PDF file: EURASNET Annual Report 2008

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315 Lamond will use a FLIM-FRET based assay to identifythe regions of highlycondensed and decondensedchromatin within interphasenuclei of live mammaliancells and use this approach tocompare chromatinorganization in vivo with theconcentrations ofspliceosomal proteins. Thiswill provide novelinformation on thetopological relation betweenhigher order chromatinorganization and geneexpression.316 Caceres will identify thetranslational targets of the SRprotein SF2/ASF. Acombination of sucrosegradients and deepsequencingwill be used tofollow polysomal shifts ofRNA that are bound andactivated at the translationallevel by SF2/ASF.317 Carmo-Fonseca will performkinetic measurements ofmolecular interactions in thespliceosome using live-cellimaging techniques.318 Luhrmann will focus on thecharacterization of the role ofreversible phosphorylation inselected spliceosomalproteins during pre-mRNAsplicing. Together withUrlaub they will alsoperform a comparativecharacterization of thephosphoproteome of yeastspliceosomes319 Stamm will identify themechanism by which PP1causes the release of RNAfrom the tra2-beta1 RRM.10 Caceres O CO 5410 Caceres O CO 5410 Caceres O CO 5410 Caceres O CO 5410 Caceres O CO 54243
320 Tazi has identified theDrosophila brain tumor (brat)gene among the proteins thatsuppress the deleteriousdevelopmental effect of B52overexpression. This geneencodes a member of theconserved NHL family ofproteins, which appears toregulate differentiation andgrowth in a variety oforganisms. Current studiesabout the mechanism bywhich Brat interfere with thefunction of B52, revealed thatBrat is required fortranslational repression of theproto-oncogene dmyc, whoseexpression is under thecontrol of B52. Ongoingexperiments are aimed atdeciphering the mechanismby which B52 modulate theexpression of dmyc.321 Srebrow will continue herreseach on the role of Akt as anovel SR protein kinase. Theywill also pursue the study ofthe connection betweenSUMOylation and splicingfactors, focusing on how SRprotein activity regulatesglobal protein SUMOylation.322 Functional analysis of brainamdmuscle-specific isoformsof the splicing regulator Fox-1(month 54)323 Selective targeting of CBP20isoforms to verify if theyprovide an essential function(month 54)324 Targeting of SR proteins totheir own genes (month 54)325 Determine the RNA isoformsgenerated from the snoRNAHBII-52 and determine theirinfluence on six target genes(month 54)326 Functions of adenovirus L4protein isoforms (month 54)327 HITS-CLIP of SF1 isoforms(month 54)328 Analysis of consequences ofalternative splicing upon theactivity of isoforms of ROD1and QKI (month 54)10 Caceres O CO 5410 Caceres O CO 5411 Valcarcel O CO 5411 Valcarcel O CO 5411 Valcarcel O CO 5411 Valcarcel O CO 5411 Valcarcel O CO 5411 Valcarcel O CO 5411 Valcarcel O CO 54244
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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
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alternative splicing.162 Compare sp
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33 Agreement on pre-mRNA substrates
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its numerous binding sites on both
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Work Package 8 Genome-wide Analyses
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173 Further development of data ana
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Problems and explanations for delay
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eveal that there is a dramatic chan
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Work Package 10 Post-translational
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mutational analysis that led to the
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Isolation of an active step I splic
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FBP11 and 21 with these sequences.
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Similarly to what observed for SF2/
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prp45-113 mutant, which is compatib
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cell lines. In contrast in the pres
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genes with roles in the development
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Structural analyses of several RRMs
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Work Package 17 Staff Exchange and
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Barralle's lab, Krämer is acting a
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alternative splicing) and higher ed
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Student Symposium “Decision Makin
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variation and suitability for use w
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Following feedback from members we
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Invited seminars: In addition to me
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Publications 2008Author Title Publi
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Author Title Publication EURASNET P
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Minutes of the General Assembly dec
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241 Evaluate available careerdevelo
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156 The EURASNET memberStamm publis
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y coarse-grained foldingsimulation.
