PDF file: EURASNET Annual Report 2008

Participant 8 – Andrea Bartaa) Work performed during the period• WP1The new EURASNET webpage has been launched and contains an area for the Public tounderstand and be informed about alternative splicing. In addition, relevant information aboutalternative splicing and disease is available on this webpage together with a hot topic section.Continuously we are creating and presenting interesting data about alternative splicing on thiswebpage.• WP2The alternative splicing panel for plant genes with about 300 AS events has been shared between thethree plant groups (JB, AB, AJ) and has lead already to interesting results, part of which are published.The protocol has been made available to the member of this network. In addition, plasmids of plantsplicing factors within a range of different vectors and different tags have been deposited in a resourcedata base.• WP4The alternative splicing panel with now about 300 known splicing events was used to test thesesplicing events under different environmental conditions and in various mutant Arabidopsis line. Inparticular, the experiments with mutants in the Non-sense mediated decay (NMD) pathway createdmany new alternative splicing events which were sequenced and annotated. Cloning and sequencing ofthese transcripts is underway and many represent novel, un-annotated AS events reflecting the morewidespread nature of AS in plants and the need for a systematic discovery programme for AS. Aspecific alternative splicing database for plants is now created locally at the Crop Research Institute inDundee (participant 14) for better storage and accessibility.• WP8The RT-PCR alternative splicing panel for plants, which had been expanded to more than 300 splicingevents was used for analysis of plants overexpression (GOF) and mutant (LOF) in various SR proteins.In particular, Arabidopsis splicing factors SRp30, RSp31, RSp32, RS2Z33 and RS2Z32 were tested onthis panel. In addition, plants treated with cycloheximide and mutants in the non-sense mediated decaypathway, ubf1 and ubf3 were tested on this panel. Thus far, around 15-20% of the transcripts studiedmay be turned over by NMD.. We also used the overexpression lines of the Arabidopsis SR proteinsfor Affymetrix gene chip analysis. The results of the SR protein experiments showed changing ASevents in genes which are in pathways which were suspected to be effected by AS through the plantphenotype.• WP9The four members of the Arabidopsis SRPK kinase family belonging to two different subfamilies weretested for their expression pattern and for their activity towards various SR proteins. The differencesseen in the in vitro assay are now being related to certain in vivo experiments where thephospoproteom of Arabidopsis has been analysed.• WP11Now knock-out mutants of the RSp and RSZ protein families in the moss Physcomitrella have beenisolated and characterization of the mutants on the phenotypical as well as on the molecular level areunderway.In addition, Genomic SELEX experiments have been started to define the binding partners of plant SRproteins, which should help to define their activity.• WP19Webpage for science and society issues.We were working together with JBr (14) on the development of the new hompage and have been responsible forfilling the homepage with contribution designed for the public. In particular, we focused on the importance of146