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Publications funded by the Labex NetRNA


2017

RNA-based antiviral immunity in drosophila and vector insects (Imler)

  • Kuhn L, Majzoub K, Einhorn E, Chicher J, Pompon J, Imler JL, Hammann P & Meignin C (2017) Definition of a RACK1 interaction network in Drosophila melanogaster using SWATH-MS G3 7:2249-2258. Abstract
  • Mussabekova A, Daeffler L & Imler JL (2017) Innate and intrinsic antiviral immunity in Drosophila Cell. Mol. Life Sci. 74:2039-2054. Abstract

RNA degradation in plants (Gagliardi)

  • De Almeida C, Scheer H, Zuber H and Gagliardi D (2017) RNA uridylation: a key post-transcriptional modification shaping the coding and non-coding transcriptome. WIREs RNA 10.1002/wrna.1440:na. Abstract

External Attractivity Team: Mechanisms of small RNA biogenesis (Blevins)

  • Blevins T*, Wang J, Pflieger D, Pontvianne F, Pikaard CS* *co-corresponding (2017) Hybrid incompatibility caused by an epiallele PNAS 114(4):3702-3707. Abstract

2016

Non-coding RNAs and viral infections (Pfeffer)

  • Gabrielle Haas, Semih Cetin, Mélanie Messmer, Béatrice Chane-Woon-Ming, Olivier Terenzi, Johana Chicher, Lauriane Kuhn, Philippe Hammann and Sébastien Pfeffer (2016) Identification of factors involved in target RNA-directed microRNA degradation Nulc. Acids Res in:press. Abstract
  • Haar J, Contrant M, Bernhardt K, Feederle R, Diederichs S, Pfeffer S, Delecluse HJ (2016) The expression of a viral microRNA is regulated by clustering to allow optimal B cell transformation. Nucl. Acids Res. in:press. Abstract

Digital biology of RNA (Ryckelynck)

  • Alexey Rozov, Natalia Demeshkina, Iskander Khusainov, Eric Westhof, Marat Yusupov & Gulnara Yusupova (2016) Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code Nat Commun 7:10457. Abstract
  • E. Westhof (2016) Perspectives and Pitfalls in Nucleic Acids Crystallography Methods Mol Biol 1320:3-8. Abstract

RNA-based antiviral immunity in drosophila and vector insects (Imler)

  • Lamiable O, Arnold J, de Faria I, Olmo R, Bergami F, Meignin C, Hoffmann JA, Marques JT, Imler JL (2016) Analysis of the contribution of hemocytes and autophagy to Drosophila antiviral immunity. Journal of Virology 90:5415-26. Abstract
  • Lamiable O, Kellenberger C, Kemp C, Troxler L, Pelte N, Boutros M, Marques JT, Daeffler L, Hoffmann JA, Roussel A & Imler JL (2016) Cytokine Diedel and a viral homologue suppress deleterious IMD-dependent gene expression in Drosophila Proc Natl Acad Sci USA 113:698-703. Abstract
  • Lamiable O, Meignin C & Imler JL (2016) WntD and Diedel: two immunomodulatory cytokines in Drosophila immunity Fly 10:187-194. Abstract
  • Marques JT & Imler JL (2016) The diversity of insect antiviral immunity: insight from viruses Current Opinion in Microbiology 32:71-76. Abstract
  • Martins N, Imler JL, Meignin C (2016) Discovery of novel targets for antivirals: learning from flies Current Opinion in Virology 20:64-70. Abstract

RNA degradation in plants (Gagliardi)

  • Scheer H, Zuber H, De Almeida C, Gagliardi D. (2016) Uridylation Earmarks mRNAs for Degradation… and More. Trends in Genetics 32:607-619. Abstract
  • Zuber H, Scheer H, Ferrier E, Sement F, Mercier P, Stupfler B and Gagliardi D (2016) URT1-mediated uridylation and PABP cooperate to repair mRNA deadenylated ends in Arabidopsis. Cell Rep. 14:2707-17. Abstract

2015

tRNA biology and pathogenesis (Frugier)

  • Alexandrova J, Paulus C, Rudinger-Thirion J, Jossinet F, Frugier M (2015) Elaborate uORF/IRES features control expression and localization of human glycyl-tRNA synthetase RNA Biol 12:1301-1313. Abstract

Non-coding RNAs and viral infections (Pfeffer)

  • Bandiera S, Pfeffer S, Baumert TF, Zeisel MB (2015) miR-122--a key factor and therapeutic target in liver disease J. Hepatol 62:448-457. Abstract
  • Girardi E, Lefèvre M, Chane-Woon-Ming B, Paro S, Claydon B, Imler JL, Meignin C, Pfeffer S (2015) Cross-species comparative analysis of Dicer proteins during Sindbis virus infection Sci Rep 5:10693. Abstract
  • Mailly L, Xiao F, Lupberger J, Wilson GK, Aubert P, Duong FH, Calabrese D, Leboeuf C, Fofana I, Thumann C, Bandiera S, Lütgehetmann M, Volz T, Davis C, Harris HJ, Mee CJ, Girardi E, Chane-Woon-Ming B, Ericsson M, Fletcher N, Bartenschlager R, Pessaux P, V (2015) Clearance of persistent hepatitis C virus infection in humanized mice using a claudin-1-targeting monoclonal antibody. Nat Biotechnol 33:549-554. Abstract

Bacterial messenger RNAs and regulatory RNAs (Romby)

  • Durand S, Braun F, Lioliou E, Romilly C, Helfer AC, Kuhn L, Quittot N, Nicolas P, Romby P, Condon C. (2015) A Nitric Oxide Regulated Small RNA Controls Expression of Genes Involved in Redox Homeostasis in Bacillus subtilis. PloS Genetics 11:e1004957. Abstract
  • Durand S, Tomasini A, Braun F, Condon C, Romby P (2015) sRNA and mRNA turnover in Gram-positive bacteria FEMS Microbiol Rev 39:316-330. Abstract
  • Duval M, Simonetti A, Caldelari I, Marzi S (2015) Multiple ways to regulate translation initiation in bacteria: Mechanisms, regulatory circuits, dynamics. Biochimie 114:18-29. Abstract
  • Nitzan M, Fechter P, Peer A, Altuvia Y, Bronesky D, Vandenesch F, Romby P, Biham O, Margalit H. (2015) A defense-offense multi-layered regulatory switch in a pathogenic bacterium. Nucleic acid Research 27:gkv001. Abstract
  • Wagner, E.G., Romby, P. (2015) Small RNAs in bacteria and archaea : who they are, what they do, and how they do it Adv Genet 90:133-208. Abstract

Digital biology of RNA (Ryckelynck)

  • Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng 7, Chojnowski G4 Chou FC, Cordero P, Cruz JA, Ferré-D'Amaré AR, Das R, Ding F, Dokholyan NV, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann TH, Masquida (2015) RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures RNA 21:1066-1084. Abstract
  • Ryckelynck M, Baudrey S, Rick C, Marin A, Coldren F, Westhof E, Griffiths AD. (2015) Using droplet-based microfluidics to improve the catalytic properties of RNA under multiple-turnover conditions RNA 21:1-12. Abstract

RNA-based antiviral immunity in drosophila and vector insects (Imler)

  • Aguiar E, Olmo R, Paro S, Viana F, Faria I, Todjro M, Pereira F, KroonE, Meignin C, Gatherer D, Imler JL and Marques J (2015) Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host Nucleic Acids Research 43:6191-6206. Abstract
  • Girardi E., Lefèvre M., Paro S., Chane-Woon-Ming B., Claydon B., Imler J.-L., Meignin C., Pfeffer S. (2015) Cross-species comparative analysis of Dicer proteins during Sindbis virus infection Scientific Reports 5:10693. Abstract
  • Paro S., Imler J.-L. & Meignin C. (2015) Sensing viral RNAs by Dicer/RIG-I like ATPases across species. Current Opinion in Immunology 32:106-113. Abstract

RNA degradation in plants (Gagliardi)

  • Branscheid A., Marchais A., Schott G., Lange H., Gagliardi D., Andersen S.U., Voinnet O. and Brodersen P. (2015) SKI2 mediates degradation of RISC 5’-cleavage fragments and prevents secondary siRNA production from miRNA targets in Arabidopsis. Nucleic Acids Res. 43(22):10975-10988. Abstract
  • Sikorski P.J., Zuber H., Philippe L., Sement F.M., Canaday J., Kufel J., Gagliardi D. and Lange H. (2015) Distinct 18S rRNA precursors are targets of the exosome complex the exoribonuclease RRP6L2 and the terminal nucleotidyltransferase TRL in Arabidopsis thaliana.. Plant J. 83(6):991-1004. Abstract

