Publications 2008

Author Title Publication
Bianchini, A., Loiarro, M., Bielli, P., Busà, R., Paronetto, M.P., Loreni, F., Geremia, R., Sette, C. Phosphorylation of eIF4E by MNKs supports protein synthesis, cell cycle progression and proliferation in prostate cancer cells. Carcinogenesis 29, 2279-88.
Jagannath, A. and Wood, M.J.A. Localization of double-stranded siRNA to cytoplasmic GW-Bodies is Ago2-dependent and induces upregulation of GW182. Molecular Cell Biology 20, 521-529.
Ivanova, G.D., Arzumanov, A., Abes, R., Yin, H., Wood, M.J.A., Lebleu, B. and Gait, M.J. Improved cell-penetrating peptide-PNA conjugates for splicing redirection in HeLa cells and exon skipping in mdx mouse muscle. Nucleic Acids Research 6(20), 6418-6428.
Yin, H.F., Moulton, H.M., Seow, Y., Boyd, C., Iverson, P. and Wood, M.J.A. Cell-penetrating peptide-conjugated antisense oligonucleotides restore systemic muscle and cardiac dystrophin expression and function. Human Molecular Genetics 17(24), 3909-3918.
Matos, P., Oliveira, C., Velho, S., Gonçalves, V., da Costa, L.T., Moyer, M.P., Seruca, R. and Jordan, P. B-RafV600E cooperates with alternative spliced Rac1b to sustain colorectal cancer cell survival. Gastroenterology 135, 899-906.
Lorkovic, Z.J., and Barta, A. Role of Cajal bodies and nucleolus in the maturation of the U1 snRNP in Arabidopsis. PLoS ONE 3(12). [e3989. Epub 2008 Dec 22]
Shaked, I., Zimmerman, G., Soreq, H. Stress-induced alternative splicing modulations in brain and periphery: acetylcholinesterase as a case study. Annals of the New York Academy of Sciences 1148, 269-81.
Bonnal, S., Martínez, C., Förch, P., Bachi, A., Wilm, M. and Valcárcel, J. LUCA-15/RBM5/H37 regulates splice site pairing after exon definition. Molecular Cell 32(1), 81-95.
Ayala, Y.M., Zago, P., D'Ambrogio, A., Xu, Y.F., Petrucelli, L., Buratti, E., Baralle, F.E. Structural determinants of the cellular localization and shuttling of TDP-43. Journal of Cell Science 121, 3778-3785. (doi: 10.1242/jcs.038950)
Raponi, M., Buratti, E., Llorian, M., Stuani, C., Smith, C.W., Baralle, D. Polypyrimidine tract binding protein regulates alternative splicing of an aberrant pseudoexon in NF1. FEBS Journal 275 (24), 6101-6108. (doi: 10.1111 /j.1742-4658.2008.06734.x)
Ittig, D., Schümperli, D. and Leumann, C.J. Tc-DNA modified siRNA. Nucleic Acids Symposium Series (Oxf). 52, 501-502.
Meyer, K., Marquis, J., Trüb, J., Nlend Nlend, R., Verp, S., Ruepp, M.-D., Imboden, H., Barde, I., Trono, D. and Schümperli, D. Rescue of a severe mouse model for Spinal Muscular Atrophy by U7 snRNA-mediated splicing modulation. Human Molecular Genetics 2008. (doi: 10.1093/hmg/ddn382)
Brooks, M., Dziembowski, A., Quevillon-Cheruel, S., Henriot, V., Faux, C., Van-Tilbeurgh, H., Séraphin, B. Structure of the yeast Pml1 splicing factor and its integration into the RES complex. Nucleic Acids Research. [in press]
Tournier, I., Vezain, M., Martins, A., Charbonnier, F., Baert-Desurmont, S., Olschwang, S., Q. Wang, Q., Buisine, M-P., Soret, J., Tazi, J., Frébourg, T., and Tosi, M. A large fraction of unclassified variants of the mismatch repair genes MLH1 and MSH2 is associated with splicing defects. Human Mutation 2008 June 16. [epub ahead of print]
Comment/review on paper below
Bushell, M., Stoneley, M., Spriggs, K.A. and Willis, A.E.
SF2/ASF TORCs Up Translation. Molecular Cell 30, 262-263.
Michlewski, G., Sanford, J.R. and Cáceres, J.F. The splicing factor SF2/ASF regulates translation initiation by enhancing phosphorylation of 4E-BP1. Molecular Cell 30, 179-189.
Hasegawa, M., Arai, T., Nonaka, T., Kametani, F., Yoshida, M., Hashizume, Y., Beach, T.G., Buratti, E., Baralle, F., Morita, M., Nakano, I., Oda, T., Tsuchiya, K., Akiyama, H. Phosphorylated TDP-43 in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Annals of Neurology 64(1), 60-70.
