Cell Biology of RNA

Genetics, cell biology and development

Our group has strong interests in gene expression mechanisms, from transcription to translation. While we are interested in the regulation of these processes and their functional consequences, the big question that moves us is to understand how they occur in the context of a living cell.

Indeed, cells are not only the individual units where gene regulation takes place, but they are also incredible objects: if we consider RNA and proteins, a typical cell contains several hundreds of thousands of different molecular species, with some present in millions of copies per cell while others in only few. In order to function with such a high complexity within a crowded molecular environment, cells rely on two main tools: (i) chaperones specialized in the control of molecular interactions; (ii) a remarkable degree of spatial organization, which also allows a high plasticity and a high dynamics of molecules. It is to get insights into these very fundamental questions that we first developed tools to image single mRNAs in live cells. With these tools in hands, and others that we developed later, we aim at imaging the basic mechanisms of gene expression directly in living cells, thereby providing a renewed vision of these fundamental processes.

Our strategy is to invest in methodological developments to access and image new facets of gene expression, usually at the levels of single molecules. These developments are mostly focused on imaging RNA metabolism and they are guided by our current scientific questions.

Methodological developments require multidisciplinary approaches, and we have therefore developed a stable network of collaborators who complement our own expertise. This includes the groups of: (i) C. Zimmer and F. Müller (Pasteur Institute, Paris; https://research.pasteur.fr/en/team/imaging-and-modeling/), a physicist team with a great expertise in image analysis; (ii) T. Walter (Curie/Ecole des Mines; Paris; http://members.cbio.mines-paristech.fr/~twalter/), an applied mathematician expert in high-content microscopy and in complex, high-dimensional dataset analysis; (iii) O. Radulescu (Montpellier University; https://systems-biology-lphi.cnrs.fr/), a mathematician expert in modeling biological processes. More recently, we initiated collaborations with chemists to develop novel RNA probes and biosensors.

Our group works in three main areas: transcriptional and translational regulation, as well as chaperone-mediated control of molecular interactions.

1-Film 1: HIV-1 transcription in live cells

Cells expressing an HIV-1 reporter and recorded for 8 hours at a rate of one 3D image stack every three minutes. The left panel shows a high contrast version of the right panel, to display single RNA molecules. The blinking bright spots correspond to transcription sites randomly switching ON and OFF.

2-Film 2: Transport of ASPM polysomes to centrosomes at the onset of mitosis

HeLa cells expressing a SunTagx32-ASPM allele and scFv-sfGFP were imaged every 0.9 seconds for 180 seconds during prophase. The black spots corresponds to ASPM polysomes being actively transported to centrosomes.

3-Film 3: Transport of ASPM polysomes to centrosomes at the onset of mitosis

HeLa cells expressing a SunTagx32-ASPM allele and scFv-sfGFP were imaged every 0.9 seconds for 180 seconds during prophase. Green spots are polysomes being actively transported on microtubules seen in red toward the centrosome.

4-Schéma 4: Description of the system HSP90/R2TP also called PAQosome and its numerous clients and adaptors. Accordind to Houry et al, Trends Biochem Sci 2018, 43,4-9.


Severine Boulon
Severine BOULON

Heloise Chasse
Heloise CHASSE

Flavia Mazzarda

Jean Salamero



Hussein Karaki
Hussein KARAKI
PhD Student

Sylvain Tartier
PhD Student

Rachel Topno
Rachel TOPNO
PhD Student

Julie Abrino


Manon Philippe
Ingénieur d'études en biologie

Oriane Pourcelot
Ingénieur en techniques de biologie moléculaire et cellulaire

Marie-Cecile ROBERT

Thomas Sabate

Floric Slimani
Ingénieur en analyse d'images biologiques

Elzéar Buvry
Elzéar BUVRY

Layal Nasr El Dine


Publications of the team

The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions.

Pichon X, Moissoglu K, Coleno E, Wang T, Imbert A, Robert MC, Peter M, Chouaib R, Walter T, Mueller F, Zibara K, Bertrand E, Mili S


The HSP90/R2TP assembly chaperone promotes cell proliferation in the intestinal epithelium.

Maurizy C, Abeza C, Lemmers B, Gabola M, Longobardi C, Pinet V, Ferrand M, Paul C, Bremond J, Langa F, Gerbe F, Jay P, Verheggen C, Tinari N, Helmlinger D, Lattanzio R, Bertrand E, Hahne M, Pradet-Balade B


Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting.

Tantale K, Garcia-Oliver E, Robert MC, L\'Hostis A, Yang Y, Tsanov N, Topno R, Gostan T, Kozulic-Pirher A, Basu-Shrivastava M, Mukherjee K, Slaninova V, Andrau JC, Mueller F, Basyuk E, Radulescu O, Bertrand E


A choreography of centrosomal mRNAs reveals a conserved localization mechanism involving active polysome transport

Adham Safieddine, Emeline Coleno, Soha Salloum, Arthur Imbert, Abdel-Meneem Traboulsi, Oh Sung Kwon, Frederic Lionneton, Virginie Georget, Marie-Cécile Robert, Thierry Gostan, Charles-Henri Lecellier, Racha Chouaib, Xavier Pichon, Hervé Le Hir, Kazem Zibara, Florian Mueller, Thomas Walter, Marion Peter, Edouard Bertrand


Exon junction complex dependent mRNA localization is linked to centrosome organization during ciliogenesis

Oh Sung Kwon, Rahul Mishra, Adham Safieddine, Emeline Coleno, Quentin Alasseur, Marion Faucourt, Isabelle Barbosa, Edouard Bertrand, Nathalie Spassky, Hervé Le Hir


Quantitative imaging of transcription in living Drosophila embryos reveals the impact of core promoter motifs on promoter state dynamics.