External Attractivity Team: Cryo-electron microscopy of translation complexes (Hashem)

  • Amedee des Georges, Vidya Dhote, Lauriane Kuhn, Christopher U. T. Hellen, Tatyana V. Pestova, Joachim Frank & Yaser Hashem (2015) Structure of mammalian eIF3 in the context of the 43S preinitiation complex Nature 525:491-495. Abstract

2014

Non-coding RNAs and viral infections (Pfeffer)

  • Alsaleh G, François A, Philippe 1, Gong YZ, Bahram S, Cetin S, Pfeffer S, Gottenberg JE, Wachsmann D, Georgel P, Sibilia J. (2014) MiR-30a-3p negatively regulates BAFF synthesis in systemic sclerosis and rheumatoid arthritis fibroblasts PLoS One 9(10):e111266. Abstract
  • Contrant M., Fender A., Chane-Woon-Ming B., Randrianjafy R., Vivet-Boudou V., Richer D. and Pfeffer S. (2014) Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs Nucleic Acids Res 42(12):7981-96. Abstract

Bacterial messenger RNAs and regulatory RNAs (Romby)

  • Fechter P, Caldelari I, Lioliou E, Romby P. (2014) Novel aspects of RNA regulation in Staphylococcus aureus . FEBS Lett 588(15):2523-2529. Abstract
  • Hammann P., Parmentier D., Cerciat M., Reimegård J., Helfer A.C., Boisset S., Guillier M., Vandenesch F., Wagner E.G., Romby P. and Fechter P. (2014) A method to map changes in bacterial surface composition induced by regulatory RNAs in Escherichia coli and Staphylococcus aureus Biochimie 106:175-179. Abstract
  • Romilly C., Lays C., Tomasini A., Caldelari I., Benito Y., Hammann P., Geissmann T., Boisset S., Romby P. and Vandenesch F. (2014) A Non-Coding RNA Promotes Bacterial Persistence and Decreases Virulence by Regulating a Regulator in Staphylococcus aureus. PLoS Pathog 10(3):e1003979. Abstract
  • Sesto N, Touchon M, Andrade JM, Kondo J, Rocha EP, Arraiano CM, Archambaud C, Westhof E, Romby P, Cossart P. (2014) A PNPase dependent CRISPR System in Listeria. PLoS Genet. 10(1):e1004065. Abstract
  • Tomasini A, François P, Howden BP, Fechter P, Romby P, Caldelari I. (2014) The importance of regulatory RNAs in Staphylococcus aureus. Infect. Genet. Evol. 21C:616-626. Abstract

Digital biology of RNA (Ryckelynck)

  • Sesto N, Touchon M, Andrade JM, Kondo J, Rocha EP, Arraiano CM, Archambaud C, Westhof E, Romby P, Cossart P. (2014) A PNPase dependent CRISPR System in Listeria. PLoS Genet. 10(1):e1004065. Abstract
  • Vicens Q. and Westhof E. (2014) Biogenesis of Circular RNAs Cell 159(1):13-14. Abstract
  • Westhof E. (2014) Isostericity and tautomerism of base pairs in nucleic acids FEBS Lett 10(1):e1004065. Abstract
  • Westhof E., Yusupov M. and Yusupova G. (2014) Recognition of Watson-Crick base pairs: constraints and limits due to geometric selection and tautomerism. F1000Prime Rep 6:19, eCollection 2014. Abstract

RNA-based antiviral immunity in drosophila and vector insects (Imler)

  • Chtarbanova S., Lamiable O., Lee K.Z., Galiana D., Troxler L., Meignin C., Hetru C., Hoffmann J.A., Daeffler L. & Imler J.-L. (2014) Drosophila C virus systemic infection leads to intestinal obstruction Journal of Virology 88:14057-14069. Abstract
  • Goto A., Fukuyama H., Imler J.-L. & Hoffmann J.A. (2014) The chromatin regulator DMAP1 modulates activity of the NF-kB transcription factor Relish in the drosophila innate immune response Journal of Biological Chemistry 289:20470-20476. Abstract
  • Majzoub K., Hafirassou M.-L., Meignin C., Goto A., Marzi S., Fedorova A., Verdier Y., Vinh J., Hoffmann J.A., Martin F., Baumert T.F., Schuster C. & Imler J.-L. (2014) RACK1 controls IRES-mediated translation of viruses Cell 159:1086-1095. Abstract

The role of RNAs in the selectivity of the Drosophila Innate Immune Response (Matt)

  • Bonnay F, Nguyen XH, Cohen-Berros E, Troxler L, Batsche E, Camonis J, Takeuchi O, Reichhart JM, Matt N. (2014) Akirin specifies NF-κB selectivity of Drosophila innate immune response via chromatin remodeling EMBO J 33(20):2349-62. Abstract
  • Tartey S, Matsushita K, Vandenbon A, Ori D, Imamura T, Mino T, Standley DM, Hoffmann JA, Reichhart JM, Akira S, Takeuchi O. (2014) Akirin2 is critical for inducing inflammatory genes by bridging IκB-ζ and the SWI/SNF complex EMBO J. 33(20):2332-48. Abstract

RNA degradation in plants (Gagliardi)

  • Lange H., Zuber H., Sement F.M., Chicher J., Kuhn L., Hammann P., Brunaud V., Bérard C., Bouteiller N., Balzergue S., Aubourg S., Martin-Magniette M.L., Vaucheret H. and Gagliardi D. (2014) The RNA Helicases AtMTR4 and HEN2 Target Specific Subsets of Nuclear transcripts for Degradation by the Nuclear Exosome in Arabidopsis thaliana. PLoS Genet. 10:e1004564. Abstract

Role of Ubiquitin in Cellular Regulation (Genschik)

  • Derrien B, Genschik P. (2014) When RNA and protein degradation pathways meet. Front Plant Sci. 5(161):1-6. Abstract

2013

tRNA biology and pathogenesis (Frugier)

  • Filisetti D, Théobald-Dietrich A, Mahmoudi N, Rudinger-Thirion J, Candolfi E, Frugier M. (2013) Aminoacylation of Plasmodium falciparum tRNA(Asn) and insights in the synthesis of asparagine repeats. J. Biol. Chem. 288(51):36361-71. Abstract

Non-coding RNAs and viral infections (Pfeffer)

  • Girardi E, Chane-Woon-Ming B, Messmer M, Kaukinen P, Pfeffer S. (2013) Identification of RNase L-dependent, 3'-end-modified, viral small RNAs in Sindbis virus-infected mammalian cells. mBio 4(6):e00698-13. Abstract
  • Kemp C, Mueller S, Goto A, Barbier V, Paro S, Bonnay F, Dostert C, Troxler L, Hetru C, Meignin C, Pfeffer S, Hoffmann JA, Imler JL. (2013) Broad RNA interference-mediated antiviral immunity and virus-specific inducible responses in Drosophila. J. Immunol. 190(2):650-8. Abstract
  • Zeisel M.B., Pfeffer S. and Baumert T.F. (2013) miR-122 acts as a tumor suppressor in hepatocarcinogenesis in vivo J Hepatol 58(4):821-823. Abstract

Bacterial messenger RNAs and regulatory RNAs (Romby)

  • Caldelari I, Chao Y, Romby P, Vogel J. (2013) RNA-mediated regulation in pathogenic bacteria. Cold Spring Harb. Perspect. Med. 3(9):a010298. Abstract
  • Duval M, Korepanov A, Fuchsbauer O, Fechter P, Haller A, Fabbretti A, Choulier L, Micura R, Klaholz BP, Romby P, Springer M, Marzi S. (2013) Escherichia coli ribosomal protein S1 unfolds structured mRNAs onto the ribosome for active translation initiation. PLoS Biol. 11(12):e1001731. Abstract
  • Lioliou E, Sharma CM, Altuvia Y, Caldelari I, Romilly C, Helfer AC, Margalit H, Romby P. (2013) In vivo mapping of RNA-RNA interactions in Staphylococcus aureus using the endoribonuclease III. Methods 63(2):135-43. Abstract

RNA-based antiviral immunity in drosophila and vector insects (Imler)

  • Kemp C, Mueller S, Goto A, Barbier V, Paro S, Bonnay F, Dostert C, Troxler L, Hetru C, Meignin C, Pfeffer S, Hoffmann JA, Imler JL. (2013) Broad RNA interference-mediated antiviral immunity and virus-specific inducible responses in Drosophila. J. Immunol. 190(2):650-8. Abstract

RNA degradation in plants (Gagliardi)

