2008 Publications

Author Title Publication
Morillas M., Eberl H., Allain F.H.-T., Glockshuber R., Kuennemann E. (2008) "Novel enzymatic activity derived from the Semliki Forest virus capsid protein" J. Mol. Biol., 376, 721-35
Auweter S.D., Allain F.H.-T. (2008) "Structure-function relationships of the polypyrimidine tract binding protein" Cell Mol Life Sci., 65, 516-27
Lapouge K., Schubert M,. Allain F.H.-T., Haas D. (2008) "Gac/Rsm signal transduction pathway of gamma-proteobacteria: from RNA recognition to regulation of social behaviour" Mol. Microbiol., 67, 241-253
Kim E, Goren A and Gil Ast. (2008) Alternative splicing and disease. RNA Biol. 2008 Mar 22;5(1) [Epub ahead of print]
Ram O, Schwartz S and Gil Ast. (2008) Multifactorial interplay controls the splicing profile of Alu derived exons. Mol Cell Biol. 2008 Mar 10; [Epub ahead of print]
Gal-Mark N, Schwartz S and Gil Ast. (2008) Alternative splicing of Alu exons--two arms are better than one. Nucleic Acids Res. 2008 Feb 14
Goren A*, Kim E*, Amit M*, Bochner R, Lev-Maor G, Ahituv N and Gil Ast. (2008) Alternative approach to a heavy weight problem. Genome Res. 2008 Feb
Kim E*, Goren A* and Gil Ast. (2008) Alternative splicing: current perspectives. Bioessays. 2008 Jan;30(1):38-47.
Kim E*, Goren A* and Gil Ast. (2008) Insights into the connection between cancer and alternative splicing. Trends Genet. 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. Proc Natl Acad Sci U S A. 2008 Apr 14; [Epub ahead of print]
Simpson, CG.,  Fuller, J., Maronova, M., Kalyna, M., Davidson, D.,McNicol, J.,,   Barta, A.,  and Brown , J W. S. (2008) Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts The Plant Journal, 53, 1035–1048
Sergio de la Fuente van Bentem,  Dorothea Anrather, Ilse Dohnal, Elisabeth Roitinger, Edina Csaszar, Jos Joore,  Joshua Buijnink,  Alessandro Carreri, Celine Forzani, Zdravko J. Lorkovic, Andrea Barta, David Lecourieux,  Andreas Verhounig, Claudia Jonak, and Heribert Hirt. Site-Specific Phosphorylation Profiling of Arabidopsis Proteins by Mass Spectrometry and Peptide Chip Analysis. J Proteome Res. 2008 Apr 24. [Epub ahead of print]
Simpson, CG.,  Lewandowska, D.,  Fuller, J., Maronova, M., Kalyna, M., Davidson, D.,McNicol, J.,,  Raczynska, D.,  Jarmolowski, A., Barta, A.,  and Brown , J W. S. (2008) Alternative Splicing in Plants Biochem Soc. Trans.  Accepted
Lorkovic, ZJ., Hilscher, J., and Barta, A. (2008) Co-localisation studies of Arabidopsis SR splicing factors reveal different types of speckles in plant cell nuclei. Exp. Cell Research accepted
M raponi, D Baralle. Biochemical Society Can donor splice site recognition occur without the involvement of U1 snRNP? Transactions 2008 Vol 36, part 3.
Romano, M., Bacalini, M.G., Verschoor, E.J., Crovella, S., Baralle, F.E. 2008 Origin and evolution of the c.844_845ins68/c.833T>C mutations within the cystathionine beta-synthase gene in great apes. FEBS Lett. 582(3), 423-426
Ayala, Y.M., Misteli, T., Baralle, F.E. 2008. TDP-43 regulates retinoblastoma protein phosphorylation through the repression of cyclin-dependent kinase 6 expression. Proc. Natl. Acad. Sci. USA 105(10), 3785-3789
Buratti, E., Baralle, F.E. 2008. Multiple roles of TDP-43 in gene expression, splicing regulation, and human disease. Front. Biosci. 13, 867-878
Simpson, C.G. and Brown, J.W.S. 2008. 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. 2008. The plant nucleolus and mRNA biogenesis. In: 'Nuclear pre-mRNA processing in plants'. Ed. Reddy, A.S.N. (in press).
Ellis,J.D., Lleres,D., Denegri,M., Lamond,A.I. and Cáceres,J.F.(2008) Spatial mapping of splicing factor complexes involved in exon and intron definition. J. Cell Biol, in press
Michlewski,G., Sanford,J.R. and Cáceres,J.F.(2008) The splicing factor SF2/ASF regulates translation initiation by enhancing phosphorylation of 4E-BP1. Mol Cell 30, 179-189
Schwartz SH, Silva J, Burstein D, Pupko T, Eyras E, Ast G. (2008). Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res. 18(1):88-103
Ellis, J.D., Lleres, D., Denegri, M., Lamond, A.I. and Caceres, J.F. (2008) Spatial mapping of splicing factor complexes involved in exon and intron definition J Cell Biol, in press
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. (2008). In vivo identification of human small ubiquitin-like modifier polymerization sites by high accuracy mass spectrometry and an in vitro to in vivo strategy. Mol Cell Proteomics 7, 132-44
Le Hir, H. and Séraphin, B. (2008) EJCs at the heart of translational control. Cell, 133 (2) 213-6. Review
Mauxion, F., Faux, C. and Séraphin, B. (2008) The BTG2 protein is a general activator of mRNA deadenylation EMBO J, 27 (7) 1039-48
Kuwasako, K., Dohmae, N., Inoue, M., Shirouzu, M., Taguchi, S., Güntert, P., Séraphin, B., Muto, Y. and Yokoyama, S. (2008) 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. (2008) Identifying Alternative Hyper-Splicing Signatures in MG-Thymoma by Exon Arrays. in press in PLOS1
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. J.Biol. Chem. 283(3): 1223-7
Chern TM, 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 (2008)
Patient S, Wieser D, Kleen M, Kretschmann E, Jesus Martin M, Apweiler R. UniProtJAPI: a remote API for accessing UniProt data. Bioinformatics. 2008 May 15;24(10):1321-2. Epub 2008 Apr 4
Côté RG, Jones P, Martens L, Apweiler R, Hermjakob H. The Ontology Lookup Service: more data and better tools for controlled vocabulary queries Nucleic Acids Res. 2008 May 8. [Epub ahead of print]
Zhang J, Li X, Mueller M, Wang Y, Zong C, Deng N, Vondriska TM, Liem DA, Yang JI, Korge P, Honda H, Weiss JN, Apweiler R, Ping P. Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria. Proteomics. 2008 Apr;8(8):1564-75.