Pimmett L., Dejean, M., Fernandez, C., Trullo, A., Bertrand, E., Radulescu, O., M. Lagha.


The box C/D snoRNP assembly factor Bcd1 interacts with the histone chaperone Rtt106 and controls its transcription dependent activity 2020

Bragantini, B., Charron, C., Bourguet, M., Paul, A., Tiotiu, D., Rothé, B., Marty, H., Terral, G., Hessmann, S., Decourty, L., Chagot, ME., Strub, JM., Massenet, S., Bertrand, E., Quinternet, M., Saveanu, C., Cianférani, S., Labialle, S., Manival, X., B. Charpentier.

RNA transport from transcription to localized translation: a single molecule perspective.

Basyuk E, Rage F, Bertrand E


Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting.

Tantale K., Garcia-Oliver, E., L’Hostis, A., Yang, Y., Robert, MC., Gostan, T., Basu, M., Kozulic-Pirher, A., Andrau, JC., Muller, F., Basyuk, E., Radulescu, O., E. Bertrand


A localization screen reveals translation factories and widespread co-translational protein targeting.

Chouaib, R., Safieddine, A., Pichon, X., Kwon, OS., Samacoits, A., Traboulsi, AM., Tsanov, N., Robert, MC., Coleno, E., Poser, I., Zimmer, C., Hyman, A. A., Le Hir, H., Zibara, K., Peter, M., Mueller, F.*, Walter, T.*, E. Bertrand


Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene.

Forero-Quintero L. S., Raymond, W., Handa, T., Saxton, M., Morisaki, T., Kimura, H., Bertrand, E., Munsky, B., T. J. Stasevich


New generations of MS2 variants and MCP fusions to detect single mRNAs in living eukaryotic cells.

Pichon X., Robert, MC., Bertrand, E., Singer, RH., Tutucci E.

NF-kB triggers a prompt and sharp transcriptional response in cell populations that emerges from heterogeneous bursting in single cells.

Zambrano S., Loffreda, A., Carelli, E., Stefanelli, G., Colombo, F., Bertrand, E., Tacchetti, C., Agresti, A., Bianchi, M. E., Molina,, N., D. Mazza.

RNA transport from transcription to localized translation: a single molecule perspective.

Basyuk, E., Rage, F., and E. Bertrand.

NOPCHAP1 is a PAQosome cofactor that helps loading NOP58 on RUVBL1/2 during box C/D snoRNP biogenesis.

Abel Y., Paiva A. C., Bizarro J., Chagot M.-E., Santo P. E., Robert M.-C., Quinternet M., Vendermoere F., Sousa P. M., Fort P., Charpentier B., Manival X., Bandeiras T. M., Bertrand E., Verheggen C.


The R2TP chaperone assembles cellular machineries in intestinal CBC stem cells and progenitors.

Maurizy C., Abeza, C., Pinet, V., Ferrand, M., Paul, C., Bremond, J., Langa, F., Gerbe, F., Jay, P., Verheggen, C., Tinari, N., Helmlinger, D., Lattanzio, R., Hahne, M., B. Pradet-Balade, Bertrand E.


A deep learning approach to identify mRNA localization patterns. 

R. Dubois, A. Imbert, A. Samacoits, M. Peter, E. Bertrand, F. Müller & T. Walter.

Live cell imaging reveals 3'-UTR dependent mRNA sorting to synapses.

Bauer, K., Segura, I., Gaspar, I., Scheuss, V., Illig, C., Ammer, G., Hutten, S., Basyuk, E., Fernández-Moya, SM., Ehses, J., Bertrand, E., Kiebler, MA.

The PAQosome, an R2TP-based chaperone for quaternary structure formation.

Houry, W.A.*, Bertrand, E.*, and Coulombe, B.* *:co-corresponding authors.

Meg3 non-coding RNA expression controls imprinting by preventing transcriptional upregulation in cis.

Sanli I, Lalevée S, Cammisa M, Perrin A, Rage F, Llères D, Riccio A, Bertrand E, Feil R.

The RPAP3-Cterminal domain identifies R2TP-like quaternary chaperones.

Maurizy, C., Quinternet, M., Abel, Y., Verheggen, C., Santo, P. E., Bourguet, M., Paiva, A. C. F., Bragantini, B., Chagot, ME., Robert, MC., Abeza, C., Fabra, P., Fort, P., Vandermoere, F., Sousa, P., Rain, JC., Charpentier, B., Cianférani, S., Bandeiras, T. M., Pradet-Balade, B., Manival, X., Bertrand, E.

Deep structural analysis of RPAP3 and PIH1D1, two components of the HSP90 co-chaperone R2TP complex.

Henri, J., Chagot, ME., Bourguet, M., Abel, Y., Terral, G., Maurizy, C., Aigueperse, C., Georgescauld, F., Vandermoere, F., Saint-Fort, R., Behm-Ansmant, I., Charpentier, B., Pradet-Balade, B., Verheggen, C., Bertrand, E., Meyer, P., Cianférani, S., Manival, X., and Quinternet, M.

The Role of Supercoiling in the Motor Activity of RNA Polymerases.

Lesne A, Victor JM, Bertrand E, Basyuk E, Barbi M.

A growing toolbox to image gene expression in single cells: sensitive approaches for demanding challenges.

Pichon, X., Lagha, M., Mueller, F. and Bertrand, E.

The splicing factor SRSF3 is functionally connected to the nuclear RNA exosome for intronless mRNA decay. Sci Rep., 2018, 8:12901.

Mure F, Corbin A, Benbahouche NEH, Bertrand E, Manet E, Gruffat H.

