PDF file: EURASNET Annual Report 2008

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Author Title Publication EURASNET Public. +/- 1 EURASNETacknowledgement 2Mauxion, F., Faux, C. and Séraphin, B.Kuwasako, K., Dohmae, N., Inoue, M.,Shirouzu, M., Taguchi, S., Güntert, P.,Séraphin, B., Muto, Y. and Yokoyama, S.Soreq, L., Gilboa-Geffen, A., Berrih-Aknin, S., Lacoste, P., Darvasi, A., Soreq,E., Bergman, H. and Soreq, H.Mor, I., Sklan, E.H., Podoly, E., Pick, M.,Kirschner, M., Yogev, L., Bar-SheshetItach, S., Diamant, S., Schreiber, L., Mor,T., Grisaru, D. and Soreq, H. (2008)Stamm, S. (2008)Chern, T.M., Paul, N., van Nimwegen, E.,Zavolan, M.Berninger, P., Gaidatzis, D., vanNimwegen, E., Zavolan, M.Patient, S., Wieser, D., Kleen, M.,Kretschmann, E., Jesus Martin, M.,Apweiler, R.Côté, R.G., Jones, P., Martens, L.,Apweiler, R., Hermjakob, H.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.Soldà, G., Suyama, M., Pelucchi, P., Boi,S., Guffanti, A., Rizzi, E., Bork, P.,Tenchini, M.L., Ciccarelli, F.D.The BTG2 protein is a general activator of mRNAdeadenylation.Complex assembly mechanism and an RNA-bindingmode of the human p14-SF3b155 spliceosomal proteincomplex identified by NMR solution structure andfunctional analyses.Identifying Alternative Hyper-Splicing Signatures inMG-Thymoma by Exon Arrays.Acetylcholinesterase-R increases germ cell apoptosisbut enhances sperm motility.Regulation of alternative splicing by reversiblephosphorylation.EMBO Journal 27(7), 1039-48.Proteins 71(4), 1617-1636.-PLoS One. (in press)Journal of Cellular andMolecular Medicine. (inpress)Journal of BiologicalChemistry 283(3), 1223-7.Computational analysis of small RNA cloning data. DNA Research. 15:63-72Computational analysis of small RNA cloning data. Methods 44, 13-21.- -- -- -- +- -- +- -UniProtJAPI: a remote API for accessing UniProt data. Bioinformatics 24(10),1321-2. - -The Ontology Lookup Service: more data and bettertools for controlled vocabulary queries.Systematic characterization of the murine mitochondrialproteome using functionally validated cardiacmitochondria.Non-random retention of protein-coding overlappinggenes in Metazoa.Nucleic Acids Research2008 May 8. [epub ahead ofprint]Proteomics 8(8), 1564-75.BMC Genomics 9:174.- -- -- -83
Author Title Publication EURASNET Public. +/- 1 EURASNETacknowledgement 2Harrington, 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.Letunic, I., Yamada, T., Kanehisa, M.,Bork, P.Muller, S., Leclerc, F., Behm-Ansmant, I.,Fourmann, J.B., Charpentier, B., Branlant,C.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.Piazzon, N., Rage, F., Schlotter, F., Moine,H., Branlant, C., Massenet, S.Heyd, F., Carmo-Fonseca, M., Moroy, T.de Almeida, S.F., Carmo-Fonseca, M.Rino, J., Desterro, J.M., Pacheco, T.R.,Gadella, T.W. Jr, Carmo-Fonseca, M.Carneiro, T., Carvalho, C., Braga, J., Rino,J., Milligan, L., Tollervey, D., Carmo-Fonseca, M.Large-scale prediction of drug-target relationships. FEBS Letters 582(8), 1283-90.PMID: 18291108. [PubMed- in process]iPath: interactive exploration of biochemical pathwaysand networks.Combined in silico and experimental identification ofthe Pyrococcus abyssi H/ACA sRNAs and their targetsites in ribosomal RNAs.The Hsp90 chaperone controls the biogenesis of L7AeRNPs through conserved machinery.In vitro and in cellulo evidences for association of thesurvival of motor neuron complex with the fragile Xmental retardation protein.Differential isoform expression and interaction with theP32 regulatory protein controls the subcellularlocalization of the splicing factor U2AF26.The CTD