PDF file: EURASNET Annual Report 2008

automated methods to update thepredictions as more genomesand transcripts becomeavailable. Finally, they willdevelop methods to relatechanges in mRNA expression tochanges in the expression ofmiRNAs (month 42).161 The Bork lab will finalize avisualization tool that candisplay and integrate variousdatasets (EST, cDNA genomicDNA etc) and computes splicepaths through the correspondingproteins. They will also examinea network of genomic sequencemotifs involved in alternativesplicing which includesprediction and validation of newalternative splicing variants(month 42).162 The Ast lab will compare splicesites and splicing factors thatbind these sites among the entireeukaryotic kingdom (incollaboration with Eyras). Theywill compare the evolution ofgenes, exon-intron structure,intron gain and loss, and theeffect of transposed elements invertebrates and invertebrates(month 42).163 The Eyras group in collaborationwith the Smith group will studythe splicing regulation of intronsin which the branch sitesequence located more than 100nucleotides from the 3’ss. Theywill use comparative methods toextract possible regulatorysequences and secondarystructres that may be involved inthe regulation. They will alsoidentify the cases that are relatedto disease. In colaboration withthe Ast group they will comparethe splicing mechanism ineukaryotes. Using multipleeukaryotic species, they willcompare the properties ofprotein factors and snRNAsinvolved in splicing. They willinvestigate the role of the SRand hnRNPs proteins in theorigin of regulated splicing(month 42).164 The Bujnicki lab will develop aprototype version of templatebasedmethod for RNA 3Dstructure prediction by fragmentmatching and a prototypeversion of template-free methodfor RNA 3D structure prediction6 42 36 Ast6 42 42 Ast6 42 40 Ast6 42 36 Ast98