Jablonski, J.A., Buratti E., Stuani C., Caputi M. The secondary structure of the Human Immunodeficiency Virus Type 1 transcript modulates viral splicing and infectivity. Journal of Virology 82(16), 8038-8050.
Marcucci, R., Romano, M. Thrombopoietin and its splicing variants: structure and functions in thrombopoiesis and beyond. Biochimica et Biophysica Acta 1782(7-8), 427-432.
Asparuhova, M.B., Barde, I., Schranz, K., Trono, D. and Schümperli, D. Development and characterisation of a triple combination gene therapy vector inhibiting HIV-1 multiplication. Journal of Gene Medicine 10, 1059-1070.
Marquis, J., Kämpfer S.S., Angehrn, L. and Schümperli, D. Doxycycline-controlled splicing modulation by regulated antisense U7 snRNA expression cassettes. Gene Therapy, 2008 Aug 14. [epub ahead of print]
Morillas M., Eberl H., Allain F.H.-T., Glockshuber R., Kuennemann E. Novel enzymatic activity derived from the Semliki Forest virus capsid protein. Journal of Molecular Biology 376, 721-35.
Auweter S.D., Allain F.H.-T. Structure-function relationships of the polypyrimidine tract binding protein. Cellular and Molecular Life Sciences 65, 516-27.
Lapouge, K., Schubert, M,. Allain, F.H.-T., Haas, D. Gac/Rsm signal transduction pathway of gamma-proteobacteria: from RNA recognition to regulation of social behaviour. Molecular Microbiology 67, 241-253.
Kim, E., Goren, A. and Ast, G. Alternative splicing and disease. RNA Biology 2008 Mar 22;5(1). [epub ahead of print]
Ram, O., Schwartz, S. and Ast. G. Multifactorial interplay controls the splicing profile of Alu derived exons. Molecular and Cellular Biology 2008 Mar 10. [epub ahead of print]
Gal-Mark, N., Schwartz, S. and Ast, G. Alternative splicing of Alu exons--two arms are better than one. Nucleic Acids Research 2008 Feb 14.
Goren, A., Kim, E., Amit, M., Bochner, R., Lev-Maor, G., Ahituv, N. and Ast, G. Alternative approach to a heavy weight problem. Genome Research 2008 Feb.
Kim, E., Goren, A. and Ast, G. Alternative splicing: current perspectives. Bioessays 30(1), 38-47.
Kim, E., Goren, A. and Ast, G.. Insights into the connection between cancer and alternative splicing. Trends in Genetics 2008 Jan.
Sanchez, G., Bittencourt, D., Laud, K., Barbier, J., Delattre, O., Auboeuf, D., Dutertre, M. Alteration of cyclin D1 transcript elongation by a mutated transcription factor up-regulates the oncogenic D1b splice isoform in cancer. Proceedings of the National Academy of Sciences USA 2008 Apr 14. [epub ahead of print]
Simpson, C.G.,  Fuller, J., Maronova, M., Kalyna, M., Davidson, D., McNicol, J.,,   Barta, A.,  and Brown , J.W.S. Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts The Plant Journal 53, 1035–1048.
de la Fuente van Bentem, S.,  Anrather, D., Dohnal, I., Roitinger, E., Csaszar, E., Joore, J., Buijnink, J., Carreri, A., Forzani, C., Lorkovic, Z.J., Barta, A., Lecourieux, D., Verhounig, A., Jonak, C., and Hirt, H. Site-Specific Phosphorylation Profiling of Arabidopsis Proteins by Mass Spectrometry and Peptide Chip Analysis. Journal of Proteome Research 2008 Apr 24. [epub ahead of print]
Simpson, C.G.,  Lewandowska, D.,  Fuller, J., Maronova, M., Kalyna, M., Davidson, D.,McNicol, J.,,  Raczynska, D.,  Jarmolowski, A., Barta, A.,  and Brown, J.W.S. Alternative Splicing in Plants Biochemical Society Transactions.  (accepted)
Lorkovic, Z.J., Hilscher, J. and Barta, A. Co-localisation studies of Arabidopsis SR splicing factors reveal different types of speckles in plant cell nuclei. Experimental Cell Research. (accepted)
Raponi, M., Baralle, D. Can donor splice site recognition occur without the involvement of U1 snRNP? Biochemical Society Transactions 36(3).
Romano, M., Bacalini, M.G., Verschoor, E.J., Crovella, S., Baralle, F.E. Origin and evolution of the c.844_845ins68/c.833T>C mutations within the cystathionine beta-synthase gene in great apes. FEBS Letters 582(3), 423-426.