  • Sement FM, Ferrier E, Zuber H, Merret R, Alioua M, Deragon JM, Bousquet-Antonelli C, Lange H, Gagliardi D. (2013) Uridylation prevents 3' trimming of oligoadenylated mRNAs. Nucleic Acids Res. 41(14):7115-27. Abstract

2012

Bacterial messenger RNAs and regulatory RNAs (Romby)

  • Jester B.C., Romby P.and Lioliou E. (2012) When ribonucleases come into play in pathogens: a survey of gram-positive bacteria. Int. J. Microbiol. 2012:592196. Abstract
  • Lioliou E, Sharma CM, Caldelari I, Helfer AC, Fechter P, Vandenesch F, Vogel J, Romby P. (2012) Global Regulatory Functions of the Staphylococcus aureus Endoribonuclease III in Gene Expression. PLoS Genet. 8(6):e1002782. Abstract
  • Romilly C, Chevalier C, Marzi S, Masquida B, Geissmann T, Vandenesch F, Westhof E, Romby P. (2012) Loop-loop interactions involved in antisense regulation are processed by the endoribonuclease III in Staphylococcus aureus. RNA Biol. 9(12):1461-72. Abstract
  • Romilly C., Caldelari I., Parmentier D., Lioliou E., Romby P., Fechter P. (2012) Current knowledge on regulatory RNAs and their machineries in Staphylococcus aureus. RNA Biol. 9(4):402-413. Abstract

Digital biology of RNA (Ryckelynck)

  • Romilly C, Chevalier C, Marzi S, Masquida B, Geissmann T, Vandenesch F, Westhof E, Romby P. (2012) Loop-loop interactions involved in antisense regulation are processed by the endoribonuclease III in Staphylococcus aureus. RNA Biol. 9(12):1461-72. Abstract

Role of Ubiquitin in Cellular Regulation (Genschik)

  • Derrien B., Baumberger N., Schepetilnikov M., Viotti C., De Cillia J., Ziegler-Graff V., Isono E., Schumacher K. and Genschik P. (2012) Degradation of the antiviral component ARGONAUTE1 by the autophagy pathway Proc. Natl. Acad. Sci. U S A 109(39):15942-6. Abstract


Other publications


2016

RNA degradation in plants (Gagliardi)

  • Hématy K, Bellec Y, Podicheti R, Bouteiller N, Anne P, Morineau C, Haslam RP, Beaudoin F, Napier J, Mockaitis K, Gagliardi D, Vaucheret H, Lange H and Faure J-D (2016) The zinc-finger protein SOP1 is required for a subset of the nuclear exosome functions in Arabidopsis. PLoS Genet. 12:e1005817. Abstract

External Attractivity Team: Mechanisms of small RNA biogenesis (Blevins)

  • Chinmayi Chandrasekhara, Gireesha Mohannath, Todd Blevins, Frederic Pontvianne and Craig S. Pikaard (2016) Chromosome-specific NOR inactivation explains selective rRNA gene silencing and dosage control in Arabidopsis Genes Dev. 30:177-190. Abstract

2015

Bacterial messenger RNAs and regulatory RNAs (Romby)

  • Romby P, Dontsova O (2015) A glimpse at long regulatory RNAs in various organisms Biochimie 117:1-2. Abstract

External Attractivity Team: Cryo-electron microscopy of translation complexes (Hashem)

  • Hstau Y Liao, Yaser Hashem, Joachim Frank (2015) Efficient Estimation of Three-Dimensional Covariance and its Application in the Analysis of Heterogeneous Samples in Cryo-Electron Microscopy. Structure 23:1129-1137. Abstract

External Attractivity Team: Mechanisms of small RNA biogenesis (Blevins)

  • Blevins T, Podicheti R, Mishra V, Marasco M, Wang J, Rusch D, Tang H, Pikaard CS (2015) Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis Elife 4:e09591. Abstract

2014

Bacterial messenger RNAs and regulatory RNAs (Romby)

  • Morfoisse F, Kuchnio A, Frainay C, Gomez-Brouchet A, Delisle MB, Marzi S, Helfer AC, Hantelys F, Pujol F, Guillermet-Guibert J, Bousquet C, Dewerchin M, Pyronnet S, Prats AC, Carmeliet P, Garmy-Susini B. (2014) Hypoxia Induces VEGF-C Expression in Metastatic Tumor Cells via a HIF-1α-Independent Translation-Mediated Mechanism. Cell Rep. 6(1):155-67. Abstract

Digital biology of RNA (Ryckelynck)

  • Gotthard Kunze, Claude Gaillardin, Małgorzata Czernicka, Pascal Durrens, Tiphaine Martin, Erik Böer, Toni Gabaldón, Jose A Cruz, Emmanuel Talla, Christian Marck, André Goffeau, Valérie Barbe, Philippe Baret, Keith Baronian, Sebastian Beier, Claudine Bleyk (2014) The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest Science 345:732-733. Abstract
  • Hartmann RK, Bindereif A, Schon A, Westhof E, eds. (2014) Handbook of RNA biochemistry (2nd edition). Wiley-VCH Verlag GmbH WESTHOF 1:...
  • Kondo J, Sauter C, Masquida B. (2014) Crystallization of RNA. In "Handbook of RNA biochemistry" (2nd edition) in press:...

RNA-based antiviral immunity in drosophila and vector insects (Imler)

  • Imler J.-L. (2014) Overview of Drosophila immunity : a historical perspective DEvelopmental and Comparative Immunology 42:3-15. Abstract
  • Lamiable O. & Imler J.-L. (2014) Induced antiviral innate immunity in Drosophila Current Opinion in Microbiology 20:62-68. Abstract

External Attractivity Team: Cryo-electron microscopy of translation complexes (Hashem)

  • Amedee Georges, Yaser Hashem, Sarah N Buss, Fabrice Jossinet, Qin Zhang, Hstau Y Liao, Jie Fu, Amy Jobe, Robert A Grassucci, Robert Langlois, Chandrajit Bajaj, Eric Westhof, Susan Madison-Antenucci, Joachim Frank (2014) High-resolution Cryo-EM Structure of the Trypanosoma brucei Ribosome: A Case Study. Computational Methods for Three-Dimensional Microscopy 99:97-132. Abstract
  • Bo Chen, Grégory Boël, Yaser Hashem, Wei Ning, Jingyi Fei, Chi Wang, Ruben L Gonzalez, John F Hunt, Joachim Frank (2014) EttA regulates translation by binding the ribosomal E site and restricting ribosome-tRNA dynamics. NSMB 21:152-159. Abstract
  • Boël G, Smith PC, Ning W, Englander MT, Chen B, Hashem Y, Testa AJ, Fischer JJ, Wieden HJ, Frank J, Gonzalez RL Jr, Hunt JF. (2014) he ABC-F protein EttA gates ribosome entry into the translation elongation cycle. NSMB 21:143-151. Abstract

2013

tRNA biology and pathogenesis (Frugier)

  • Riley LG, Menezes MJ, Rudinger-Thirion J, Duff R, de Lonlay P, Rotig A, Tchan MC, Davis M, Cooper ST, Christodoulou J. (2013) Phenotypic variability and identification of novel YARS2 mutations in YARS2 mitochondrial myopathy, lactic acidosis and sideroblastic anaemia. Orphanet J. Rare Dis. 8:193. Abstract

Non-coding RNAs and viral infections (Pfeffer)

  • Bonnet ME, Gossart JB, Benoit E, Messmer M, Zounib O, Moreau V, Behr JP, Lenne-Samuel N, Kedinger V, Meulle A, Erbacher P, Bolcato-Bellemin AL. (2013) Systemic delivery of sticky siRNAs targeting the cell cycle for lung tumor metastasis inhibition. J. Control. Release 170(2):183-90. Abstract
  • Kedinger V, Meulle A, Zounib O, Bonnet ME, Gossart JB, Benoit E, Messmer M, Shankaranarayanan P, Behr JP, Erbacher P, Bolcato-Bellemin AL. (2013) Sticky siRNAs targeting survivin and cyclin B1 exert an antitumoral effect on melanoma subcutaneous xenografts and lung metastases. BMC Cancer 13:338. Abstract
  • Philippe L, Alsaleh G, Bahram S, Pfeffer S, Georgel P. (2013) The miR-17 ∼ 92 Cluster: A Key Player in the Control of Inflammation during Rheumatoid Arthritis. Front. Immunol. 4:70. Abstract
  • Philippe L, Alsaleh G, Pichot A, Ostermann E, Zuber G, Frisch B, Sibilia J, Pfeffer S, Bahram S, Wachsmann D, Georgel P. (2013) MiR-20a regulates ASK1 expression and TLR4-dependent cytokine release in rheumatoid fibroblast-like synoviocytes. Ann. Rheum. Dis. 72(6):1071-9. Abstract
  • Stik G, Dambrine G, Pfeffer S, Rasschaert D. (2013) The oncogenic microRNA OncomiR-21 overexpressed during Marek's disease lymphomagenesis is transactivated by the viral oncoprotein Meq. J. Virol. 87(1):80-93. Abstract

