IBENS - ENS

Olivier Bensaude

Alice Lebreton — 2017-06-01T11:55:25Z

Biologie cellulaire de la transcription

Contexte

Depuis une vingtaine d'années, il est bien établi chez les eucaryotes que le facteur positif d'élongation de la transcription (P-TEFb) joue un rôle essentiel dans ce processus fondamental, discontinu et régulé à plusieurs étapes. Le P-TEFb contrecarre, en les phosphorylant, les facteurs négatifs de l'élongation (NELF) qui fréquemment interrompent la transcription par l'ARN polymérase II (Pol II) eucaryotique. En outre, le P-TEFb est impliqué dans le couplage de la transcription à la maturation des pré-messagers (épissage, terminaison, transport) par phosphorylation du domaine C-terminal de la Pol II. Depuis 2001, l'équipe d'Olivier Bensaude concentre ses recherches sur la régulation de P-TEFb, dont l'hyper activation est impliquée dans la transformation cancéreuse et l'hypertrophie cardiaque.

Résultats marquants

En 2001, cette équipe a montré que l'activité du P-TEFb était régulée en réponse à une inhibition de la transcription et que cette régulation impliquait l'ARN 7SK, un ARN nucléaire non codant. Identifié dès 1976, cet ARN, très conservé chez les vertébrés, n'avait pas de fonction connue jusque là. Cette équipe a ensuite identifié une nouvelle protéine cellulaire, Hexim1. L'association d'Hexim1 avec l'ARN 7SK provoque un changement de conformation d'Hexim1 qui, en se liant à la sous-unité cycline T, bloque l'activité kinase du P-TEFb. Il apparaît donc que, dans les cellules, P-TEFb co-existe sous deux formes : l'une active, constituée uniquement de la kinase Cdk9 et d'une cycline (T1ou T2) et l'autre inactive, formée par un complexe Cdk9/Cycline T/Hexim1/7SK. Ce dernier se dissocie in vivo lorsque la transcription est inhibée. Cette dissociation est liée à la formation de complexes entre l'ARN 7SK et certaines des ribonucléoprotéines nucléaires hétérologues (hnRNP) qui chaperonnent les ARN prémessagers. En effet, lorsque la transcription est inhibée, les hnRNP libérées en grande quantité piègent l'ARN 7SK au détriment de l'assemblage du complexe CDK9/Cycline T/Hexim1/7SK.
Où et comment ce complexe est-il dissocié et se reforme-t-il ? Comment s'organisent les différents partenaires ? L'équipe étudie les modalités de recrutement de P-TEFb sur un site donné de transcription par deux stratégies complémentaires, l'immunoprécipitation de chromatine (ChIP) et l'imagerie par microscopie de fluorescence. Par une analyse bioinformatique, cette équipe a identifié des homologues de la protéine Hexim et de l'ARN 7SK chez les nématodes. Ces homologues dont les séquences sont très divergentes, ont-ils les mêmes fonctions ? Un résultat positif ouvrirait d'intéressantes perspectives structurales. Parallèlement, cette équipe recherche des ARN non codants capables d'entrer en interaction directe avec l'ARN pol II. Ainsi, elle a établi que le snARN U1 impliqué dans l'épissage était associé à cette enzyme même lorsqu'elle transcrit un gène qui ne s'épisse pas. Les bases moléculaires et les conséquences fonctionnelles de cette interaction sont à l'étude.

KOBBI L, DEMEY-THOMAS E, BRAYE F, PROUX F, KOLESKINOVA O, VINH J, POTERSZMAN A, BENSAUDE O. An evolutionary conserved Hexim1 peptide binds to the Cdk9 catalytic site to inhibit P-TEFb. Proc Natl Acad Sci U S A. (2016) 113, 12721-12726. doi : 10.1073/pnas.1612331113. Epub 2016 Oct 25

GU B, EICK D, BENSAUDE O CTD serine-2 plays a critical role in splicing and termination factor recruitment to RNA polymerase II in vivo. Nucleic Acids Res, (2013) 41, 1591-1603.