Ayala, Y.M., Misteli, T., Baralle, F.E. TDP-43 regulates retinoblastoma protein phosphorylation through the repression of cyclin-dependent kinase 6 expression. Proceedings of the National Academy of Sciences USA 105(10), 3785-3789.
Buratti, E., Baralle, F.E. Multiple roles of TDP-43 in gene expression, splicing regulation, and human disease. Frontiers in Bioscience 13, 867-878.
Simpson, C.G. and Brown, J.W.S. Plant U12-dependent (AT-AC) introns. In: Nuclear pre-mRNA processing in plants. Ed. Reddy, A.S.N. (in press)
Brown, J.W.S. and Shaw, P.J. The plant nucleolus and mRNA biogenesis. In: Nuclear pre-mRNA processing in plants. Ed. Reddy, A.S.N. (in press)
Schwartz, S.H., Silva, J., Burstein, D., Pupko, T., Eyras, E., Ast, G. Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Research 18(1), 88-103.
Ellis, J.D., Lleres, D., Denegri, M., Lamond, A.I. and Caceres, J.F. Spatial mapping of splicing factor complexes involved in exon and intron definition. Journal of Cell Biology 181(6), 921-34.
Matic, I., van Hagen, M., Schimmel, J., Macek, B., Ogg, S. C., Tatham, M. H., Hay, R. T., Lamond, A. I., Mann, M. and Vertegaal, A. C. In vivo identification of human small ubiquitin-like modifier polymerization sites by high accuracy mass spectrometry and an in vitro to in vivo strategy. Molecular and Cellular Proteomics 7, 132-44.
Le Hir, H. and Séraphin, B. EJCs at the heart of translational control. Cell 133(2), 213-6.
Mauxion, F., Faux, C. and Séraphin, B. The BTG2 protein is a general activator of mRNA deadenylation. EMBO Journal 27(7), 1039-48.
Kuwasako, K., Dohmae, N., Inoue, M., Shirouzu, M., Taguchi, S., Güntert, P., Séraphin, B., Muto, Y. and Yokoyama, S. Complex assembly mechanism and an RNA-binding mode of the human p14-SF3b155 spliceosomal protein complex identified by NMR solution structure and functional analyses. Proteins 71(4), 1617-1636.
Soreq, L., Gilboa-Geffen, A., Berrih-Aknin, S., Lacoste, P., Darvasi, A., Soreq, E., Bergman, H. and Soreq, H. Identifying Alternative Hyper-Splicing Signatures in MG-Thymoma by Exon Arrays. PLoS One. (in press)
Mor, I., Sklan, E.H., Podoly, E., Pick, M., Kirschner, M., Yogev, L., Bar-Sheshet Itach, S., Diamant, S., Schreiber, L., Mor, T., Grisaru, D. and Soreq, H. (2008) Acetylcholinesterase-R increases germ cell apoptosis but enhances sperm motility. Journal of Cellular and Molecular Medicine. (in press)
Stamm, S. (2008) Regulation of alternative splicing by reversible phosphorylation. Journal of Biological Chemistry 283(3), 1223-7.
Chern, T.M., Paul, N., van Nimwegen, E., Zavolan, M. Computational analysis of small RNA cloning data. DNA Research. (in press)
Berninger, P., Gaidatzis, D., van Nimwegen, E., Zavolan, M. Computational analysis of small RNA cloning data. Methods 44, 13-21.
Patient, S., Wieser, D., Kleen, M., Kretschmann, E., Jesus Martin, M., Apweiler, R. UniProtJAPI: a remote API for accessing UniProt data. Bioinformatics 24(10), 1321-2.
Côté, R.G., Jones, P., Martens, L., Apweiler, R., Hermjakob, H. The Ontology Lookup Service: more data and better tools for controlled vocabulary queries. Nucleic Acids Research 2008 May 8. [epub ahead of print]
Zhang, J., Li, X., Mueller, M., Wang, Y., Zong, C., Deng, N., Vondriska, T.M., Liem, D.A., Yang, J.I., Korge, P., Honda, H., Weiss, J.N., Apweiler, R., Ping, P. Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria. Proteomics 8(8), 1564-75.
Soldà, G., Suyama, M., Pelucchi, P., Boi, S., Guffanti, A., Rizzi, E., Bork, P., Tenchini, M.L., Ciccarelli, F.D. Non-random retention of protein-coding overlapping genes in Metazoa. BMC Genomics 9:174.
Harrington, E.D., Jensen, L.J., Bork, P. Predicting biological networks from genomic data. FEBS Letters 582(8), 1251-8.
PMID: 18294967. [PubMed - in process]
Kuhn, M., Campillos, M., González, P., Jensen, L.J., Bork, P. Large-scale prediction of drug-target relationships.

FEBS Letters 582(8), 1283-90.