Bacterial messenger RNAs and regulatory RNAs (Romby)

  • Ruiz de los Mozos I, Vergara-Irigaray M, Segura V, Villanueva M, Bitarte N, Saramago M, Domingues S, Arraiano CM, Fechter P, Romby P, Valle J, Solano C, Lasa I, Toledo-Arana A. (2013) Base pairing interaction between 5'- and 3'-UTRs controls icaR mRNA translation in Staphylococcus aureus. PLoS Genet. 9(12):e1004001. Abstract
  • Simonetti A, Marzi S, Billas IM, Tsai A, Fabbretti A, Myasnikov AG, Roblin P, Vaiana AC, Hazemann I, Eiler D, Steitz TA, Puglisi JD, Gualerzi CO, Klaholz BP. (2013) Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor. Proc. Natl. Acad. Sci. U S A 110(39):15656-61. Abstract
  • Simonetti A, Marzi S, Fabbretti A, Hazemann I, Jenner L, Urzhumtsev A, Gualerzi CO, Klaholz BP. (2013) Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms. Acta Crystallogr. D Biol. Crystallogr. 69(Pt 6):925-33. Abstract

Digital biology of RNA (Ryckelynck)

  • Anokhina M, Bessonov S, Miao Z, Westhof E, Hartmuth K, Lührmann R. (2013) RNA structure analysis of human spliceosomes reveals a compact 3D arrangement of snRNAs at the catalytic core. EMBO J. 32(21):2804-18. Abstract
  • Cattenoz PB, Taft RJ, Westhof E, Mattick JS. (2013) Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage. RNA 19(2):257-70. Abstract
  • Daldrop P, Masquida B, Lilley DM. (2013) The functional exchangeability of pk- and k-turns in RNA structure. RNA Biol. 10(3):445-52. Abstract
  • Demeshkina N, Jenner L, Westhof E, Yusupov M, Yusupova G. (2013) New structural insights into the decoding mechanism: translation infidelity via a G·U pair with Watson-Crick geometry. FEBS Lett. 587(13):1848-57. Abstract
  • Gabaldón T, Martin T, Marcet-Houben M, Durrens P, Bolotin-Fukuhara M, Lespinet O, Arnaise S, Boisnard S, Aguileta G, Atanasova R, Bouchier C, Couloux A, Creno S, Almeida Cruz J, Devillers H, Enache-Angoulvant A, Guitard J, Jaouen L, Ma L, Marck C, Neuvégl (2013) Comparative genomics of emerging pathogens in the Candida glabrata clade. BMC Genomics 14(1):623. Abstract
  • Hashem Y, des Georges A, Fu J, Buss SN, Jossinet F, Jobe A, Zhang Q, Liao HY, Grassucci RA, Bajaj C, Westhof E, Madison-Antenucci S, Frank J. (2013) High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Nature 594(7437):385-9. Abstract
  • Kondo J, Dock-Bregeon AC, Willkomm DK, Hartmann RK, Westhof E. (2013) Structure of an A-form RNA duplex obtained by degradation of 6S RNA in a crystallization droplet. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 69(Pt 6):634-9. Abstract
  • Ngondo RP, Carbon P. (2013) Transcription factor abundance controlled by an auto-regulatory mechanism involving a transcription start site switch. Nucleic Acids Res. in press:... Abstract
  • Ngondo-Mbongo RP, Myslinski E, Aster JC, Carbon P. (2013) Modulation of gene expression via overlapping binding sites exerted by ZNF143, Notch1 and THAP11. Nucleic Acids Res. 41(7):4000-14. Abstract
  • Smekalova EM, Malyavko AN, Zvereva MI, Mardanov AV, Ravin NV, Skryabin KG, Westhof E, Dontsova OA. (2013) Specific features of telomerase RNA from Hansenula polymorpha. RNA 19(11):1563-74. Abstract

RNA-based antiviral immunity in drosophila and vector insects (Imler)

  • Petrillo J.E., Venter P.A., Short J.A., Gopal R., Deddouche S., Lamiable O., Imler J.-L. & Schneeman A. (2013) Cytoplasmic granule formation and translational inhibition of nodaviral RNAs in the absence of the dsRNA binding protein B2 Journal of Virology 87:13409-13421. Abstract

The role of RNAs in the selectivity of the Drosophila Innate Immune Response (Matt)

  • Bonnay F, Cohen-Berros E, Hoffmann M, Kim SY, Boulianne GL, Hoffmann JA, Matt N and Reichhart JM (2013) Big bang modulates gut immune tolerance in Drosophila PNAS 110:2957-62. Abstract

Role of Ubiquitin in Cellular Regulation (Genschik)

  • Genschik P, Marrocco K, Bach L, Noir S, Criqui MC. (2013) Selective protein degradation: a rheostat to modulate cell-cycle phase transitions. J. Exp. Bot. in press:... Abstract
  • Tromas A, Paque S, Stierlé V, Quettier AL, Muller P, Lechner E, Genschik P, Perrot-Rechenmann C. (2013) Auxin-Binding Protein 1 is a negative regulator of the SCF(TIR1/AFB) pathway Nat. Commun. 4:2496. Abstract

External Attractivity Team: Cryo-electron microscopy of translation complexes (Hashem)

  • Amédée des Georges, Yaser Hashem, Anett Unbehaun, Robert A Grassucci, Derek Taylor, Christopher U T Hellen, Tatyana V Pestova, Joachim Frank (2013) Structure of the mammalian ribosomal pre-termination complex associated with eRF1•eRF3•GDPNP. Nucleic Acids Research 42:3409-3418. Abstract
  • Jesper Pallesen, Yaser Hashem, Gürkan Korkmaz, Ravi Kiran Koripella, Chenhui Huang, Måns Ehrenberg, Suparna Sanyal, Joachim Frank (2013) Cryo-EM visualization of the ribosome in termination complex with apo-RF3 and RF1. eLife Sciences 2:e00411. Abstract
  • Yaser Hashem, Amedee des Georges, Jie Fu, Sarah N. Buss, Fabrice Jossinet, Amy Jobe, Qin Zhang, Hstau Y. Liao, Robert A. Grassucci, Chandrajit Bajaj, Eric Westhof, Susan Madison-Antenucci, Joachim Frank (2013) High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Nature 494:385-389. Abstract
  • Yaser Hashem, Amedee des Georges, Vidya Dhote, Robert Langlois, Hstau Y Liao, Robert A Grassucci, Christopher U T Hellen, Tatyana V Pestova, Joachim Frank (2013) Structure of the Mammalian Ribosomal 43S Preinitiation Complex Bound to the Scanning Factor DHX29. Cell 153:1108-1119. Abstract
  • Yaser Hashem, Amedee des Georges, Vidya Dhote, Robert Langlois, Hstau Y Liao, Robert A Grassucci, Tatyana V Pestova, Christopher U T Hellen, Joachim Frank (2013) Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit. Nature 503:539-543. Abstract

2012

Non-coding RNAs and viral infections (Pfeffer)

  • Da Costa D, Turek M, Felmlee DJ, Girardi E, Pfeffer S, Long G, Bartenschlager R, Zeisel MB, Baumert TF. (2012) Reconstitution of the entire hepatitis C virus life cycle in nonhepatic cells. J. Virol. 86(21):11919-25. Abstract
  • Marcinowski L, Tanguy M, Krmpotic A, Rädle B, Lisnić VJ, Tuddenham L, Chane-Woon-Ming B, Ruzsics Z, Erhard F, Benkartek C, Babic M, Zimmer R, Trgovcich J, Koszinowski UH, Jonjic S, Pfeffer S, Dölken L. (2012) Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo. PLoS Pathog. 8(2):e1002510. Abstract
  • Ostermann E, Tuddenham L, Macquin C, Alsaleh G, Schreiber-Becker J, Tanguy M, Bahram S, Pfeffer S, Georgel P. (2012) Deregulation of Type I IFN-Dependent Genes Correlates with Increased Susceptibility to Cytomegalovirus Acute Infection of Dicer Mutant Mice PLoS One 7(8):e43744. Abstract
  • Philippe L., Alsaleh G., Suffert G., Meyer A., Georgel P., Sibilia J., Wachsmann D. and Pfeffer S (2012) TLR2 Expression Is Regulated by MicroRNA miR-19 in Rheumatoid Fibroblast-like Synoviocytes. J. Immunol. 188(1):454-461. Abstract
  • Tuddenham L., Jung J.S., Chane-Woon-Ming B., Dölken L. and Pfeffer S. (2012) Small RNA deep-sequencing identifies microRNAs and other small non-coding RNAs from human herpesvirus 6 (HHV-6B). J. Virol. 86:1638-1649. Abstract