SPILUTTINI, B., GU, B., BELAGAL, P., SIRNOVA, A., NGUYEN, V.T., HEBERT, C., SCHMIDT, U., BERTRAND, E., DARZACQ, X. & BENSAUDE, O. Splicing-independent recruitment of U1 snRNP to a transcription unit in living cells. J Cell Science (2010) 123, 2085-93.

BARRANDON C, BONNET F, NGUYEN VT, LABAS V and BENSAUDE O. The transcription-dependent dissociation of P-TEFb.HEXIM1.7SK RNA relies upon formation of hnRNP.7SK RNA complexes. Mol Cell Biol, (2007) 27 : 6996-7006.

MICHELS AA, FRALDI A, LI Q, ADAMSON TE, BONNET F, NGUYEN VT, SEDORE SC, PRICE JP, PRICE DH, LANIA L & BENSAUDE O. Binding of the 7SK snRNA turns the HEXIM1 protein into a P-TEFb (CDK9/Cyclin T) inhibitor. EMBO J, (2004) 23 : 2608-2619.

MICHELS AA, NGUYEN VT, FRALDI A, LABAS V, EDWARDS M, BONNET F, LANIA L & BENSAUDE O MAQ1(‘ménage à quatre') and 7SK RNA interact with CDK9/Cyclin T complexes in a transcription-dependent manner. Mol Cell Biol, (2003) 23 : 4859-69.

NGUYEN VT, KISS T, MICHELS, AA & BENSAUDE O. 7SK snRNA binds to and inhibits the activity of Cdk9/cyclin T complexes. Nature, (2001) 414 : 322-325.

Publications

Hervé Le Hir — 2014-12-18T07:06:59Z

Chemical inhibition of Exon Junction Complex assembly impairs mRNA localization and neural stem cells ciliogenesis
Villa T, Pourcelot O, Dierks D, Faucourt M, Burel C, Slimani F, Guyonnet L, Spassky N, Schwartz S, Bertrand E, Bensaude O, Le Hir H. (2025).
Nucleic Acids Research

Most Upf1-associated mRNAs have short poly(A) tails, lack a premature termination codon and are targeted by NMD
Gouhier T, Cornille A, Gauthier E, Saveanu C, Badis G. (2025).
BioRxiv

Polysome sorting controls mRNA localization and protein fate
Safieddine A, Bizarro J, Salloum S, Le Hir H, Bertrand E. (2025).
Trends in Cell Biology

RNA anchoring of Upf1 facilitates recruitment of Dcp2 in the NMD decapping complex
Ruiz-Gutierrez N, Dupas J, Auquier E, Barbarin-Bocahu I, Gaudon-Plesse C, Saveanu C, Graille M, Le Hir H. (2025).
Nucleic Acids Research

Deadenylation rate is not a major determinant of RNA degradation in yeast
Audebert L, Feuerbach F, Decourty L, Namane A, Permal E, Badis G, Saveanu C. (2024).
EMBO Journal

Structure of the Nmd4-Upf1 complex supports conservation of the nonsense-mediated mRNA decay pathway between yeast and humans
Barbarin-Bocahu I, Ulryck N, Rigobert A, Ruiz-Gutierrez N, Decourty L, Raji M, Garkhal B, Le Hir H, Saveanu C, Graille M. (2024).
PLOS Biology

Exon-junction complex association with stalled ribosomes and slow translation-independent disassembly
Bensaude O, Barbosa I, Morillo L, Dikstein R, Le Hir H. (2024).
Nature Communications

Comprehensive mapping of exon junction complex binding sites reveals universal EJC deposition in Drosophila
Morillo L, Paternina T, Alasseur Q, Genovesio A, Schwartz S, Le Hir H. (2023).
BMC Biology

