PDF file: EURASNET Annual Report 2008

system, Bindereif incollaboration with StefanKaufmann, Max-Planck-Institutefor Infection Biology, Berlin(month 42).2. ExonArray analysis of thetranscriptome of a mouse modelof breast cancer (Auboeuf,month 36)176 Exon Array (and junction array,if available) microarray analysisof effects of SF1 knockdownupon alternative splicing(Krämer, month 42)177 Validation of array predictionsof AS changes in epithelialmesenchymaltransition,focusing mainly on alternativesplicing of SR-proteinstranscripts (Biamonti, month42).178 We will develop simulations ofalternative splice form samplingto study the theoretical limits ofdeep sequencing approaches toprofiling of alternatively splicedisoforms (Zavolan).179 Application of Roche/454 and/orSolexa/Illumina sequencing forquantitative comparison of HeLacell control and splicingregulator knockdown samples(PTB/nPTB, Smith, Valcarcel,Zavolan; hnRNP-L, Bindereif).(Month 36)180 Application of deep sequencingto CLIP tags of SF1 andU2AF65 (Krämer, month 42)181 Use of CLIP to identify RNAtargets for the shuttling SRprotein SF2/ASF. Use of CLIPwill be complemented withsubcellular fractionation toidentify nuclear, cytoplasmicand polysomal targets (Caceres,month 42).182 Use of CLIP to identify RNAtargets for hnRNP A1. Use ofCLIP will be complementedwith subcellular fractionation toidentify nuclear, cytoplasmicand polysomal targets.Furthermore, we will identifyRNA targets in cells subjected tostress, due to the reported role ofhnRNP A1 in the stress response(Caceres, month 42).184 Continue to complete analysesof Arabidopsis NMD mutantsand hyl1; SR protein8 42 on target Smith8 42 36 Smith8 42 36 Smith8 42 36 Smith8 42 42 Smith8 42 36 Smith8 42 36 Smith8 42 42 Smith100