Bacterial messenger RNAs and regulatory RNAs (Romby)

  • Caldelari I, Fechter P, Lioliou E, Chevalier C, Gaspin C, Romby P. (2012) A current overview of regulatory RNAs in Staphylococcus aureus. In "Regulatory RNAs in prokaryotes" (Marchfelder A., Hess W.R., eds.) 1:51-75.
  • Lioliou E, Romilly C, Geissman T, Vandenesch F, Romby P. (2012) RNA-mediated regulation of virulence gene expression: another layer of complexity. In "Bacterial Regulatory Networks" (Filloux A., eds.) 1:143-166.
  • Marzi S., Romby P. (2012) RNA mimicry, a decoy for regulatory proteins. Mol. Microbiol. 83(1):1-6. Abstract
  • Song J., Lays C., Vandenesch F., Benito Y., Bes M., Chu Y., Lina G., Romby P., Geissmann T. and Boisset S. (2012) The Expression of Small Regulatory RNAs in Clinical Samples Reflects the Different Life Styles of Staphylococcus aureus in Colonization vs. Infection. PLos One 7(5):e37294. Abstract

Digital biology of RNA (Ryckelynck)

  • Auffinger P. (2012) Ions in molecular dynamics simulations of RNA systems. In "RNA 3D Structure Analysis and Prediction (Nucleic Acids and Molecular Biology)" 27:299-318.
  • Cartault, F., Munier, P., Benko, E., Desguerre, I., Hanein, S., Boddaert, N., Bandiera, S., Vellayoudom, J., Krejbich-Trotot, P., Bintner, M., Hoarau, J.J., Girard, M., Génin, E., de Lonlay, P., Fourmaintraux, A., Naville, M., Rodriguez, D., Feingold, J., (2012) Mutation in a primate-conserved retrotransposon reveals a noncoding RNA as a mediator of infantile encephalopathy. Proc. Natl. Acad. Sci. U S A 109(13):4980-4985. Abstract
  • Cruz, J.A., Blanchet, M.F., Boniecki, M., Bujnicki, J.M., Chen, S.J., Cao, S., Das, R., Ding, F., Dokholyan, N.V., Flores, S.C., Huang, L., Lavender, C.A., Lisi, V., Major, F., Mikolajczak, K., Patel, D.J., Philips, A., Puton, T., Santalucia, J., Sijenyi, (2012) RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction. RNA 18(4):610-625. Abstract
  • Demeshkina, N., Jenner, L., Westhof, E., Yusupov, M., Yusupova, G. (2012) A new understanding of the decoding principle on the ribosome. Nature 484(7393):256-259. Abstract
  • Lamiable, A., Barth, D., Denise, A., Quessette, F., Vial, S., Westhof, E. (2012) Automated prediction of three-way junction topological families in RNA secondary structures. Comput. Biol. Chem. 37:1-5. Abstract
  • Leontis N, Westhof E, eds. (2012) RNA 3D Structure Analysis and Prediction (Nucleic Acids and Molecular Biology). Springer, Berlin WESTHOF 1:...
  • Louis, V. L., Despons, L., Friedrich, A., Martin, T., Durrens, P., Casarégola, S., Neuvéglise, C., Fairhead, C., Marck, C., Cruz, J. A., Straub, M. L., Kugler, V., Sacerdot, C., Uzunov, Z., Thierry, A., Weiss, S., Bleykasten, C., De Montigny, J., Jacques, (2012) Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization. G3 (Bethesda) 2(2):299-311. Abstract
  • Mertz D, Cui J, Yan Y, Devlin G, Chaubaroux C, Dochter A, Alles R, Lavalle P, Voegel JC, Blencowe A, Auffinger P, Caruso F. (2012) Protein capsules assembled via isobutyramide grafts: sequential growth, biofunctionalization, and cellular uptake. ACS Nano 6(9):7584-94. Abstract
  • Meyer, M., Westhof, E., Masquida, B. (2012) A structural module in RNase P expands the variety of RNA kinks. RNA Biol. 9(3):254-260. Abstract
  • Salian S, Matt T, Akbergenov R, Harish S, Meyer M, Duscha S, Shcherbakov D, Bernet BB, Vasella A, Westhof E, Böttger EC. (2012) Structure-activity relationships among the kanamycin aminoglycosides: role of ring I hydroxyl and amino groups. Antimicrob. Agents Chemother. 56(12):6104-8. Abstract
  • Vallejos M, Auffinger P, Ho PS. (2012) Part 23. Structural analysis and classification Chapter 23.6. Halogen interactions in biomolecular crystal structures. In "International Tables for Crystallography F: Crystallography of biological macromolecules" 1:821-826.
  • Westhof E, Auffinger P. (2012) Transfer RNA structure. In "Encyclopedia of Life Sciences" John Wiley & Sons 1:...
  • Westhof, E. (2012) RNA modeling, naturally. Proc. Natl. Acad. Sci. U S A 109(8):2691-2692. Abstract
  • Westhof, E. (2012) Ribozymes, catalytically active RNA molecules. Introduction. Meth. Mol. Biol. 848:1-4. Abstract

RNA-based antiviral immunity in drosophila and vector insects (Imler)

  • Coste F., Kemp C., Bobezeau V., Hetru C., Kellenberger C., Imler J.-L. & Roussel A. (2012) Crystal structure of Diedel, a marker of the immune response of Drosophila melanogaster PLoS ONE 7:e33416. Abstract
  • Goto A. & Imler J.-L. (2012) Toll signaling in flies and mammals: two sorts of MyD88. Immunity 36:555-557. Abstract
  • Imler, J.-L. & Hoffmann, J.A. (2012) Chapter 14 : Antiviral responses in invertebrates Nucleic Acid Sensors and Antiviral Immunity In press:...

The role of RNAs in the selectivity of the Drosophila Innate Immune Response (Matt)

  • Deleury E., Dubreuil G., Elangovan N., Wajnberg E., Reichhart JM., Gourbal B., Duval D., Baron OL., Gouzy J and Coustau C. (2012) Specific versus Non-Specific Immune Responses in an Invertebrate Species Evidenced by a Comparative de novo Sequencing Study. PLOS One 7:e32512. Abstract
  • Zuniga A., Laurent F., Lopez-Rios J., Klasen C., Matt N and Zeller R. (2012) Conserved cis-regulatory regions in a large genomic landscape control SHH and BMP-regulated Gremlin1 expression in mouse limb buds. BMC Dev. Biol. 12:23. Abstract

Role of Ubiquitin in Cellular Regulation (Genschik)

  • Bjerkan K.N., Jung-Roméo S., Jürgens G., Genschik P. and Grini P.E (2012) Arabidopsis WD REPEAT DOMAIN55 Interacts with DNA DAMAGED BINDING PROTEIN1 and Is Required for Apical Patterning in the Embryo. Plant Cell 24(3):1013-33. Abstract
  • Marrocco K., Criqui M.C., Zervudacki J., Schott G., Eisler H., Parnet A., Dunoyer P. and Genschik P. (2012) APC/C-mediated degradation of dsRNA-binding protein 4 (DRB4) involved in RNA silencing. PloS One 7(4):e35173. Abstract
  • Wild M, Davière JM, Cheminant S, Regnault T, Baumberger N, Heintz D, Baltz R, Genschik P, Achard P. (2012) The Arabidopsis DELLA RGA-LIKE3 is a direct target of MYC2 and modulates jasmonate signaling responses. Plant Cell 24(8):3307-19. Abstract

External Attractivity Team: Cryo-electron microscopy of translation complexes (Hashem)

  • Bussiere C, Hashem Y, Arora S, Frank J, Johnson AW. (2012) Integrity of the P-site is probed during maturation of the 60S ribosomal subunit. Journal of Cell Biology 197:747-759. Abstract

2011

tRNA biology and pathogenesis (Frugier)

  • Bonnefond L., Schellenberger P., Basquin J., Demangeat G., Ritzenthaler C., Chênevert R., Balg C., Frugier M., Rudinger-Thirion J., Giegé R., Lorber B. and Sauter C. (2011) Exploiting protein engineering and crystal polymorphism for successful X-ray structure determination. Crystal Growth & Design 11(10):4334-4343.
  • Jackson K.E., Habib S., Frugier M., Hoen R., Khan S., Pham J.S., Pouplana L.R., Royo M., Santos M.A., Sharma A. and Ralph S.A. (2011) Protein translation in Plasmodium parasites Trends Parasitol. 27(10):467-476. Abstract
  • Rudinger-Thirion J., Lescure A., Paulus C., Frugier M. (2011) Misfolded human tRNA isodecoder binds and neutralizes a 3' UTR-embedded Alu element. Proc. Natl. Acad. Sci. U S A 108(40):E794-802. Abstract