Exclusion of m6A from splice-site proximal regions by the exon junction complex dictates m6A topologies and mRNA stability
Uzonyi A, Dierks D, Nir R, Kwon OS, Toth U, Barbosa I, Burel C, Brandis A, Rossmanith W, Le Hir H, Slobodin B, Schwartz S. (2023).
Molecular Cell

Novel approaches to study helicases using magnetic tweezers
Ruiz-Gutierrez N, Rieu M, Ouellet J, Allemand J-F, Croquette V, Le Hir H (2022)
Methods in Enzymology

Exon junction complex dependent mRNA localization is linked to centrosome organization during ciliogenesis
Kwon OS, Mishra R, Safieddine A, Coleno E, Alasseur Q, Faucourt M, Barbosa I, Bertrand E, Spassky N, Le Hir H. (2021).
Nature Communications

NCBP3 positively impacts mRNA biogenesis
Dou Y, Barbosa I, Jiang H, Iasillo C, Molloy KR, Schulze WM, Cusack S, Schmid M, Le Hir H, LaCava J, Jensen TH (2020)
Nucleic Acids Research

A localization screen reveals translation factories and widespread co-translational protein targeting
Chouaib R, Saffieddine A, Pichon X, Kwon OS, Samacoits A, Traboulsi AM, Tsanov N, Robert MC, Poser I, Zimmer C, Hyman AA, Le Hir H, Walter T, Zibara K, Mueller F, Peter M, and Bertrand E (2020)
Develomental Cell

Structural and functional insights into CWC27/CWC22 heterodimer linking the exon junction complex to spliceosomes
Busetto V, Barbosa I, Basquin J, Marquenet É, Hocq R, Hennion M, Paternina JA, Namane A, Conti E, Bensaude O, Le Hir H (2020)
Nucleic Acids Research

ALFA : annotation landscape for aligned reads
Bahin M, Noël BF, Murigneux V, Bernard C, Bastianelli L, Le Hir H, Lebreton A, Genovesio A (2019)
BMC genomics

Antisense transcriptional interference mediates condition-specific gene repression in budding yeast
Nevers A, Doyen A, Malabat C, Néron B, Kergrohen T, Jacquier A, Badis G. (2018)
Nucleic Acids Research

Nonsense-mediated mRNA decay involves two distinct Upf1-bound complexes
Dehecq M, Decourty L, Namane A, Proux C, Kanaan J, Le Hir H, Jacquier A, Saveanu C (2018)
EMBO Journal

Monitored eCLIP : high accuracy mapping of RNA-protein interactions
Hocq R, Paternina J, Alasseur Q, Genovesio A, Le Hir H (2018)
Nucleic Acids Research

UPF1-like helicase grip on nucleic acids dictates processivity
Kanaan J, Raj S, Decourty L, Saveanu C, Croquette V, Le Hir H (2018)
Nature Communications

Exon Junction Complexes can have distinct functional flavours to regulate specific splicing events
Wang Z, Ballut L, Barbosa I, Le Hir H (2018)
Scientific Reports

HTLV-1 Tax plugs and freezes UPF1 helicase leading to Nonsense-Mediated mRNA Decay inhibition
Fiorini F, Robin JP, Kanaan J, Borowiak M, Croquette V, Le Hir H, Jalinot P, Mocquet V. (2018)
Nature Communications.

A conserved structural element in the RNA helicase UPF1 regulates its catalytic activity in an isoform-specific manner
Gowravaram M, Bonneau F, Kanaan J, Maciej VD, Fiorini F, Raj S, Croquette V, Le Hir H, Chakrabarti S. (2018)
Nucleic Acids Research.

A mechanistic study of helicases with magnetic traps.
Hodeib S, Raj S, Manosas M, Zhang W, Bagchi D, Ducos B, Fiorini F, Kanaan J, Le Hir H, Allemand JF, Bensimon D, Croquette V. (2017)
Protein Science

Mutations in the Spliceosome Component CWC27 Cause Retinal Degeneration with or without Additional Developmental Anomalies.
Xu M, Xie YA, Abouzeid H, et al. (2017)
American Journal of Human Genetics

Insights into the design and interpretation of iCLIP experiments.
Haberman N, Huppertz I, Attig J, König J, Wang Z, Hauer C, Hentze MW, Kulozik AE, Le Hir H, Curk T, Sibley CR, Zarnack K, Ule J. (2017)
Genome Biology

The exon junction complex as a node of postranscriptional networks.
Le Hir H, Saulière J, Wang Z. (2016)
Nature Review in Molecular and Cellular Biology.