A computational framework to study sub-cellular mRNA localization.

Samacoits, A., Chouaib, R., Safieddine, A., Traboulsi, A., Ouyang, W., Zimmer, C., Peter, M., Bertrand, E.*, Walter, T.*, Mueller, F.* *. co-corresponding authors.

Assembly and trafficking of box C/D and H/ACA snoRNPs

Massenet S., Bertrand E., Verheggen C.

Mutually exclusive CBC-containing complexes contribute to RNA fate.

Giacometti, S., Benbahouche, N. H., Domanski, M., Robert, M-C., Meola, N., Lubas, M., Bukenborg, J., Andersen, J. S., Schultze, W. M., Verheggen, C., Kudla, G.*, Jensen, T. H.*, Bertrand, E.* *:co-corresponding authors

Assembly of the U5 snRNP component PRPF8 is controlled by the HSP90/R2TP chaperones.

Malinová, A., Cvačková, Z., Matějů, D., Hořejší, Z., Abéza, C., Vandermoere, F., Bertrand, E.*, Staněk, D.*, Verheggen, C.* *. co-corresponding authors.

ARS2 is a general suppressor of pervasive transcription.

Iasillo, C., Schmid, M., Yahia, Y., Maqbool, M., Descotes, N., Karadoulama, E., Bertrand, E., Andrau, JC., Jensen, T.

P-Body Purification Reveals the Condensation of Repressed mRNA Regulons.

Hubstenberger, A., Courel ,M., Bénard, M., Souquere, S., Ernoult-Lange, M., Chouaib, R., Yi, Z., Morlot, JB., Munier, A., Fradet M., Daunesse, M., Bertrand, E., Pierron, G., Mozziconacci, J., Kress, M., Weil, D.

The in vivo dynamics of TCERG1, a factor that couples transcriptional elongation with splicing.

Sánchez-Hernández N., Boireau S., Schmidt U., Muñoz-Cobo JP, Hernández-Munain C, Bertrand E., Suñé C.

A real-time, single molecule view of transcription reveals convoys of RNA polymerases and multiscale bursting.

Tantale, K., Müller, F., Kozulic-Pirher, A., Lesne, A., Victor, JL., Robert, MC., Capozi, S., Bäcker, V., Mateos-Langerak, J., Darzacq, X., Zimmer, C., Basyuk, E., Bertrand, E.

Imaging HIV-1 RNA dimerization in cells by multicolor super-resolution and fluctuation microscopies.

Ferrer M, Clerté C, Chamontin C, Basyuk E, Lainé S, Hottin J, Bertrand E, Margeat E, Mougel M.

SmiFISH and FISH-quant -  a flexible single mRNA detection approach with super-resolution capability.

Tsanov, N., Samacoits, A., Chouaib, R., Traboulsi, A.M., Gostan, T., Weber, C., Zimmer, C., Zibara, K., Walter, T., Peter, M.*, Bertrand, E.*, Mueller, F* *. co-corresponding authors.

Visualization of single polysomes reveals translation dynamics of endogenous mRNAs in living human cells.

Pichon X., Bastide A., Safieddine A., Chouaib R., Samacoits A., Basyuk E., Peter M., Mueller F., Bertrand E.


Long lasting control of viral rebound with a new drug ABX464 targeting Rev-mediated viral RNA biogenesis.

Campos N, Myburgh R, Garcel A, Vautrin A, Lapasset L, Nadal ES, Mahuteau-Betzer F, Najman R, Fornarelli P, Tantale K, Basyuk E, Séveno M, Venables JP, Pau B, Bertrand E, Wainberg MA, Speck RF, Scherrer D, Tazi J.

NUFIP and the HSP90/R2TP chaperone bind the SMN complex and facilitate assembly of U4-specific proteins.

Bizarro, J., Dodré, M., Huttin, A., Charpentier, B., Schlotter, F., Branlant, C., Verheggen, C., Massenet, S., Bertrand, E.

SnoRNPs, ZNHIT proteins and the R2TP pathway.

Verheggen, C., Pradet-Balade, B., Bertrand E.

Identification of the interface between Snu13p/15.5K and Rsa1p/NUFIP and demonstration of its functional importance for snoRNP assembly.

Rothé, B., Back, R., Quinternet, M., Bizarro, J., Robert, M-C., Blaud, M., Romier, C., Manival, X.*, Charpentier, B.*, Bertrand, E.*, Branlant, C. *: co-corresponding authors.

Stable assembly of HIV-1 export complexes occurs co-transcriptionally.

Nawroth, I., Mueller, F., Basyuk, E., Beerens, N., Rahbek, U. Darzacq, X., Bertrand, E.*, Kjems, J.* and Schmidt, U.* *: co-corresponding authors.

Characterization of spaghetti function in Drosophila supports a role for Hsp70 in R2TP/Hsp90-assisted assembly of cellular machineries.

Benbahouche, H., Iliopoulos, I., Török, I., Marhold, J., Kajava, A., Kempf, T., Schnölzer, M., Kiss, I., Bertrand, E.*, Mechler*, B. M.*, Pradet-Balade, B.* *: co-corresponding authors.

MLN51 triggers P-body disassembly and formation of a new type of RNA granules.

Cougot N, Daguenet E, Baguet A, Cavalier A, Thomas D, Bellaud P, Fautrel A, Godey F, Bertrand E, Tomasetto C, Gillet R.

Hypermethylated-capped selenoprotein mRNAs in mammals.

Wurth L, Gribling-Burrer AS, Verheggen C, Leichter M, Takeuchi A, Baudrey S, Martin F, Krol A, Bertrand E, Allmang C.

Proteomic and 3D structure analyses highlight the C/D box snoRNP assembly mechanism and its control.