Non-coding RNAs and viral infections (Pfeffer)

  • John M., Pfeffer S. (2011) Detection of viral microRNA with S1 nuclease protection assay. Methods Mol. Biol. 721:173-82. Abstract
  • Semaan N., Frenzel L., Alsaleh G., Suffert G., Gottenberg J.E., Sibilia J., Pfeffer S., Wachsmann D. (2011) miR-346 Controls Release of TNF-α Protein and Stability of Its mRNA in Rheumatoid Arthritis via Tristetraprolin Stabilization. PLoS One 6(5):e19827. Abstract
  • Suffert G., Malterer G., Hausser J., Viiliäinen J, Fender A., Contrant M., Ivacevic T., Benes V., Gros F., Voinnet O., Zavolan M., Ojala P.M., Haas J.G. and Pfeffer S. (2011) Kaposi's sarcoma herpesvirus microRNAs target caspase 3 and regulate apoptosis. PLoS Pathog. 6(5):e19827. Abstract
  • Tuddenham L., Pfeffer S. (2011) Roles and regulation of microRNAs in cytomegalovirus infection. Biochim. Biophys. Acta 1809(11-12):613-622. Abstract

Bacterial messenger RNAs and regulatory RNAs (Romby)

  • Avesson L., Schumacher H.T., Fechter P., Romby P., Hellman U., Söderbom F. (2011) Abundant class of non-coding RNA regulates development in the social amoeba dictyostelium discoideum. RNA Biol. 8(6):1094-1104. Abstract
  • Felden B., Vandenesch F., Bouloc P., Romby P. (2011) The Staphylococcus aureus RNome and its commitment to virulence. PLoS Pathog. 7(3):e1002006. Abstract
  • Simonetti A, Marzi S, Myasnikov A, Menetret JF, Klaholz BP. (2011) Insights into translation initiation and termination complexes and into the polysome architecture. In "Ribosomes Structures, Function, and Dynamics" (Rodnina M. Wintermeyer W. Green R., eds.) 1:113-128.

Digital biology of RNA (Ryckelynck)

  • Auffinger P, Grover N, Westhof E. (2011) Metal ion binding to RNA In "Structural and Catalytic Roles of Metal Ions in RNA" (Metal Ions in Life Sciences) 9:1-35.
  • Beckert B. and Masquida B. (2011) Synthesis of RNA by in vitro transcription. Methods Mol. Biol. 703:29-41. Abstract
  • Birgisdottir A.B., Nielsen H., Beckert B., Masquida B. and Johansen S.D. (2011) Intermolecular interaction between a branching ribozyme and associated homing endonuclease mRNA. Biol. Chem. 392(6):491-499. Abstract
  • Cruz J.A. and Westhof E. (2011) Identification and annotation of noncoding RNAs in Saccharomycotina. C. R. Biol. 334(8-9):671-8. Abstract
  • Cruz J.A. and Westhof E. (2011) Sequence-based identification of 3D structural modules in RNA with RMDetect. Nature Methods 8(6):513-519. Abstract
  • Hoehndorf R., Batchelor C., Bittner T., Dumontier M., Eilbeck K., Knight R., Mungall C.J., Richardson J.S., Stombaugh J., Westhof E., Zirbel C.L. and Leontis N. (2011) The RNA ontology (RNAO) : An ontology for integrating RNA sequence and structure data. Applied Ontology 6(1):53-89.
  • Kondo, J., Westhof, E. (2011) Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes. Nucleic Acids Res. 39(19):8628-8637. Abstract
  • Masquida, B., Westhof, E. (2011) RNase P: At last, the key finds its lock. RNA 17(9):1615-1618. Abstract
  • Szychowski, J., Kondo, J., Zahr, O., Auclair, K., Westhof, E., Hanessian, S., Keillor, J.W. (2011) Inhibition of Aminoglycoside-Deactivating Enzymes APH(3')-IIIa and AAC(6')-Ii by Amphiphilic Paromomycin O2''-Ether Analogues. ChemMedChem 6(11):1961-1966. Abstract
  • Theil E.C., Westhof E. (2011) New dimensions of RNA in molecular recognition and catalysis. Acc. Chem. Res. 44(12):1255-6. Abstract
  • Westhof E., Fritsch, V. (2011) The Endless Subtleties of RNA-Protein Complexes. Structure 19(7):902-903. Abstract
  • Westhof E., Masquida B. and Jossinet F. (2011) Predicting and modeling RNA architecture. Cold Spring Harb. Perspect. Biol. 3(2):309-320. Abstract
  • Wright J.E., Gaidatzis D., Senften M., Farley B.M., Westhof E., Ryder S.P. and Ciosk R. (2011) A quantitative RNA code for mRNA target selection by the germline fate determinant GLD-1. EMBO J. 30(3):533-545. Abstract

RNA-based antiviral immunity in drosophila and vector insects (Imler)

  • Chtarbanova S. & Imler J.-L. (2011) Immunité innée antivirale chez la drosophile Virologie 15:296-306.
  • Chtarbanova S. & Imler J.-L. (2011) Microbial sensing by Toll receptors: a historical perspective. Arteriosclerosis, Thrombosis and Vascular Biology 31:1734-1738. Abstract
  • Eleftherianos I., Won S., Chtarbanova S., Squiban B., Ocorr K., Bodmer R., Beutler B., Hoffmann J.A. & Imler J.-L. (2011) ATP-sensitive potassium channel (K(ATP))-dependent regulation of cardiotropic viral infections. Proc. Natl. Acad. Sci. U S A 108:12024-12029. Abstract
  • Imler J.-L. & Ferrandon D. (2011) Le printemps de l’immunité innée couronné à Stockholm. Médecine/Sciences 27:1019-1024.

The role of RNAs in the selectivity of the Drosophila Innate Immune Response (Matt)

  • Bou Aoun R., Hetru C., Troxler L., Doucet D., Ferrandon D and Matt N. (2011) Analysis of the thioester-containing proteins, TEPs, during the innate immune response of Drosophila melanogaster. J. Innate Immun. 3(1):52-64. Abstract
  • Boyer L., Magoc L., Dejardin S., Cappillino M., Paquette N., Hinault C., Charriere GM., Ip WK., Fracchia S., Hennessy E., Erturk-Hasdemir D., Reichhart JM., Silverman N., Lacy-Hulbert A, and Stuart LM. (2011) Pathogen-derived effectors trigger protective immunity via activation of the Rac2 enzyme and the IMD or Rip kinase signaling pathway. Immunity 35:536-49. Abstract
  • Kellenberger C., Leone P., Coquet L., Jouenne T., Reichhart JM and Roussel A. (2011) Structure-function analysis of grass clip serine protease involved in Drosophila Toll pathway activation. J. Biol. Chem. 286(14):12300-7. Abstract
  • Ogawa M., Yoshikawa Y., Kobayashi T., Mimuro H., Fukumatsu M., Kiga K., Piao Z., Ashida H., Yoshida M., Kakuta S., Koyama T., Goto Y., Nagatake T., Nagai S., Kiyono H., Kawalec M., Reichhart JM and Sasakawa C. (2011) A tecpr1-dependent selective autophagy pathway targets bacterial pathogens. Cell Host Microbe 9(5):376-89. Abstract
  • Reichhart JM., Gubbs D and Leclerc V (2011) The drosophila serpins : multiple functions in immunity and morphogenesis. Methods in Enzymology 499:205-225. Abstract

Role of Ubiquitin in Cellular Regulation (Genschik)