Human Upf1 is a highly processive RNA helicase and translocase with RNP remodelling activities.
Fiorini F, Bagchi D, Le Hir H*, Croquette V*. (2015)
Nature Communications.
*Corresponding authors

CLIP-seq to discover transcriptome-wide imprinting of RNA binding proteins in living cells.
Saulière J, Le Hir H. (2015)
Methods Molecular Biology.

Transcriptome-wide modulation of splicing by the Exon Junction Complex.
Wang Z, Murigneux V, Le Hir H. (2014)
Genome Biol.

Crystal structure of the human eIF4AIII-CWC22 complex shows how a DEAD-box protein is inhibited by a MIF4G domain.
Buchwald G, Schüssler S, Basquin C, Le Hir H, Conti E. (2013)
Proc Natl Acad Sci U S A

Transcriptome-wide identification of RNA binding sites by CLIP-seq.
Murigneux V, Saulière J, Roest Crollius H, Le Hir H. (2013)
Methods

EJC core component MLN51 interacts with eIF3 and activates translation.
Chazal PE, Daguenet E, Wendling C, Ulryck N, Tomasetto C, Sargueil B, Le Hir H. (2013)
Proc Natl Acad Sci U S A

Tight intramolecular regulation of the human Upf1 helicase by its N- and C-terminal domains.
Fiorini F, Boudvillain M, Le Hir H. (2013)
Nucleic Acids Res.

CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex.
Saulière J, Murigneux V, Wang Z, Marquenet E, Barbosa I, Le Tonquèze O, Audic Y, Paillard L, Roest Crollius H, Le Hir H. (2012)
Nature structural & molecular biology

Human CWC22 escorts the helicase eIF4AIII to spliceosomes and promotes exon junction complex assembly.
Barbosa I, Haque N, Fiorini F, Barrandon C, Tomasetto C, Blanchette M, Le Hir H. (2012)
Nature structural & molecular biology

The human T-lymphotropic virus type 1 tax protein inhibits nonsense-mediated mRNA decay by interacting with INT6/EIF3E and UPF1.
Mocquet V, Neusiedler J, Rende F, Cluet D, Robin JP, Terme JM, Duc Dodon M, Wittmann J, Morris C, Le Hir H, Ciminale V, Jalinot P. (2012)
J Virol.

Perispeckles are major assembly sites for the exon junction core complex.
Daguenet E, Baguet A, Degot S, Schmidt U, Alpy F, Wendling C, Spiegelhalter C, Kessler P, Rio MC, Le Hir H, Bertrand E, Tomasetto C. (2012)
Mol Biol Cell.

Proteins associated with the exon junction complex also control the alternative splicing of apoptotic regulators.
Michelle L, Cloutier A, Toutant J, Shkreta L, Thibault P, Durand M, Garneau D, Gendron D, Lapointe E, Couture S, Le Hir H, Klinck R, Elela SA, Prinos P, Chabot B. (2012)
Mol Cell Biol.