Bizarro, J., Charron, C., Boulon, S., Westman, B., Pradet-Balade, B., Vandermoere, F., Chagot, ME., Hallais, M., Ahmad, Y., Leonhardt, H., Lamond, A., Manival, X., Branlant, C., Charpentier, B., Verheggen*, C., Bertrand*, E. *: co-corresponding authors.

FISH-quant : automated counting of transcripts in 3D images.

Mueller, F., Senecal, A., Tantale, K., Marie-Nelly, H., Ly, N., Collin, O., Basyuk, E., Bertrand, E.*, Darzacq, X.* and Zimmer, C*. *: co-corresponding authors.

Genome-wide identification of mRNAs associated with the Survival of Motor.

Rage, F., Boulisfane, N., Rihan, K., Neel, H., Gostan, T., Bertrand, E., Bordonné, R., and Soret, J.

The human cap-binding complex is functionally connected to the nuclear RNA exosome.

Refsing Andersen, P., Domanski, M., Kristiansen, M., Storvall, E., Ntini, E., Verheggen, C., Bunkenborg, J., Poser, I., Hallais, M., Sandberg, R., Hyman, A., LaCava, J., Rout, M. P., Andersen, J. S., Bertrand, E., and Jensen, T. H.

CBC-ARS2 stimulate 3'-end maturation of multiple RNA families and favor cap-proximal processing.

Hallais, M., Pontvianne, F., Refsing Andersen, P., Clerici, M., Lener, D., Benbahouche, H., Gostan, T.,Vandermoere, F., Robert, M-C., Cusack, S., Verheggen, C., Jensen, T. H. and Bertrand, E.

Retroviral GAG proteins recruit AGO2 on viral RNAs without affecting RNA accumulation and translation (2012).

Bouttier M., Saumet A., Peter M., Courgnaud V., Schmidt U., Cazevieille C., Bertrand E., Lecellier CH.

HSP90 and the R2TP co-chaperone complex: building multi-protein machineries essential for cell growth and gene expression.

Boulon, S., Bertrand, E.*, and B. Pradet-Balade*. *: co-corresponding authors

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.

Microprocessor dynamics and interactions at endogenous imprinted C19MC microRNA genes.

Bellemer C, Bortolin-Cavaillé ML, Schmidt U, Jensen SM, Kjems J, Bertrand E, Cavaillé J.

CRM1 plays a nuclear role in transporting snoRNPs to nucleoli in higher eukaryotes.

Verheggen C, Bertrand E.

Nuclear retention prevents premature cytoplasmic appearance of mRNA.

Kallehauge,T., Robert, M-C., Bertrand*, E., Jensen*, T. H. *: co-corresponding authors.

Real-time imaging of the HIV-1 transcription cycle in living cells.

Maiuri P, Knezevich A, Bertrand E, Marcello A.

Real-time imaging of co-transcriptional splicing reveals a kinetic model that reduces noise: implication for alternative splicing regulation.

Schmidt, U., Basyuk, E., Robert, MC., Yoshida, M., Villemin, JP., Auboeuf, D., Aitken, S. and Bertrand, E.

CRM1 controls the composition of nucleoplasmic pre-snoRNA complexes to licence them for nucleolar transport.

Pradet-Balade, B., Girard, C., Boulon, S., Paul, C., Azzag, K., Bordonne, R., Bertrand, E.*, and Verheggen, C* *: co-corresponding authors.

Processivity and coupling in messenger RNA transcription.

Aitken, S., Robert, M-C., Ross D. Alexander, Igor Goryanin, E.Bertrand, Jean D. Beggs.

Establishment of a protein frequency library and its application in the reliable identification of specific protein interaction partners.

Boulon S, Ahmad Y, Trinkle-Mulcahy L, Verheggen C, Cobley A, Gregor P, Bertrand E, Whitehorn M, Lamond AI.

A Proteomic Screen for Nucleolar SUMO Targets shows SUMOylation modulates the function of Nop5/Nop58.

Westman, B.J., Verheggen, C., Hutten, S.,Lam, Y. W., Bertrand, E., Lamond, A. I.

Splicing independent recruitment of U1 snRNA to a transcription unit in living cells.

Spiluttini B, Gu B, Belagal P, Smirnova AS, Nguyen VT, Hébert C, Schmidt U, Bertrand E, Darzacq X, Bensaude O.

RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3'-end formation processing in S. Cerevisiae.

Alexander RD, Barrass JD, Dichtl B, Kos M, Obtulowicz T, Robert MC, Koper M, Karkusiewicz I, Mariconti L, Tollervey D, Dichtl B, Kufel J, Bertrand E, Beggs JD

HSP90 and its R2TP/Prefoldin-like co-chaperone are involved in the cytoplasmic assembly of RNA polymerase II.

Boulon, S., Pradet-Balade, B., Verheggen, C., Molle, D., Boireau, S., Georgieva, M., Azzag, K., Robert, M-C., Ahmad, Y., Neel, H., Lamond, A.I., Bertrand, E.

Crosstalk between mRNA 3'-end processing and transcription initiation.

Mapendano, C., Lykke-Andersen, S., Kjems, J., Bertrand, E. and T. H. Jensen.

DNA Damage Regulates Alternative Splicing through Changes in Pol II Elongation. Cell, 2009, 137:708-20.

Muñoz, M. J., Pérez Santangelo, S. M., de la Mata, M., Bird, G., Bentley, D., Boireau, S., Bertrand, E., Kornblihtt, A. R.

Endosomal trafficking of HIV-1 Gag and genomic RNAs regulates viral egress. J. Biol Chem, 2009, 284:19727-43.