PMID: 18291108. [PubMed - in process]

Letunic, I., Yamada, T., Kanehisa, M., Bork, P. iPath: interactive exploration of biochemical pathways and networks. Trends in Biochemical Sciences 33(3), 101-3.
PMID: 18276143. [PubMed - in process]
Muller, S., Leclerc, F., Behm-Ansmant, I., Fourmann, J.B., Charpentier, B., Branlant, C. Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in ribosomal RNAs. Nucleic Acids Research 36(8), 2459-75.
Boulon, S., Marmier-Gourrier, N., Pradet-Balade, B., Wurth, L., Verheggen, C., Jády, B.E., Rothé, B., Pescia, C., Robert, M.C., Kiss, T., Bardoni, B., Krol, A., Branlant, C., Allmang, C., Bertrand, E., Charpentier, B. The Hsp90 chaperone controls the biogenesis of L7Ae RNPs through conserved machinery. Journal of Cell Biology 180(3), 579-95.
Piazzon, N., Rage, F., Schlotter, F., Moine, H., Branlant, C., Massenet, S. In vitro and in cellulo evidences for association of the survival of motor neuron complex with the fragile X mental retardation protein. Journal of Biological Chemistry 283(9), 5598-610.
Heyd, F., Carmo-Fonseca, M., Moroy, T. Differential isoform expression and interaction with the P32 regulatory protein controls the subcellular localization of the splicing factor U2AF26. Journal of Biological Chemistry 2008 May 6. [epub ahead of print]
de Almeida, S.F., Carmo-Fonseca, M. The CTD role in cotranscriptional RNA processing and surveillance. FEBS Letters 2008 Apr 22. [epub ahead of print]
Rino, J., Desterro, J.M., Pacheco, T.R., Gadella, T.W. Jr, Carmo-Fonseca, M. Splicing factors SF1 and U2AF associate in extraspliceosomal complexes. Molecular and Cellular Biology 28(9), 3045-57.
Carneiro, T., Carvalho, C., Braga, J., Rino, J., Milligan, L., Tollervey, D., Carmo-Fonseca, M. Inactivation of cleavage factor I components rna14p and rna15p induces sequestration of small nucleolar ribonucleoproteins at discrete sites in the nucleus. Molecular Biology of the Cell 19(4), 1499-508.
Jankowska, A., Gunderson, S.I., Andrusiewicz, M., Burczynska, B., Szczerba, A., Jarmolowski, A., Nowak-Markwitz, E., Warchol, J.B. Reduction of human chorionic gonadotropin beta subunit expression by modified U1 snRNA caused apoptosis in cervical cancer cells. Molecular Cancer 7:26.
Pearson, J.L., Robinson, T.J., Muñoz, M.J., Kornblihtt, A.R., Garcia-Blanco, M.A. Identification of the cellular targets of the transcription factor TCERG1 reveals a prevalent role in mRNA processing. Journal of Biological Chemistry 283(12), 7949-61.
Baldin, V., Militello, M., Thomas, Y., Doucet, C., Fic, W., Boireau, S., Jariel-Encontre, I., Piechaczyk, M., Bertrand, E., Tazi, J., Coux, O. A Novel Role for PA28{gamma}-Proteasome in Nuclear Speckle Organization and SR Protein Trafficking. Molecular Biology of the Cell 19(4), 1706-16.
Di Segni, G., Gastaldi, S., Tocchini-Valentini, G.P. Cis- and trans-splicing of mRNAs mediated by tRNA sequences in eukaryotic cells. Proceedings of the National Academy of Sciences USA 2008 May 5. [epub ahead of print]
Mathew, R., Hartmuth, K., Möhlmann, S., Urlaub, H., Ficner, R., Lührmann, R. Phosphorylation of human PRP28 by SRPK2 is required for integration of the U4/U6-U5 tri-snRNP into the spliceosome. Nature Structural and Molecular Biology 15(5), 435-43.
Mukherjee, K., Sharma, M., Urlaub, H., Bourenkov, G.P., Jahn, R., Südhof, T.C., Wahl, M.C. CASK Functions as a Mg2+-independent neurexin kinase. Cell 133(2), 328-39.
Bessonov, S., Anokhina, M., Will, C.L., Urlaub, H., Lührmann, R. Isolation of an active step I spliceosome and composition of its RNP core. Nature 452(7189), 846-50.
Martin, N., Schwamborn, K., Urlaub, H., Gan, B., Guan, J.L., Dejean, A. Spatial interplay between PIASy and FIP200 in the regulation of signal transduction and transcriptional activity. Molecular and Cellular Biology 28(8), 2771-81.
Ben-Dov, C., Hartmann, B., Lundgren, J., Valcárcel, J. Genome-wide analysis of alternative pre-mRNA splicing. Journal of Biological Chemistry 283(3), 1229-33.