Biochemical characterization of the RNA helicase UPF1 involved in nonsense-mediated mRNA decay.
Fiorini F, Bonneau F, Le Hir H. (2012)
Methods in Enzymology

Molecular mechanisms for the RNA-dependent ATPase activity of Upf1 and its regulation by Upf2.
Chakrabarti S, Jayachandran U, Bonneau F, Fiorini F, Basquin C, Domcke S, Le Hir H, Conti E (2012)
Mol Cell

The structure of the ASAP core complex reveals the existence of a Pinin-containing PSAP complex.
Murachelli AG, Ebert J, Basquin C, Le Hir H, Conti E (2011)
Nature structural & molecular biology

The exon junction complex differentially marks spliced junctions.
Saulière J, Haque N, Harms S, Barbosa I, Blanchette M, Le Hir H, (2010)
Nature structural & molecular biology

Insights into the recruitment of the NMD machinery from the crystal structure of a core EJC-UPF3b complex.
Buchwald G, Ebert J, Basquin C, Sauliere J, Jayachandran U, Bono F, Le Hir H, Conti E, (2010)
Proceedings of the National Academy of Sciences of the United States of America

A UPF3-mediated regulatory switch that maintains RNA surveillance.
Chan WK, Bhalla AD, Le Hir H, Nguyen LS, Huang L, Gécz J, Wilkinson MF, (2009)
Nature structural & molecular biology

Mechanism of ATP turnover inhibition in the EJC.
Nielsen KH, Chamieh H, Andersen CB, Fredslund F, Hamborg K, Le Hir H, Andersen GR, (2009)
RNA (New York, N.Y.)

EJCs at the heart of translational control.
Le Hir H, Séraphin B, (2008)
Cell

Structural insights into the exon junction complex.
Le Hir H, Andersen GR, (2008)
Current opinion in structural biology

NMD factors UPF2 and UPF3 bridge UPF1 to the exon junction complex and stimulate its RNA helicase activity.
Chamieh H, Ballut L, Bonneau F, Le Hir H, (2008)
Nature structural & molecular biology

The exon-junction-complex-component metastatic lymph node 51 functions in stress-granule assembly.
Baguet A, Degot S, Cougot N, Bertrand E, Chenard MP, Wendling C, Kessler P, Le Hir H, Rio MC, Tomasetto C, (2007)
Journal of cell science

Identification and characterization of human Mex-3 proteins, a novel family of evolutionarily conserved RNA-binding proteins differentially localized to processing bodies.
Buchet-Poyau K, Courchet J, Le Hir H, Séraphin B, Scoazec JY, Duret L, Domon-Dell C, Freund JN, Billaud M, (2007)
Nucleic acids research

Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA.
Andersen CB, Ballut L, Johansen JS, Chamieh H, Nielsen KH, Oliveira CL, Pedersen JS, Séraphin B, Le Hir H, Andersen GR, (2006)
Science (New York, N.Y.)

The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity.
Ballut L, Marchadier B, Baguet A, Tomasetto C, Séraphin B, Le Hir H, (2005)
Nature structural & molecular biology

Expression of GFRalpha1 receptor splicing variants with different biochemical properties is modulated during kidney development.
Charlet-Berguerand N, Le Hir H, Incoronato M, di Porzio U, Yu Y, Jing S, de Franciscis V, Thermes C, (2004)
Cellular signalling

Association of the breast cancer protein MLN51 with the exon junction complex via its speckle localizer and RNA binding module.
Degot S, Le Hir H, Alpy F, Kedinger V, Stoll I, Wendling C, Seraphin B, Rio MC, Tomasetto C, (2004)
The Journal of biological chemistry

Splicing enhances translation in mammalian cells : an additional function of the exon junction complex.
Nott A, Le Hir H, Moore MJ, (2004)
Genes & development

DcpS can act in the 5 -3 mRNA decay pathway in addition to the 3 -5 pathway.
van Dijk E, Le Hir H, Séraphin B, (2003)
Proceedings of the National Academy of Sciences of the United States of America

How introns influence and enhance eukaryotic gene expression.
Le Hir H, Nott A, Moore MJ, (2003)
Trends in biochemical sciences

5 exon interactions within the human spliceosome establish a framework for exon junction complex structure and assembly.
Reichert VL, Le Hir H, Jurica MS, Moore MJ, (2002)
Genes & development

5 -End RET splicing : absence of variants in normal tissues and intron retention in pheochromocytomas.
Le Hir H, Charlet-Berguerand N, de Franciscis V, Thermes C, (2002)
Oncology