  • Castells E., Molinier J., Benvenuto G., Bourbousse C., Zabulon G., Zalc A., Cazzaniga S., Genschik P., Barneche F. and Bowler C. (2011) The conserved factor DE-ETIOLATED 1 cooperates with CUL4-DDB1DDB2 to maintain genome integrity upon UV stress. EMBO J. 30:1162-1172. Abstract
  • Cheminant S., Wild M., Bouvier F., Pelletier S., Renou J.P., Erhardt M., Hayes S., Terry M.J., Genschik P. and Achard P. (2011) DELLAs regulate chlorophyll and carotenoid biosynthesis to prevent photo-oxidative damage during seedling deeliolation. Plant Cell 23:1849-1860. Abstract
  • Dumbliauskas E., Lechner E., Jaciubek M., Berr A., Pazhouhandeh M., Alioua A., Cognat V., Brukhin V., Koncz C., Grossniklaus U., Molinier J. and Genschik P. (2011) The Arabidopsis CUL4-DDB1 complex interacts with MSI1 and is required to maintain MEDEA parental imprinting. Embo J. 30:731-743. Abstract
  • Iwata E., Ikeda S., Matsunaga S., Kurata M., Yoshioka Y., Criqui M.C., Genschik P. and Ito M. (2011) GIGAS CELL 1 a novel negative regulator of the Anaphase-promoting Complex/Cyclosome, is required for proper mitotic progression and cell fate determination in Arabidopsis thaliana. Plant Cell 23:4382-4393. Abstract
  • Lechner E., Leonhardt N., Eisler H., Parmentier Y., Alioua M., Jacquet H., Leung J. and Genschik P. (2011) MATH/BTB CRL3 receptors target the homeodomain-leucine zipper ATHB6 to modulate abscisic acid signalling. Dev Cell 13:1116-1128. Abstract
  • Lingam S., Mohrbacher J., Brumbarova T., Potuschak T., Fink-Straube C., Blondet E., Genschik P. and Bauer P. (2011) Interaction between the bHLH Transcription Factor FIT and ETHYLENE INSENSITIVE3/ETHYLENE INSENSITIVE3-LIKE1 Reveals Molecular Linkage between the Regulation of Iron Acquisition and Ethylene Signaling in Arabidopsis. Plant Cell 23:1815-1829. Abstract
  • Pazhouhandeh M., Molinier J., Berr A. and Genschik P. (2011) MSI4/FVE interacts with CUL4-DDB1 and a PRC2-like complex to control epigenetic regulation of flowering time in Arabidopsis. Proc. Natl. Acad. Sci. U S A 108(8):3430-3435. Abstract
  • Roberts D., Pedmale U.V., Morrow J., Sachdev S., Lechner E., Tang X., Zheng N., Hannink M., Genschik P. and Liscum E. (2011) Modulation of phototropic responsiveness in Arabidopsis through ubiquitination of phototropin 1 by the CUL3-ring E3 ubiquitin ligase CRL3 NPH3. Plant Cell 23:3627-3640. Abstract
  • Sasabe M., Boudolf V., De Veylder L., Inzé D., Genschik P. and Machida Y. (2011) Phosphorylation of a mitotic kinesin-like protein and a MAPKKK by cyclin-dependentkinases (CDKs) is involved in the transition to cytokinesis in plants. Proc. Natl. Acad. Sci. U S A 108(43):17844-17849. Abstract

External Attractivity Team: Cryo-electron microscopy of translation complexes (Hashem)

  • Jie Fu, Yaser Hashem, Jacek Wower, Joachim Frank (2011) tmRNA on its way through the ribosome Two steps of resume and what next? RNA biology 8:586-590. Abstract

2010

tRNA biology and pathogenesis (Frugier)

  • Frugier M., Bour T., Ayach M., Santos M.A., Rudinger-Thirion J., Theobald-Dietrich A. and Pizzi E. (2010) Low Complexity Regions behave as tRNA sponges to help co-translational folding of plasmodial proteins. FEBS Lett. 584(2):448-54. Abstract
  • Garcia Silva M.R., Tosar J.P., Frugier M., Pantano S., Bonilla B., Esteban L., Serra E., Rovira C., Robello C. and Cayota A. (2010) Cloning, characterization and subcellular localization of a Trypanosoma cruzi argonaute protein defining a new subfamily distinctive of trypanosomatids. Gene 466(1-2:26-35. Abstract
  • Garcia-Silva M.R., Frugier M., Tosar J.P., Correa-Dominguez A., Ronalte-Alves L., Parodi-Talice A., Rovira C., Robello C., Goldenberg S. and Cayota A. (2010) A population of tRNA-derived small RNAs is actively produced in Trypanosoma cruzi and recruited to specific cytoplasmic granules. Mol. Biochem. Parasitol. 171(2):64-73. Abstract
  • Riley L.G., Cooper S., Hickey P., Rudinger-Thirion J., McKenzie M., Compton A., Lim S.C., Thorburn D., Ryan M.T., Giege R., Bahlo M. and Christodoulou J. (2010) Mutation of the mitochondrial tyrosyl-tRNA synthetase gene, YARS2, causes myopathy, lactic acidosis, and sideroblastic anemia--MLASA syndrome. Am J Hum Genet 87(1):52-9. Abstract

Non-coding RNAs and viral infections (Pfeffer)

  • Buck AH, Perot J, Chisolm M, Kumar DS, Tuddenham L, Cognat V, Marcinowski L, Dölken L, Pfeffer S. (2010) Post-transcriptional regulation of miR-27 in murine cytomegalovirus infection. RNA 16(2):307-15. Abstract
  • Dölken L., Krmpotic A., Kothe S., Tuddenham L., Tanguy M., Marcinowski L., Ruzsics Z., Elefant N., Altuvia Y., Margalit H., Koszinowski U.H., Jonjic S., Pfeffer S. (2010) Cytomegalovirus microRNAs facilitate persistent virus infection in salivary glands. PLoS pathog. 6(10):e1001150. Abstract
  • Dölken L., Malterer G., Erhard F., Kothe S., Friedel C.C., Suffert G., Marcinowski L., Motsch N., Barth S., Beitzinger M., Lieber D., Bailer S.M., Hoffmann R., Ruzsics Z., Kremmer E., Pfeffer S., Zimmer R., Koszinowski U.H., Grässer F., Meister G., Haas J (2010) Systematic analysis of viral and cellular microRNA targets in cells latently infected with human gamma-herpesviruses by RISC immunoprecipitation assay. Cell Host Microbe 7(4):324-34. Abstract
  • Mueller S., Gausson V., Vodovar N., Deddouche S., Troxler L., Perot J., Pfeffer S., Hoffmann J.A., Saleh M.C., Imler J.L. (2010) RNAi-mediated immunity provides strong protection against the negative-strand RNA vesicular stomatitis virus in Drosophila. Proc. Natl. Acad. Sci. U S A 107(45):19390-5. Abstract
  • Pfeffer S. (2010) RNA silencing as a natural antiviral defense system in mammals: where are we now? Mol Ther. 18(5):871-2. Abstract
  • Pfeffer S. and Baumert T.F. (2010) Antagonizing microRNA-122 and treatment of hepatitis C virus infection. Hepatology 51(4):1461-3. Abstract
  • Pfeffer S. and Baumert T.F. (2010) Impact of microRNAs for pathogenesis and treatment of hepatitis C virus infection. Gastroenterol Clin Biol. 34(8-9):431-5. Abstract
  • Tanguy M, Pfeffer S. (2010) The properties and roles of virus-encoded microRNAs. In "RNA Interference and Viruses: Current Innovations and Future Trends" (Martinez M.A., eds.) 1:47-66.

Bacterial messenger RNAs and regulatory RNAs (Romby)

  • Beaume M., Hernandez D., Farinelli L., Deluen C., Linder P., Gaspin C., Romby P., Schrenzel J., Francois P. (2010) Cartography of methicillin-resistant S. aureus transcripts: detection, orientation and temporal expression during growth phase and stress conditions. PLoS One 5(5):e10725. Abstract
  • Chevalier C., Boisset S., Romilly C., Masquida B., Fechter P., Geissmann T., Vandenesch F. and Romby P. (2010) Staphylococcus aureus RNAIII binds to two distant regions of coa mRNA to arrest translation and promote mRNA degradation. PLoS Pathog. 6(3):e1000809. Abstract
  • Giuliodori A.M., Di Pietro F., Marzi S., Masquida B., Wagner R., Romby P., Gualerzi C.O. and Pon C.L. (2010) The cspA mRNA is a thermosensor that modulates translation of the cold-shock protein CspA. Mol. Cell 37(1):21-33. Abstract
  • Lioliou E., Romilly C., Romby P. and Fechter P. (2010) RNA-mediated regulation in bacteria: from natural to artificial systems. N. Biotechnol. 27(3):222-235. Abstract
  • Romby P., Charpentier E. (2010) An overview of RNAs with regulatory functions in gram-positive bacteria. Cell Mol. Life Sci. 67(2):217-237. Abstract
  • Westhof E. and Romby P. (2010) The RNA structurome: high-throughput probing. Nat. Methods 7(12):965-7. Abstract

Digital biology of RNA (Ryckelynck)