Molle, D., Segura-Morales, C., Camus, G., Berlioz-Torrent, C., Kjems, J., Basyuk, E., Bertrand, E.

Assembly of an export-competent mRNP is needed for efficient release of the 3'-end processing complex after polyadenylation. Mol Cell Biol. 2009, 19:5327-38.

Qu X, Lykke-Andersen S, Nasser T, Saguez C, Bertrand E, Jensen TH, Moore C.

Characterization of a short isoform of human Tgs1 hypermethylase associating with snoRNPs core proteins and produced by limited proteasome processing. J Biol. Chem, 2008, 283(4):2060-9.

Girard, C., Verheggen, C., Vagner, C., Bertrand, E., and Bordonné, R.

A novel role for PA28gamma-proteasome in nuclear speckle organization and SR protein trafficking. Mol Biol Cell. 2008, 19(4):1706-16.

Baldin V, Militello M, Thomas Y, Doucet C, Fic W, Boireau S, Jariel-Encontre I, Piechaczyk M, Bertrand E, Tazi J, Coux O.

The HSP90 chaperone controls the biogenesis of L7Ae RNPs through a conserved machinery. J. Cell Biol, 2008, 180(3):579-95.

Boulon, S., Marmier-Gourrier, N., Wurth, L., Pradet-Balade, B., Verheggen, C., Jády, B., Rothé, B., Pescia, C., Robert, M-C., Kiss, T., Bardoni, B., Krol, A., Branlant, C., Allmang, C., Charpentier, B., and Bertrand, E.

Mutations in a small region of the exportin Crm1p disrupt the daughter cell specific nuclear localization of the transcription factor Ace2p in Saccharomyces cerevisiae. Biol Cell. 2008, 100(6):343-54.

Bourens, M., Racki, W., Bécam, AM., Panozzo, C., Boulon, S., Bertrand, E., Herbert, CJ.

Translationally repressed mRNA transiently cycles through stress granules during stress. Mol Biol Cell. 2008, 19(10):4469-79.

Mollet S, Cougot N, Wilczynska A, Dautry F, Kress M, Bertrand E, Weil D.

Dendrites of mammalian neurons contain specialized P-Body-LikesStructures that respond to neuronal activation. J. Neurosci. 2008, 28:13793-13804.

Cougot N, Bhattacharyya SN, Tapia-Arancibia L, Bordonné R, Filipowicz W, Bertrand E, Rage F.

Suv39H1 and HP1gamma are responsible for chromatin-mediated HIV-1 transcriptional silencing and post-integration latency. EMBO J. 2007, 26:424-35.

Du Chene, I., Basyuk, E., Lin, Y., Triboulet, R., Knezevich, A., Chable-Bessia, C., Mettling, C., Baillat, V., Reynes, J., Corbeau, P., Bertrand, E., Marcello, A., Emiliani, S., Kiernan, R., and Benkirane, M.

Bsr, a novel nuclear-restricted RNA with mono-allelic expression. Mol Biol Cell, 2007, 18:2817-27.

Royo, H., Basyuk, E., Marty, E., Marques, M., Bertrand, E., and Cavaille, J.

A real-time view of the TAR:Tat:P-TEFb complex at HIV-1 transcription sites. Retrovirology. 2007, 4:36.

Molle, D., Maiuri, P., Boireau, S., Bertrand, E., Knezevich, A., Marcello, A., and Basyuk, E.

The clathrin adaptor complex AP-1 binds HIV-1 and MLV Gag and facilitates their budding. Mol Biol Cell. 2007, 18:3193-203.

Camus, G., Segura-Morales, C., Molle, D., Lopez-Verges, S., Begon-Pescia, C., Cazevieille, C., Schu, P., Bertrand, E., Berlioz-Torrent, C., and Basyuk, E.

A dynamic scaffold of pre-snoRNP factors facilitates human box C/D snoRNP assembly. Mol Cell Biol. 2007, 27:6782-93.

McKeegan, K., Debieux, C., Boulon, S., Bertrand, E., and Watkins, NJ.

The exon-junction-complex-component metastatic lymph node 51 functions in stress-granule assembly. J Cell Sci. 2007, 120:2774-84.

Baguet, A., Degot, S., Cougot, N., Bertrand, E., Chenard, MP., Wendling, C., Kessler, P., Le Hir, H., Rio, M-C., and Tomasetto, C.

Inhibition of nonsense-mediated mRNA decay (NMD) by a new chemical molecule reveals the dynamic of NMD factors in P-bodies. J Cell Biol. 2007, 178:1145-60.

Durand, S., Cougot, N., Mahuteau-Betzer, F., Nguyen, C.H., Grierson, D.S., Bertrand, E., Tazi, J., and Lejeune, F.

The transcriptional cycle of HIV-1 in real-time and live cells. J. Cell Biol. 2007, 179:291-304.

Boireau, S., Maiuri, P., Basyuk, E., de la Mata, M., Knezevich, A., Pradet-Balade, B., Bäcker, V., Kornblihtt, A., Marcello, A., and Bertrand E.

Cell cycle-dependent recruitment of telomerase RNA and Cajal bodies to human telomeres. Mol Biol Cell. 2006, 17:944-54.

Jady, B., Richard, P., Bertrand, E., and Kiss, T.

The exonuclease ISG20 mainly localizes in the nucleolus and the Cajal (Coiled) bodies and is associated with nuclear SMN protein-containing complexes. J Cell Biochem. 2006, 98:1320-33.

Espert, L., Eldin, P., Gongora, C., Bayard, B., Harper, F., Chelbi-Alix, M., Bertrand, E., Degols, G., and Mechti, N.

Depletion of SMN by RNA interference in HeLa cells induces defects in Cajal body formation. Nucleic Acids Res. 2006, 34:2925-32.

