography for proteinaceous capsids in interaction with an approaching nanoscale substrate

Speaker: Horacio V. Guzman (Universidad Autonoma de Madrid | Jozef Stefan Institute)

10:30 → 11:00 Coffee break

11:00 → 11:45 Integrative modeling strategies and RNA polymorphism

Speaker: Samuela Pasquali

Trento_2023.pdf

11:00 → 12:30 Session VIII

11:45 → 12:30 RNA Composer-based modeling of RNA 3D structures in CASP15

Speaker: Maciej Antczak

RNA-Workshop-Trento-Antczak.pptx

12:30 → 14:30 Lunch break

14:30 → 15:15 Differential SHAPE probing to screen computationally designed RNA and to detect pseudoknot and non-canonical interactions

Speaker: Bruno Sargeuil

Sargueil_Trento.pdf

14:30 → 16:00 Session IX

15:15 → 16:00 Discussion

16:00 → 16:30 Coffee break

16:30 → 17:30 Discussion

Moderators: Samuela Pasquali, Luca Tubiana, Anže Božič

Thursday 2 February

09:00 → 09:45 Deciphering the mechanism of influenza A genome packaging using genome-wide approaches

Speaker: Roland Marquet

09:00 → 10:15 Session XI

09:45 → 10:15 Computational 3D structure characterization of CCMV RNA2 fragment

Speaker: Giovanni Mattiotti

Mattiotti_CCMV_simulations.pdf

10:15 → 10:45 Coffee break

10:45 → 11:15 Knot or not in RNA?

Speaker: Wanda Niemyska

10:45 → 11:45 Short talks 2

11:15 → 11:45 RNA Abstractions for Structural Comparison and Classification

Speaker: Michela Quadrini

Quadrini_Structure_ Topology_RNA2 (1).pdf