  • Armache J.P., Jarasch A., Anger A.M., Villa E., Becker T., Bhushan S., Jossinet F., Habeck M., Dindar G., Franckenberg S., Marquez V., Mielke T., Thomm M., Berninghausen O., Beatrix B., Soding J., Westhof E., Wilson D.N. and Beckmann R. (2010) Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome.. Proc. Natl. Acad. Sci. U S A 107(46):19754-9. Abstract
  • Armache J.P., Jarasch A., Anger A.M., Villa E., Becker T., Bhushan S., Jossinet F., Habeck M., Dindar G., Franckenberg S., Marquez V., Mielke T., Thomm M., Berninghausen O., Beatrix B., Soding J., Westhof E., Wilson D.N. and Beckmann R. (2010) Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution. Proc. Natl. Acad. Sci. U S A 107(46):19748-53. Abstract
  • Chevalier C., Boisset S., Romilly C., Masquida B., Fechter P., Geissmann T., Vandenesch F. and Romby P. (2010) Staphylococcus aureus RNAIII binds to two distant regions of coa mRNA to arrest translation and promote mRNA degradation. PLoS Pathog. 6(3):e1000809. Abstract
  • Denoeud F., Henriet S., Mungpakdee S., Aury J.M., Da Silva C., Brinkmann H., Mikhaleva J., Olsen L.C., Jubin C., Canestro C., Bouquet J.M., Danks G., Poulain J., Campsteijn C., Adamski M., Cross I., Yadetie F., Muffato M., Louis A., Butcher S., Tsagkogeor (2010) Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate. Science 330(6009):1381-5. Abstract
  • Dutheil J.Y., Jossinet F., Westhof E. (2010) Base pairing constraints drive structural epistasis in ribosomal RNA sequences. Mol. Biol. Evol. 27(8):1868-76. Abstract
  • Fritsch V, Westhof E. (2010) The architectural motifs of folded RNAs. In "The Chemical Biology of Nucleic Acids" (Mayer G., eds.) 1:141-174.
  • Giuliodori A.M., Di Pietro F., Marzi S., Masquida B., Wagner R., Romby P., Gualerzi C.O. and Pon C.L. (2010) The cspA mRNA is a thermosensor that modulates translation of the cold-shock protein CspA. Mol. Cell 37(1):21-33. Abstract
  • Hanessian S., Pachamuthu K., Szychowski J., Giguere A., Swayze E.E., Migawa M.T., Francois B., Kondo J., Westhof, E. (2010) Structure-based design, synthesis and A-site rRNA co-crystal complexes of novel amphiphilic aminoglycoside antibiotics with new binding modes: a synergistic hydrophobic effect against resistant bacteria. Bioorg. Med. Chem. Lett. 20(23):7097-101. Abstract
  • Jossinet F., Ludwig T.E. and Westhof E. (2010) Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinformatics 26(16):2057-9. Abstract
  • Kondo J. and Westhof E. (2010) Base pairs and pseudo pairs observed in RNA-ligand complexes. J. Mol. Recognit. 23(2):241-52. Abstract
  • Masquida B, Jossinet F, Westhof E. (2010) Over a decade of bacterial ribonuclease P modeling. In "Ribonuclease P, Protein Reviews" (Liu F., Altman S., eds.) 10:41-62.
  • Masquida B., Beckert B. and Jossinet F. (2010) Exploring RNA structure by integrative molecular modelling. N. Biotechnol. 27(3):170-83. Abstract
  • O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJ. (2010) Visualization of macromolecular structures. Nat. Methods 7(3 Suppl):S42-55. Abstract
  • Procter J.B., Thompson J., Letunic I., Creevey C., Jossinet F. and Barton G.J. (2010) Visualization of multiple alignments, phylogenies and gene family evolution. Nat. Methods 7(3 Suppl):S16-25. Abstract
  • Westhof E. (2010) Toward atomic accuracy in RNA design. Nat. Methods 7(4):272-3. Abstract
  • Westhof E. (2010) The amazing world of bacterial structured RNAs. Genome Biol. 11(3):108. Abstract
  • Westhof E. and Romby P. (2010) The RNA structurome: high-throughput probing. Nat. Methods 7(12):965-7. Abstract

RNA-based antiviral immunity in drosophila and vector insects (Imler)

  • Hyvert, Y. & Imler, J.L. (2010) Chapter 53: Toll family receptors. In "Functioning of transmembrane receptors in cell signaling" Editors: R.A. Bradshaw and E. Dennis. 1:421-425.
  • Hyvert, Y. & Imler, J.L. (2010) Chapter 159: Toll family receptors. In "Handbook of cellular Signaling" Editors: R.A. Bradshaw and E. Dennis. (Elsevier, Inc.) 2:1275-1280.
  • Mueller S., Gausson V., Vodovar N., Deddouche S., Troxler L., Perot J., Pfeffer S., Hoffmann J.A., Saleh M.-C. & Imler J.-L. (2010) RNAi mediated immunity provides strong protection against the negative strand RNA virus VSV in drosophila. Proc. Natl. Acad. Sci. U S A 107:19390-19395. Abstract

The role of RNAs in the selectivity of the Drosophila Innate Immune Response (Matt)

  • Baeza Garcia A., Pierce RJ., Gourbal B., Werkmeister E., Colinet D., Reichhart JM., Dissous C and Coustau C. (2010) Involvement of the cytokine MIF in the snail host immune response to the parasite Schistosoma mansoni. PLoS Pathog. 6(9):e1001115. Abstract
  • Paquette N, Broemer M, Aggarwal K, Chen L, Husson M, Ertürk-Hasdemir D, Reichhart JM, Meier P, Silverman N (2010) Caspase-mediated cleavage, IAP binding, and ubiquitination: linking three mechanisms crucial for Drosophila NF-kappaB signaling. Mol. Cell 37(2):172-82. Abstract
  • Silverman GA, Whisstock JC, Bottomley SP, Huntington JA, Kaiserman D, Luke CJ, Pak SC, Reichhart JM, Bird PI (2010) Serpins flex their muscle: I. Putting the clamps on proteolysis in diverse biological systems. J. Biol. Chem. 285(32):24299-305. Abstract
  • Whisstock JC., Silverman GA., Bird PI., Bottomley SP., Kaiserman D., Luke CJ., Pak SC., Reichhart JM and Huntington JA. (2010) Serpins flex their muscle: II. Structural insights into target peptidase recognition, polymerization, and transport functions. J. Biol. Chem. 285(32):24307-12. Abstract
  • Zannetti C., Bonnay F., Takeshita F., Parroche P., Ménétrier-Caux C., Tommasino M and Hasan UA. (2010) C/EBP{delta} and STAT-1 are required for TLR8 transcriptional activity. J. Biol. Chem. 285(45):34773-80. Abstract

RNA degradation in plants (Gagliardi)

  • Lange H. and Gagliardi D. (2010) The exosome and 3'-to-5' RNA degradation in plants. Adv Exp Med Biol. 702:50-62. Abstract

Role of Ubiquitin in Cellular Regulation (Genschik)

  • Castells E., Molinier J., Drevensek S., Genschik P., Barneche F. and Bowler C. (2010) det1-1-induced UV-C hyposensitivity through UVR3 and PHR1 photolyase gene over-expression. Plant J. 63:392-404. Abstract
  • Marrocco K., Bergdoll M., Achard P., Criqui M.C. and Genschik P. (2010) Selective proteolysis sets the tempo of the cell cycle. Curr. Opin. Plant Biol. 13:631-639. Abstract
  • Roodbarkelari F., Bramsiepe J., Weinl C., Marquardt S., Novak B., Jakoby M. J., Lechner E., Genschik P. and A Schnittger (2010) CULLIN 4-RING FINGER-LIGASE plays a key role in the control of endoreplication cycles in Arabidopsis trichomes. Proc. Natl. Acad. Sci. U S A 107:15275-15280. Abstract

External Attractivity Team: Cryo-electron microscopy of translation complexes (Hashem)

  • Jie Fu, Yaser Hashem, Iwona Wower, Jianlin Lei, Hstau Y Liao, Christian Zwieb, Jacek Wower, Joachim Frank (2010) Visualizing the transfer-messenger RNA as the ribosome resumes translation. The EMBO Journal 29:3819-3825. Abstract

2009

External Attractivity Team: Cryo-electron microscopy of translation complexes (Hashem)

  • Yaser Hashem, Pascal Auffinger (2009) A short guide for molecular dynamics simulations of RNA systems Methods 47:187-197. Abstract

2007

External Attractivity Team: Cryo-electron microscopy of translation complexes (Hashem)

  • Pascal Auffinger, Yaser Hashem (2007) SwS: a solvation web service for nucleic acids. Bioinformatics 23:1035-1037. Abstract
  • Pascal Auffinger, Yaser Hashem (2007) Nucleic acid solvation: from outside to insight Current Opinion in Structural Biology 17:325-333. Abstract