The protein Mago provides a link between splicing and mRNA localization.
Le Hir H, Gatfield D, Braun IC, Forler D, Izaurralde E, (2001)
EMBO reports

The DExH/D box protein HEL/UAP56 is essential for mRNA nuclear export in Drosophila.
Gatfield D, Le Hir H, Schmitt C, Braun IC, Köcher T, Wilm M, Izaurralde E, (2001)
Current biology : CB

The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay.
Le Hir H, Gatfield D, Izaurralde E, Moore MJ, (2001)
The EMBO journal

The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions.
Le Hir H, Izaurralde E, Maquat LE, Moore MJ, (2001)
The EMBO journal

Relative expression of the RET9 and RET51 isoforms in human pheochromocytomas.
Le Hir H, Charlet-Berguerand N, Gimenez-Roqueplo A, Mannelli M, Plouin P, de Franciscis V, Thermes C, (2000)
Oncology

Pre-mRNA splicing alters mRNP composition : evidence for stable association of proteins at exon-exon junctions.
Le Hir H, Moore MJ, Maquat LE, (2000)
Genes & development

Collaborations

Hervé Le Hir — 2014-12-18T07:05:01Z

Vincent CROQUETTE (LPS)
Nathalie SPASSKY (IBENS)
Edouard BERTRAND (IGMM, Montpellier) site web
Elena CONTI (MPI for Biochemistry - Martinsried, Germany) site web
Cosmin SAVEANU (Institut Pasteur, Paris) site web
Marc GRAILLE (Ecole Polytechnique, Palaiseau) site web
Schraga SCHWARTZ (Weizmann Institute of Science, Israel) site web
Jan KADLEC (Institut de Biologie Structurale, Grenoble) site web
Zoher GUEROUI (Department of Chemistry, Ecole Nrmale Superieure, Paris) site web

Membres de l'équipe

Hervé Le Hir — 2014-07-10T12:25:08Z

Hervé LE HIR DR CNRS Chef d'équipe	Isabelle BARBOSA Ingénieure d'Études CNRS	Olivier BENSAUDE DR Émérite
Gwenael BADIS-BREARD CR CNRS	Tommaso VILLA CR CNRS	Clara REY Doctorante 3e année
Dina KARI Ingénieure Bioinformatique	Quentin ALASSEUR Ingénieur de Recherche	Chloé SEJOURNET Assistant ingénieure

Anciens membres

Cindy BUREL (Ingénieure d'études, CDD)
Lionel BALLUT (Post-Doc)
Charlotte BARRANDON (Post-Doc)
Leïla BASTIANELLI (Ingénieure d'études, CDD)
Fabien BONNEAU (Ingénieur d'études, CDD)
Virginia BUSETTO (Doctorante)
Hala CHAMIEH (Post-Doc)
Pierre-Etienne CHAZAL (Doctorant)
Francesca FIORINI (Post-Doc)
Toni GOUHIER (Doctorant)
Rémi HOCQ (Ingénieur d'études, CDD)
Joanne KANAAN (Doctorante)
Oh Sung KWON (Post-Doc)
Maëva LE GOFF (Ingénieure d'études, CDD)
Brice MARCHADIER (Doctorant)
Emélie MARQUENET (Post-Doc)
Rahul MISHRA (Doctorant)
Lucia MORILLO (Doctorante)
Valentine MURIGNEUX (Ingénieure d'études, CDD)
Toni PATERNINA (Doctorant)
Nadia RUIZ-GUTIERREZ (Doctorante)
Jérôme SAULIERE (CR INSERM)
Raphaël SERVIGNAT D'AOUT (Ingénieur d'études, CDD)
Lorita VELAYOUDON (Ingénieure d'études, CDD)
Zhen WANG (Post-Doc)

Réunion des 10 ans du laboratoire

ON RECRUTE ! Si vous voulez rejoindre le laboratoire contactez Hervé LE HIR

BBQ d'été 2021