Soldà G, Suyama M, Pelucchi P, Boi S, Guffanti A, Rizzi E, Bork P, Tenchini ML, Ciccarelli FD. Non-random retention of protein-coding overlapping genes in Metazoa BMC Genomics. 2008 Apr 16;9:174.
Harrington ED, Jensen LJ, Bork P. Predicting biological networks from genomic data. FEBS Lett. 2008 Apr 9;582(8):1251-8. Epub 2008 Feb 21.
PMID: 18294967 [PubMed - in process]
Kuhn M, Campillos M, González P, Jensen LJ, Bork P. Large-scale prediction of drug-target relationships. FEBS Lett. 2008 Apr 9;582(8):1283-90. Epub 2008 Feb 20. PMID: 18291108 [PubMed - in process]
Letunic I, Yamada T, Kanehisa M, Bork P. iPath: interactive exploration of biochemical pathways and networks. Trends Biochem Sci. 2008 Mar;33(3):101-3. Epub 2008 Feb 13.
PMID: 18276143 [PubMed - in process]
Muller S, Leclerc F, Behm-Ansmant I, Fourmann JB, 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 Res. 2008 May;36(8):2459-75. Epub 2008 Feb 27.
Boulon S, Marmier-Gourrier N, Pradet-Balade B, Wurth L, Verheggen C, Jády BE, Rothé B, Pescia C, Robert MC, 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. J Cell Biol. 2008 Feb 11;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. J Biol Chem. 2008 Feb 29;283(9):5598-610. Epub 2007 Dec 19.
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. J Biol Chem. 2008 May 6. [Epub ahead of print]
de Almeida SF, Carmo-Fonseca M. The CTD role in cotranscriptional RNA processing and surveillance. FEBS Lett. 2008 Apr 22. [Epub ahead of print]
Rino J, Desterro JM, Pacheco TR, Gadella TW Jr, Carmo-Fonseca M. Splicing factors SF1 and U2AF associate in extraspliceosomal complexes. Mol Cell Biol. 2008 May;28(9):3045-57. Epub 2008 Feb 19.
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. Mol Biol Cell. 2008 Apr;19(4):1499-508. Epub 2008 Jan 30.
Jankowska A, Gunderson SI, Andrusiewicz M, Burczynska B, Szczerba A, Jarmolowski A, Nowak-Markwitz E, Warchol JB. Reduction of human chorionic gonadotropin beta subunit expression by modified U1 snRNA caused apoptosis in cervical cancer cells. Mol Cancer. 2008 Mar 14;7:26.
Pearson JL, Robinson TJ, Muñoz MJ, Kornblihtt AR, Garcia-Blanco MA. Identification of the cellular targets of the transcription factor TCERG1 reveals a prevalent role in mRNA processing. J Biol Chem. 2008 Mar 21;283(12):7949-61. Epub 2008 Jan 10.
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. Mol Biol Cell. 2008 Apr;19(4):1706-16. Epub 2008 Feb 6.
Di Segni G, Gastaldi S, Tocchini-Valentini GP. Cis- and trans-splicing of mRNAs mediated by tRNA sequences in eukaryotic cells. Proc Natl Acad Sci U S A. 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. Nat Struct Mol Biol. 2008 May;15(5):435-43. Epub 2008 Apr 20.
Mukherjee K, Sharma M, Urlaub H, Bourenkov GP, Jahn R, Südhof TC, Wahl MC. CASK Functions as a Mg2+-independent neurexin kinase. Cell. 2008 Apr 18;133(2):328-39.
Bessonov S, Anokhina M, Will CL, Urlaub H, Lührmann R. Isolation of an active step I spliceosome and composition of its RNP core. Nature. 2008 Apr 17;452(7189):846-50. Epub 2008 Mar 5.
Martin N, Schwamborn K, Urlaub H, Gan B, Guan JL, Dejean A. Spatial interplay between PIASy and FIP200 in the regulation of signal transduction and transcriptional activity. Mol Cell Biol. 2008 Apr;28(8):2771-81. Epub 2008 Feb 19.
Ben-Dov C, Hartmann B, Lundgren J, Valcárcel J. Genome-wide analysis of alternative pre-mRNA splicing. J Biol Chem. 2008 Jan 18;283(3):1229-33. Epub 2007 Nov 16. Review