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overexpressor and mutant lines(mont
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machinery with particularrespect to
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alternative splicing, using theEDI
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contemporary findings withinthe EUR
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Licht K, Medenbach J, Lührmann R,K
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9 TABULAR OVERVIEW OF MAJOR COST IT
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total costs * 18.891,12 52778.60 41
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other (the rest) 48,57 0 56.539,43t
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travel 6.964,91overhead 3.081,07oth
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Participant 1A Type of expenditure
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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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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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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
Page 194 and 195: + overhead 4.730= total eligible co
Page 196 and 197: Claudia Tamaro (PhD) has begun work
Page 198 and 199: ETHZIIMCBUPFSOTON-HGDTOTALJoint Pro
Page 200 and 201: Direct eligible costs 53.240,48 0,0
Page 202 and 203: Direct eligible costs 18.720,07 0,0
Page 204 and 205: 13 REPORT ON THE DISTRIBUTION OF TH
Page 206 and 207: Report on the Distribution of the C
Page 208 and 209: For most work packages here follows
Page 210 and 211: pathways (eg, Reactome ).While PAND
Page 212 and 213: The possible dependence of the effe
Page 214 and 215: In some treatments or mutants, simi
Page 216 and 217: Work Package 12: Mis-splicing and D
Page 218 and 219: acid. Furthermore, using antibodies
Page 220 and 221: At the 2007 annual meeting in Ile d
Page 222 and 223: Partner 13 has extensively studied
Page 224 and 225: inhibitors/modulators of RNA splici
Page 226 and 227: 18 MONTH JPA: WORKPACKAGE TIMECOURS
Page 228 and 229: 15.3 GRAPHICAL PRESENTATION OF WORK
Page 230 and 231: 15.4 TABLE OF MILESTONES (MONTH 37-
Page 232 and 233: 156 The EURASNET memberStamm publis
Page 234 and 235: 194 Bertrand will analyze indetail
Page 236 and 237: 216 Aubeouf and Neugebauer willcoll
Page 238 and 239: 238 Establishing joint PhDcommittee
Page 240 and 241: 283 A unified browser for allknown
Page 242 and 243: 296 Group 12a (Branlant) willuse th
Page 246 and 247: 329 GROUP 7 (F. BARALLE)will contin
Page 248 and 249: 333 GROUP 27 (GABELLINI)will:1) foc
Page 250 and 251: 345 Schümperli’s group isplannin
Page 252 and 253: 366 Quarterly network e-mail atmont
Page 254 and 255: 2. Sharing Resources, Technology an
Page 256 and 257: 5. Ensuring DurabilityWorkpackage d
Page 258 and 259: 7. Molecular Characterization of Sp
Page 260 and 261: 8. Genome-wide Analyses of Splicing
Page 262 and 263: 9. Complexity of Spliceosomal Prote
Page 264 and 265: 202 Srebrow will investigate the ro
Page 266 and 267: 12. Mis-splicing and DiseaseWorkpac
Page 268 and 269: 13. Co-transcriptional Mechanisms o
Page 270 and 271: 14. Chemical Biology and Therapeuti
Page 272 and 273: 15. Development of Enabling Technol
Page 274 and 275: 269 IFMs in 20091. “Alternative a
Page 276 and 277: 18. Career DevelopmentWorkpackage d
Page 278 and 279: 20. SMEs and Technology TransferWor
Page 280 and 281: 21. Reachout to the Broader RNA Com
Page 282 and 283: 15.7 WORK PACKAGE LIST (MONTHS 37-5
Page 284 and 285: ETHZIIMCBUPFSOTON-HGDTOTALJoint Pro
Page 286 and 287: AMU 5 29 8 42UAAR 5 145 16 1665 29
Page 288 and 289: Joint Programme of Activities RESEA
Page 290 and 291: 60 month period 18 month periodRequ
Page 292 and 293: 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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