Girard, C., Neel, H., Bertrand, E., and Bordonne, R.

ADAR2-mediated editing of RNA substrates in the nucleolus is inhibited by C/D small nucleolar RNA. J. Cell Biol. 2005, 169:745-753.

Vitali, P., Basyuk, E., Le Meur, E., Bertrand, E., Muscatelli, F., Cavaille, J., and Huttenhofer, A.

Tsg101 and Alix interact with MLV Gag and cooperate with Nedd4 ubiquitin-ligases during budding. J. Biol. Chem, 2005, 280:27004-12.

Segura-morales, C., Pescia, C., Chatellard-Causse, C., Sadoul, R., Bertrand, E. and Basyuk, E.

Inhibition of translational initiation by Let-7 microRNA in human cells. Science, 2005, 309:1573-6.

Pillai, R., Battacharrya, S., Artus, C., Zoller, T., Cougot, N., Basyuk, E., Bertrand, E., Filipowicz, W.

The packaging signal of MLV is an integrated module that mediates intracellular transport of genomic RNAs. J. Mol. Biol., 2005, 354:330-9.

Basyuk, E., Boulon, S., Pedersen, F. S., Bertrand, E., and Rasmussen, S. V.

Photo-conversion of YFP proteins into CFP-like species during acceptor photo-bleaching FRET experiments. Nature Methods, 2005, 2:801.

Valentin, G., Verheggen, C., Piolot, T., Neel, H., Coppey-Moisan, M., and Bertrand, E.

Human telomerase RNA and box H/ACA scaRNAs share a common Cajal body localization signal. J. Cell Biol, 2004, 164(5):647-52.

Jady, B., Bertrand, E., and Kiss, T.

From silencing to gene expression: real-time analysis in single cells. Cell, 2004, 116(5):683-98.

Janicki, S., Tsukamoto, T., Salghetti, S., Tansey, W., Sachidanandam, R., Prasanth, K., Ried, T., Shav-Tal, Y., Bertrand, E., Singer, R., and Spector, D.

Human box H/ACA pseudouridylation guide RNA machinery. Mol Cell Biol. 2004 Jul;24(13):5797-807.

Kiss AM, Jady BE, Bertrand E, Kiss T.

Nuclear localization properties of a conserved protuberance in the Sm core complex. Exp Cell Res. 2004 299(1):199-208.

Girard C, Mouaikel J, Neel H, Bertrand E, Bordonne R.

La localisation des ARN dans le cytoplasme. M/S, 2004, 20:669-73.

Eugenia Basyuk, Brigitte Lavoie, Remy Bordonné, et Edouard Bertrand.

Polarité cellulaire et localisation intracellulaire des ARNm de l'actine. M/S, 2004, 20:539-43.

Brigitte Lavoie, Eugenia Basyuk, Remy Bordonné, et Edouard Bertrand.

A co-transcriptional model for 3'-end processing of the Saccharomyces cerevisiae pre-ribosomal RNA precursor. RNA. 2004 Oct;10(10):1572-85.

Henras AK, Bertrand E, Chanfreau G.

PHAX and CRM1 are required sequentially to transport U3 snoRNA to nucleoli. Mol Cell, 2004, 16:777-787.

Boulon, S., Verheggen, C., Jady, B., Girard, C., Pescia, C., Paul, C., Ospina, J., Kiss, T., Matera, A. G., Bordonné, R. and Bertrand, E.

Single mRNA molecules demonstrate probabilistic movement in living mammalian cells Current Biology, 2003, 13(2):161-7.

D. Fusco, N. Accornéro, S. Shenoy, JM Blanchard, RH Singer and E. Bertrand.

Exportin-5 mediates nuclear export of minihelix-containing RNAs. J. Biol Chem. 2003, 278(8):5505-8.

Gwizdek C, Ossareh-Nazari B, Brownawell AM, Doglio A, Bertrand E, Macara IG, Dargemont C.

The RasGAP-associated endoribonuclease G3BP assembles stress granules. J Cell Biol. 2003, 160(6):823-31.

Tourriere H, Chebli K, Zekri L, Courselaud B, Blanchard JM, Bertrand E, Tazi J.

Modification of Sm small nuclear RNAs occurs in the nucleoplasmic Cajal body following import from the cytoplasm. EMBO J., 2003, 22(8):1878-88.

Jady BE, Darzacq X, Tucker KE, Matera AG, Bertrand E, Kiss T.

Interaction between the small-nuclear-RNA cap hypermethylase and the spinal muscular atrophy protein, survival of motor neuron. EMBO Rep., 2003, 4(6):616-22.

Mouaikel J, Narayanan U, Verheggen C, Matera AG, Bertrand E, Tazi J, Bordonne R.

A common sequence motif determines the Cajal body-specific localisation of box H/ACA scaRNAs EMBO J. 2003, 22:4283-93.

Richard, P., Xavier Darzacq, X., Bertrand, E., Jády, B., Verheggen, C., and Kiss, T.

Retroviral genomic RNAs are transported to the plasma membrane by endosomal vesicles. Dev. Cell, 2003, 5:161-174.

Basyuk, E., Galli, T., Mougel, M., Blanchard, JM., Sitbon, M., and Bertrand E.

Human let-7 stem-loop precursors harbor features of RNase III cleavage products. Nucleic Acids Res. 2003, 31(22):6593-7.

Basyuk, E., Suavet, F., Doglio, A., Bordonné, R, Bertrand E.

Hypermethylation of the cap structure of both snRNAs and snoRNAs in yeast requires a conserved methyltransferase that locates in the nucleolus. Mol. Cell, 2002, 9:891-901.

