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NMR structure determination of protein-RNA complexes involved in pre-mRNA splicing and translation regulation

English title NMR structure determination of protein-RNA complexes involved in pre-mRNA splicing and translation regulation
Applicant Allain Frédéric
Number 149921
Funding scheme Project funding
Research institution Institut für Molekularbiologie und Biophysik ETH Zürich
Institution of higher education ETH Zurich - ETHZ
Main discipline Molecular Biology
Start/End 01.10.2013 - 30.09.2016
Approved amount 751'000.00
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All Disciplines (2)

Discipline
Molecular Biology
Biophysics

Keywords (8)

NMR structure; mRNA splicing; translation regulation; IRES; splicing regulation; U1snRNP; RNP; protein-RNA recognition

Lay Summary (French)

Lead
Structure RMN de complexes ARN-proteines impliques dans l'epissage alternatif et la regulation de la traduction.
Lay summary

Comprendre les mecanismes de la regulation post-transcriptionelles est tres important pour la sante humaine car ils sont a l'origine de nombreuses maladies genetiques. Les proteines qui se lient a l'ARN sont des facteurs essentiels du controle de cette regulation.

Nous proposons ici de determiner la structure tridimentionelle de plusieurs facteurs proteiques en liaison avec l'ARN (PTB, Unr, DND1, hnRNPA1 et hnRNP C). La connaissance precise de ces structures permettra non seulement de comprendre leur mode d'action mais aussi de pouvoir elaborer de nouvelles voies therapeutiques contre certaines maladies genetiques.

 

 

Direct link to Lay Summary Last update: 01.10.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Evidence for cooperative tandem binding of hnRNP C RRMs in mRNA processing.
Cieniková Zuzana, Jayne Sandrine, Damberger Fred Franz, Allain Frédéric Hai-Trieu, Maris Christophe (2015), Evidence for cooperative tandem binding of hnRNP C RRMs in mRNA processing., in RNA (New York, N.Y.), 21(11), 1931-42.
A fly trap mechanism provides sequence-specific RNA recognition by CPEB proteins.
Afroz Tariq, Skrisovska Lenka, Belloc Eulàlia, Guillén-Boixet Jordina, Méndez Raúl, Allain Frédéric H-T (2014), A fly trap mechanism provides sequence-specific RNA recognition by CPEB proteins., in Genes & development, 28(13), 1498-514.
EPR-aided approach for solution structure determination of large RNAs or protein-RNA complexes.
Duss Olivier, Yulikov Maxim, Jeschke Gunnar, Allain Frédéric H-T (2014), EPR-aided approach for solution structure determination of large RNAs or protein-RNA complexes., in Nature communications, 5, 3669-3669.
Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition.
Duss Olivier, Michel Erich, Diarra dit Konté Nana, Schubert Mario, Allain Frédéric H-T (2014), Molecular basis for the wide range of affinity found in Csr/Rsm protein-RNA recognition., in Nucleic acids research, 42(8), 5332-46.
Structural and mechanistic insights into poly(uridine) tract recognition by the hnRNP C RNA recognition motif.
Cieniková Zuzana, Damberger Fred F, Hall Jonathan, Allain Frédéric H-T, Maris Christophe (2014), Structural and mechanistic insights into poly(uridine) tract recognition by the hnRNP C RNA recognition motif., in Journal of the American Chemical Society, 136(41), 14536-44.
Structural basis of the non-coding RNA RsmZ acting as a protein sponge.
Duss Olivier, Michel Erich, Yulikov Maxim, Schubert Mario, Jeschke Gunnar, Allain Frédéric H-T (2014), Structural basis of the non-coding RNA RsmZ acting as a protein sponge., in Nature, 509(7502), 588-92.

Collaboration

Group / person Country
Types of collaboration
Gunnar Jeschke Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Adrian Krainer/CSHL United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
Witek Filipowicz/FMI Basel Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Raul Mendez Spain (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Rudolf Aebersold Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
ICMRBS 2016 Talk given at a conference Structures of Protein-RNA complexes using NMR, EPR and Mass Spectrometry 28.08.2016 Kyoto, Japan Allain Frédéric;
RNA society 2016 Talk given at a conference structure of DnD1 28.06.2016 Kyoto, Japan Duszczyk Malgorzata;
EMBO Conference NON coding RNA Talk given at a conference Structures of protein-RNA complexes binding non-coding RNA using NMR and EPR 21.10.2015 Heidelberg, Germany Allain Frédéric;
RNA society 2015 Talk given at a conference NMR study of U1snRNP 26.05.2015 Madison, United States of America Campagne Sébastien;
EMBO conference life of mRNA Talk given at a conference Translation regulation by small RNA binding proteins 05.10.2014 Heidelberg, Germany Allain Frédéric;
ICMRBS 2014 Talk given at a conference Translation regulation by small RNA binding proteins 24.08.2014 Dallas, United States of America Allain Frédéric;


Associated projects

Number Title Start Funding scheme
136222 Elucidating the biological function of FUS and its role in neurodegeneration 01.09.2011 Sinergia
141942 Post-transcriptional regulation of germ cell apoptosis in C. elegans 01.11.2012 Sinergia
170130 NMR structure determination of protein-RNA complexes involved in pre-mRNA splicing and translation regulation 01.10.2016 Project funding
170808 Acquisition of a Talos Arctica transmission electron microscope for single particle analysis and cryo-tomography 01.05.2017 R'EQUIP
133134 NMR structure determination of protein-RNA complexes involved in pre-mRNA editing and translation regulation 01.10.2010 Project funding
141898 NMR studies of GPCRs: Structure, dynamics and interactions with ligands and signaling proteins 01.12.2012 Sinergia

Abstract

Understanding the molecular mechanisms regulating gene expression at the posttranscriptional level is a major question in molecular biology, defects in these mechanisms being at the origin of many genetic diseases. This proposal focuses on two of these processes: pre-mRNA splicing regulation and translation regulation. Posttranscriptional gene regulation plays a major role in many diverse cellular processes such as embryonic development, cell differentiation and synapse activation. We focus here on aspects of translational and splicing regulation under the control of proteins binding the mRNA and pre-mRNA. At the mRNA 5’UTR, we are interested in how hnRNP proteins (PTB and UNR) control IRES-mediated translation initiation of viral and cellular mRNAs. At the mRNA 3’UTR, we are interested in how RNA binding proteins like Dnd1 regulate translation by counteracting translation repression by miRNA. In splicing regulation, we wish to understand how alternative-splicing factors like hnRNP A1 or C assemble upon pre-mRNA binding but also how factors like PTB or SR proteins interact with the splicing machinery and in particular with U1snRNP.We are proposing here to determine the NMR structures of several key protein-RNA complexes involved in translation and splicing regulation. First, we aim at understanding how PTB and Unr bind IRES to facilitate or repress translation initiation, second, how DND1 binds mRNA 3’end to counteract miRNAs, third how multimers of hnRNPA1 or hnRNP C assemble on the pre-mRNA and finally how U1snRNP assembles, recognizes the 5’ splice-site and interacts with various alternative-splicing factors (PTB, SR proteins, TIA-1). To solve the smaller protein-RNA complexes, we will apply the same NOE-based approach that we have used successfully with others ranging in size from 15 to 30 kDa. For the larger complexes, we will start by determining the structures of stable smaller sub-complexes and subsequently use them as building blocks to reassemble the largest complex using RDCs, EPR, PRE and/or SAXS data.
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