role in cotranscriptional RNA processing andsurveillance.Splicing factors SF1 and U2AF associate inextraspliceosomal complexes.Inactivation of cleavage factor I components rna14pand rna15p induces sequestration of small nucleolarribonucleoproteins at discrete sites in the nucleus.Trends in BiochemicalSciences 33(3), 101-3.PMID: 18276143. [PubMed- in process]- -- -- -Nucleic Acids Research36(8), 2459-75. - -Journal of Cell Biology180(3), 579-95.Journal of BiologicalChemistry 283(9), 5598-610.Journal of BiologicalChemistry 2008 May 6.[epub ahead of print]FEBS Letters 2008 Apr 22.[epub ahead of print]Molecular and CellularBiology 28(9), 3045-57.- -- -- -- +- -Molecular Biology of theCell 19(4), 1499-508. - -84
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TABLE OF CONTENTSA. PERIODIC ACTIVI
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1 PUBLISHABLE EXECUTIVE SUMMARY EUR
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Dr. Davide Gabellini(28) Swiss Inst
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WP7 Molecular characterization of s
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To identify protein-protein interac
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expressed in a particular tissue. T
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Duchenne muscular dystrophy (DMD).
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WP21 Reachout to the broader RNA co
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4.1 TABLE OF MILESTONES JPA MONTH 2
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Numerous plasmids, constructs, extr
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collaboration between EURASNET and
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5.1 WORK PACKAGE REPORTSWork Packag
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• Ongoing regular addition of new
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Work Package 4 The Alternative Spli
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Work Package 6 In silico approaches
Page 33 and 34: alternative splicing.162 Compare sp
Page 35 and 36: 33 Agreement on pre-mRNA substrates
Page 37 and 38: its numerous binding sites on both
Page 39 and 40: Work Package 8 Genome-wide Analyses
Page 41 and 42: 173 Further development of data ana
Page 43 and 44: Problems and explanations for delay
Page 45 and 46: eveal that there is a dramatic chan
Page 47 and 48: Work Package 10 Post-translational
Page 49 and 50: mutational analysis that led to the
Page 51 and 52: Isolation of an active step I splic
Page 53 and 54: FBP11 and 21 with these sequences.
Page 55 and 56: Similarly to what observed for SF2/
Page 57 and 58: prp45-113 mutant, which is compatib
Page 59 and 60: cell lines. In contrast in the pres
Page 61 and 62: genes with roles in the development
Page 63 and 64: Structural analyses of several RRMs
Page 65: Work Package 17 Staff Exchange and
Page 69 and 70: Barralle's lab, Krämer is acting a
Page 71 and 72: alternative splicing) and higher ed
Page 73 and 74: Student Symposium “Decision Makin
Page 75 and 76: variation and suitability for use w
Page 77 and 78: Following feedback from members we
Page 79 and 80: Invited seminars: In addition to me
Page 81 and 82: Publications 2008Author Title Publi
Page 83: Author Title Publication EURASNET P
Page 87 and 88: Author Title Publication EURASNET P
Page 93 and 94: Minutes of the General Assembly dec
Page 96 and 97: 241 Evaluate available careerdevelo
Page 98 and 99: 156 The EURASNET memberStamm publis
Page 100 and 101: y coarse-grained foldingsimulation.
