PDF file: EURASNET Annual Report 2008

Work Package 6 In silico approaches to alternative splicingLead Participant: Gil Astdeliverables: N6 Computational structural model of splicing regulatorshnRNP-L and hnRNP-L-like in complex with RNA (month30)N7 Computational modeling and experimental testing of novelRNA binding domains (month 30)159 The Stamm lab will experimentally validated snoRNAtarget predictions generated by the Zavolan lab. This willbe performed to identify the cis-elements that control HBII-52-dependent alternative splicing. The algorithm todetermine snoRNA tartgets will be used with two othersnoRNAs in the Prader-Willi critical region, HBII-438 andHBII-85. In addition, the algorithm to predict singlestrandednesswill be implemented in a suitable databaseand combined with binding motifs to analyse DNA arrayresults for tra2-beta1 (month 42).160 The Zavolan lab implemented a snoRNA-mRNA bindingmodel, and applied this method to the prediction ofsnoRNA targets in mouse (in collaboration with Stamm).They will apply this method to other systems such asplants. These latter predictions will be tested by the Brownlab in the plant Arabidopsis thaliana. In addition they willimprove the quality of the miRNA target predictions, andwill develop automated methods to update the predictionsas more genomes and transcripts become available. Finally,they will develop methods to relate changes in mRNAexpression to changes in the expression of miRNAs (month42).161 The Bork lab will finalize a visualization tool that candisplay and integrate various datasets (EST, cDNAgenomic DNA etc) and computes splice paths through thecorresponding proteins. They will also examine a networkof genomic sequence motifs involved in alternative splicingwhich includes prediction and validation of new alternativesplicing variants (month 42).162 The Ast lab will compare splice sites and splicing factorsthat bind these sites among the entire eukaryotic kingdom(in collaboration with Eyras). They will compare theevolution of genes, exon-intron structure, intron gain andloss, and the effect of transposed elements in vertebratesand invertebrates (month 42).163 The Eyras group in collaboration with the Smith group willstudy the splicing regulation of introns in which the branchsite sequence located more than 100 nucleotides from the3’ss. They will use comparative methods to extractpossible regulatory sequences and secondary structres thatmay be involved in the regulation. They will also identifythe cases that are related to disease. In colaboration withthe Ast group they will compare the splicing mechanism ineukaryotes. Using multiple eukaryotic species, they willcompare the properties of protein factors and snRNAsinvolved in splicing. They will investigate the role of theSR and hnRNPs proteins in the origin of regulated splicing(month 42).164 The Bujnicki lab will develop a prototype version oftemplate-based method for RNA 3D structure prediction bymonthplanned achieved30 3030 3042 3642 4242 3642 4242 4042 3630