RNA has puzzled and surprised many generations of scientists as a molecule of unanticipated structural and functional versatility combined with high complexity and dynamic behaviour. Genomics has boosted RNA research in an unforeseen manner as small and large non-protein-coding RNAs were found to regulate gene expression on many unexpected levels. The PhD thesis is an important crossroad in the career of students, as it is the time where science permeates their life and sets the stage for their future. The RNA Biology doctoral program provides the optimal opportunity, conditions and support to embark on an adventure in science in which RNA related problems will challenge and boost their scientific reasoning.
Post-transcriptional processing enlarges gene product numbers encoded by the genome. We are focussing on the question how alternative splicing influences protein diversity and mRNA isoform transcript levels in the model plant Arabidopsis thaliana and how these specifics are regulated by developmental and environmental cues. High through-put RNAseq techniques are used to define the rules and targets of alternative splicing. In addition, we are investigating SR (Ser/Arg) proteins, an important family of splicing factors, and several regulatory proteins like SRPK kinases, helicases and cyclophilins that are essential to drive and regulate the splicing process. Some of the plant SR proteins and cyclophilins are currently characterized in greater detail to elucidate their mechanisms of action in particular during flowering and UV-stress response. Importantly, light signalling pathways and the regulation of alternative splicing events by light are under investigation as they are key in plant development.
Andrea Barta performed her PhD in Biochemistry at the University of Vienna and did a Post-doc at the University of California San Francisco and Santa Cruz. From 1981 on she was an independent group leader at the Medical Faculty at the University of Vienna, now from 2005 at the Max Perutz Labs, Medical University of Vienna. Since 2006 she is leading the structured PhD program in RNA Biology at the Vienna BioCenter.
She is an elected member of EMBO and the Austrian Academy of Sciences, member of the Academy Council, Deputy Chairwoman of the University Council of the University of Veterinary Medicine, Vienna, Deputy Chairwoman of the Senate of the Christian Doppler Society, and President of OPEN SCIENCE – Life Science in Dialog, a Science Communication Society operating the Vienna Open Lab.
Exitrons are exon-like introns located within protein-coding exons. Removal or retention of exitrons through alternative splicing increases proteome complexity and thus adds to phenotypic diversity. Exitron abundance and characteristics are conserved between Arabidopsis and humans. Exitron splicing occurs in many important human protein-coding genes including those involved in cancer.
Alternative splicing may cause retention of complete introns (IR). IR often results in transcripts with signatures for Non-sense Mediated Decay (NMD), however our analyses have shown that they are not degraded by NMD. By using molecular beacons with confocal laser scanning microscopy we show that these IR transcripts stay in the nucleus therefore avoiding NMD in the cytoplasm.
In plants light influences many adaptation processes. Our work shows that light/dark conditions affect alternative splicing of several genes. This requires functional chloroplasts and is also observed in roots when signaling through the photosynthetic tissue is not interrupted. We show that the reduced pool of plastoquinones initiates retrograde signaling regulating nuclear alternative splicing.
In rare cases cyclophilins (peptidyl-prolyl cis/trans isomerases; PPIase) possess an RNA binding domain. Previously, we have identified Cyp59 as a regulator of transcription, changing phosphorylation of Pol II. Here we identify the RNA binding motif of Cyp59 which is highly conserved and present in 70 % of mRNAs. Binding of the RNA motif inhibits PPIase activity in vitro, suggesting an important function in transcription regulation.
The Cyclin Dependent Kinase G group defines a thermo-sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU2AF65A.
Cavallari, Nicola; Nibau, Candida; Fuchs, Armin; Dadarou, Despoina; Barta, Andrea; Doonan, John H
A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing.
Zhang, Runxuan; Calixto, Cristiane P G; Marquez, Yamile; Venhuizen, Peter; Tzioutziou, Nikoleta A; Guo, Wenbin; Spensley, Mark; Entizne, Juan Carlos; Lewandowska, Dominika; Ten Have, Sara; Frei Dit Frey, Nicolas; Hirt, Heribert; James, Allan B; Nimmo, Hugh G; Barta, Andrea; Kalyna, Maria; Brown, John W S
Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity.
Marquez, Yamile; Höpfler, Markus; Ayatollahi, Zahra; Barta, Andrea; Kalyna, Maria
A chloroplast retrograde signal regulates nuclear alternative splicing.
Petrillo, Ezequiel; Herz, Micaela A Godoy; Fuchs, Armin; Reifer, Dominik; Fuller, John; Yanovsky, Marcelo J; Simpson, Craig; Brown, John W S; Barta, Andrea; Kalyna, Maria; Kornblihtt, Alberto R
Andrea Barta is scientific supervisor of the FWF funded Doctoral Program "RNA Biology".
The Group Barta participates in the Special Research Program (SFB) "RNA-Reg - RNA regulation of the transcriptome" funded by the Austrian Science Fund FWF. SFB's are peer-reviewed, highly interactive research networks, established to foster long-term, interdisciplinary co-operation of local research groups working on the frontiers of their thematic areas.
Member and Vice-Chair of the Senate of the Christian Doppler Society a funding agency for translational research.