Page 102 and 103: overexpressor and mutant lines(mont
Page 104 and 105: machinery with particularrespect to
Page 106 and 107: alternative splicing, using theEDI
Page 108 and 109: contemporary findings withinthe EUR
Page 118 and 119: Licht K, Medenbach J, Lührmann R,K
Page 122 and 123: 9 TABULAR OVERVIEW OF MAJOR COST IT
Page 124 and 125: total costs * 18.891,12 52778.60 41
Page 126 and 127: other (the rest) 48,57 0 56.539,43t
Page 128 and 129: travel 6.964,91overhead 3.081,07oth
Page 130 and 131: Participant 1A Type of expenditure
Page 132 and 133: Participant 1B - Karla Neugebauera)
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Participant 2 - Juan Valcarcela) Wo
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Participant 3 - Stefan Stamma) Work
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Participant 4 - Göran Akusjärvia)
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Participant 5A/B - Peer Bork/Rolf A
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Major cost items• ResearchPersonn
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Participant 7 - Francisco Barallea)
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Francisco Baralle gave a talk to a
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alternative splicing on human disea
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J. Beggs has had frequent contact w
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Page 154 and 155:
Page 156 and 157:
Participant 12A - Jamal Tazia) Work
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Participant 12B - Bertrand Séraphi
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Participant 12C - Christiane Branla
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Participant 12D - Edouard Bertranda
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Participant 13 - Daniel Schümperli
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Participant 14 - John W. S. Browna)
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Participant 15 - Javier F. Cáceres
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• ResearchPersonnelName WP Person
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MiscellaneousOligonucleotidesUse of
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Major cost items• ResearchConsuma
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Page 178 and 179:
Participant 21 - Angela Krämera) W
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Participant 22 - Angus Lamonda) Wor
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Participant 23 - Chris Smitha) Work
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ChemicalsEnzymesLaboratory supplies
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Participant 26 - Didier Auboeufa) W
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tool for the molecular analysis of
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Participant 29 - Frédéric Allaina
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protein and instead possesses the d
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+ overhead 4.730= total eligible co
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Claudia Tamaro (PhD) has begun work
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ETHZIIMCBUPFSOTON-HGDTOTALJoint Pro
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Direct eligible costs 53.240,48 0,0
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Direct eligible costs 18.720,07 0,0
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13 REPORT ON THE DISTRIBUTION OF TH
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Report on the Distribution of the C
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For most work packages here follows
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pathways (eg, Reactome ).While PAND
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The possible dependence of the effe
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In some treatments or mutants, simi
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Work Package 12: Mis-splicing and D
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acid. Furthermore, using antibodies
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At the 2007 annual meeting in Ile d
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Partner 13 has extensively studied
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inhibitors/modulators of RNA splici
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18 MONTH JPA: WORKPACKAGE TIMECOURS
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15.3 GRAPHICAL PRESENTATION OF WORK
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15.4 TABLE OF MILESTONES (MONTH 37-
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156 The EURASNET memberStamm publis
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194 Bertrand will analyze indetail
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216 Aubeouf and Neugebauer willcoll
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238 Establishing joint PhDcommittee
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283 A unified browser for allknown
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296 Group 12a (Branlant) willuse th
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315 Lamond will use a FLIM-FRET bas
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329 GROUP 7 (F. BARALLE)will contin
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333 GROUP 27 (GABELLINI)will:1) foc
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345 Schümperli’s group isplannin
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366 Quarterly network e-mail atmont
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2. Sharing Resources, Technology an
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5. Ensuring DurabilityWorkpackage d
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7. Molecular Characterization of Sp
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8. Genome-wide Analyses of Splicing
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9. Complexity of Spliceosomal Prote
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202 Srebrow will investigate the ro
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12. Mis-splicing and DiseaseWorkpac
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13. Co-transcriptional Mechanisms o
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14. Chemical Biology and Therapeuti
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15. Development of Enabling Technol
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269 IFMs in 20091. “Alternative a
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18. Career DevelopmentWorkpackage d
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20. SMEs and Technology TransferWor
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21. Reachout to the Broader RNA Com
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15.7 WORK PACKAGE LIST (MONTHS 37-5
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ETHZIIMCBUPFSOTON-HGDTOTALJoint Pro
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AMU 5 29 8 42UAAR 5 145 16 1665 29
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Joint Programme of Activities RESEA
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60 month period 18 month periodRequ
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Integration1. Young Investigator Pr
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UCAM-DBIOC 2350,000x1/3 € 50,000x
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the management team. Audit costs ar
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