John Mouaikel, Céline Verheggen, Edouard Bertrand, Jamal Tazi and Rémy Bordonné.

Mammalian and yeast U3 snoRNPs are matured in specific and related nuclear compartments. EMBO J., 2002, 21: 2736-45.

Verheggen, C., Lafontaine, D., Samarsky, S., Mouaikel, J., Blanchard, JM., Bordonné, R., and Bertrand E.

Cajal body-specific small nuclear RNAs: a novel class of 2’-o-methylation and pseudouridylation guide RNAs. EMBO J., 2002, 21:2746-56.

Xavier Darzacq, Beáta E. Jády, Céline Verheggen, Arnold M. Kiss, Edouard Bertrand and Tamás Kiss

An active precursor in assembly of yeast nuclear ribonuclease P. RNA. 2002; 8(10):1348-60.

Srisawat C, Houser-Scott F, Bertrand E, Xiao S, Singer RH, Engelke DR.

A Cajal body-specific pseudouridylation guide RNA is composed of two box H/ACA snoRNA-like domains.. Nucleic Acids Res. 2002, 30(21):4643-9.

Kiss AM, Jady BE, Darzacq X, Verheggen C, Bertrand E, Kiss T.

Terminal minihelix, a novel RNA motif that directs polymerase III transcripts to the cell cytoplasm. J Biol Chem. 2001, 276(28):25910-8.

Bertrand E, Gwizdek C, Dargemont C, Lefebvre JC, Blanchard JM, Singer RH, Doglio A.

A Well-Connected and Conserved Nucleoplasmic Helicase is Required for Production of Box C/D and H/ACA snoRNAs and Localization of snoRNP Proteins. Mol. Cell Biol. 2001, 21:7731-46.

King, T., Decatur, W., Bertrand, E., Maxwell, E.S. and Fournier, M.J.

Box C/D small nucleolar RNA trafficking involves small nucleolar RNP proteins, nucleolar factors and a novel nuclear domain. EMBO J. 2001, 20:5480-5490.

Verheggen, C., Mouaikel, J., Thiry, M., Blanchard, J-M., Tollervey, D., Bordonné, R., Lafontaine, D., and Bertrand, E.

Alcaline fixation drastically enhances the signal of in situ hybridization.

Basyuk, E., Bertrand, E., Journot, L.

A CBF5 mutation that disrupts nucleolar localization of early tRNA biosynthesis in yeast also suppresses tRNA gene-mediated transcriptional silencing.

Ann Kendall, Melissa W. Hull, Edouard Bertrand, Paul D.Good, Robert H.Singer, and David R.Engelke.

A snoRNA:ribozyme hybrid cleaves a nucleolar RNA target in vivo with near-perfect efficiency.

Samarsky D, Ferbeyre G, Bertrand E, Singer RH, Cedergren R, Fournier MJ.

mRNA localization signals can enhance the intracellular effectiveness of hammerhead ribozymes.

Lee NS, Bertrand E, Rossi J.

The snoRNA box C/D motif directs nucleolar targeting and also couples snoRNA synthesis and localization.

Samarsky DA, Fournier MJ, Singer RH, Bertrand E.

Nucleolar localization of early tRNA processing.

Bertrand E, Houser-Scott F, Kendall A, Singer RH, Engelke DR.

Monitoring retroviral RNA dimerization in vivo via hammerhead ribozyme cleavage.

Pal BK, Scherer L, Zelby L, Bertrand E, Rossi JJ.

3’-end modification of the adenoviral VAI gene affects its expression in human cells: consequences for the design of chimeric VAI RNA-ribozymes.

Barcellini-Couget S, Bertrand E, Singer RH, Lebfevre JC, Doglio A.

Localization of ASH1 mRNA particles in living yeast.

Bertrand E, Chartrand P, Shaefer M, Shenoy S, Singer RH, Long R.

Expression of small, therapeutic RNAs in human cell nuclei.

Good P, Krikos AJ, Li S, Bertrand E, Lee N, Giver L, Ellington A, Zaia JA, Rossi JJ, Engelke DR.

The expression cassette determines the functional activity of ribozymes in mammalian cells by controlling their intra-cellular localization.

Bertrand E, Castanotto D, Zhou C, Carbonelle C, Lee NS, Good P, Chaterjee S, Grange T, Pictet R, Kohn D, Engelke DR, Rossi JJ.

Can hammerhead ribozymes be efficient tools to inactivate gene function ?

Bertrand E, Pictet R, Grange T.

Facilitation of hammerhead ribozyme catalysis by the nucleocapsid protein of HIV-1 and the heterogeneous nuclear ribonucleoprotein A1.

Bertrand E, Rossi JJ

Polystyrene reverse-phase ion-pair chromatography of chimeric ribozymes.

Swiderski PM, Bertrand E, Kaplan BE

A highly sensitive method for mapping the 5' termini of mRNAs.

Fromont-Racine, M., Bertrand, E., Pictet, R., and Grange, T.

Visualization of the in vivo interaction of a regulatory protein with RNA.

Bertrand, E., Fromont-Racine, M., Pictet, R., and Grange, T.

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1- Génomique computationnelle:

En dehors des promoteurs de gène codant pour les protéines annotées, de nombreux sites du génome peuvent être transcrits pour générer divers ARN, par ex. les ARN des enhancers, les microARN et divers ARN longs non codants. D'autre part, des études d'association à l'échelle du génome montrent que les loci associés aux traits phénotypiques, y compris ceux liés à des maladies humaines, peuvent être trouvés en dehors des régions canoniques codant pour des protéines. Ces découvertes récentes suggèrent que les régions non codantes du génome humain abritent une pléthore d'éléments fonctionnellement significatifs, qui peuvent avoir un impact considérable sur les régulations et les fonctions du génome, mais restent encore à explorer. Dans ce projet, nous visons à étudier ces éléments en combinant des expériences à haut débit avec des approches d'apprentissage automatique et d'intelligence artificielle.

Ce travail est effectué dans le cadre de l'équipe Computational Regulatory Genomics:

2- La transcription dans les cellules vivantes

La transcription était longtemps considérée comme un processus déterministe. Cependant, les dix dernières années de recherche et l'avènement des technologies d'imagerie à molécule unique ont révélé une réalité bien différente: l'expression des gènes est stochastique. En effet, un gène actif n'est pas constamment transcrit mais fluctue entre les périodes d'activité et d'inactivité. Ces fluctuations sont dues à l'existence d'états actifs et inactifs des promoteurs, qui peuvent alterner de manière aléatoire. Cette découverte fondamentale a des conséquences phénotypiques clé car elle crée une variabilité incontrôlée de cellule à cellule. Dans le cas du VIH-1 par exemple, des données suggèrent que le bruit transcriptionnel aléatoire détermine la latence virale.

Pour mieux comprendre comment la transcription fonctionne réellement dans les cellules vivantes, nous visualisons la transcription dans les cellules vivantes par des méthodes d'imagerie molécule unique, grâce à des versions améliorées du système MS2-GFP. En combinant ces méthodes avec de la modélisation mathématique, nous pouvons caractériser en détail la dynamique des états du promoteur sur plusieurs échelles de temps, de la seconde au jour. Dans le cas du VIH-1 par exemple, nous avons observé que le promoteur viral présente des fluctuations stochastiques multi-échelles et que chaque échelle temporelle, minute ou heure, est régulée indépendamment. Notre objectif général est de caractériser les différentes sources de bruit stochastique, les mécanismes moléculaires en jeu et les conséquences fonctionnelles au niveau des cellules individuelles.


3- La traduction dans les cellules vivantes

La plupart des ARNm se distribuent au hasard dans le cytoplasme, mais certains se localisent dans des structures cellulaires spécifiques. La localisation des ARN est liée au métabolisme de l'ARN, par exemple pour son stockage ou sa dégradation, ou au métabolisme des protéines, pour synthétiser une protéine localement. Une telle synthèse locale joue un rôle dans de très nombreux processus cellulaires, comme la polarité cellulaire, la mitose et la plasticité synaptique. Pour mieux comprendre la localisation de l'ARN et la compartimentation de la traduction dans le cytoplasme, nous avons développé une version à haut débit du smFISH, qui permet de détecter toutes les molécules d'un ARN donné dans des cellules fixée, ainsi que des outils pour visualiser la traduction de molécules unique d'ARNm dans les cellules vivantes. Nous avons découvert que la traduction est un processus stochastique à l'échelle des molécules unique d'ARNm, et en réalisant des cribles combinés à la vision par ordinateur et à l'apprentissage automatique, nous avons découvert des ARNm localisés dans une variété de compartiments: protubérances cytoplasmiques, contours cellulaires, appareil de Golgi, endosomes, enveloppe nucléaire, centrosomes, etc. De manière surprenante, nous avons observé que la localisation de l'ARN nécessite fréquemment le polypeptide naissant en cours de traduction, et s'effectue par le transport actif et motorisé des polysomes. Nous avons également révélé l'existence d'usines de traduction, de petites structures cytoplasmiques dédiées à la traduction d'ARNm spécifiques et jouant des rôles particuliers dans le métabolisme des protéines naissantes. Nous visons maintenant à caractériser la compartimentation de la traduction dans le cytoplasme à l'échelle nanoscopique.  

4- Le système HSP90 / R2TP: contrôle des interactions moléculaires par chaperon

Après la traduction, les protéines doivent se replier vers leur structure native pour devenir fonctionnelles. La plupart des protéines ne fonctionnent pas seules mais sont rassemblées dans de grands assemblages macromoléculaires, comme les nano-machines cellulaires et les condensats micrométriques. Ces processus nécessitent des chaperons dédiés qui aident les polypeptides à acquérir leur structure tertiaire et à s'assembler en complexes macromoléculaires. Plus largement, dans un environnement cellulaire encombré, les chaperons participent au contrôle des interactions moléculaires, et sont donc susceptibles de jouer un rôle dans la régulation de la formation des condensats, ainsi que dans l'agrégation des protéines dans des conditions physiologiques et pathologiques.

Nous nous intéressons à une co-chaperone de HSP90, nommée R2TP, qui a la propriété unique parmi les chaperons de participer à la formation de complexes macromoléculaires. Le R2TP est composé de quatre sous-unités: (i) RUVBL1 et RUVBL2, qui sont des AAA + ATPases avec une activité chaperon; (ii) RPAP3 et PIH1D1, qui servent d'adaptateurs et de régulateurs. Nous et d'autres avons montré que le chaperon HSP90/R2TP est impliqué dans l'assemblage de plusieurs complexes multi-sous-unités, comme les snoRNP, les snRNP, les ARN polymérases et les PIKKs. Notre hypothèse est que le chaperon HSP90/R2TP participe au contrôle qualité de l'assemblage de complexes multi-protéiques, et ce dans différents contextes: (i) pour construire des nano-machines composées de plusieurs sous-unités; (ii) pour réguler la formation de condensat; (iii) lors de stress protéotoxiques liés au cancer, où il pourrait jouer un rôle important dans le développement des tumeurs. Pour aborder ces hypothèses, nous effectuons des études de protéomique quantitative, des tests fonctionnels, et nous collaborons avec cinq laboratoires en biologie structurale pour déchiffrer les mécanismes impliqués.