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What determines the complexity of higher organisms? No correlation has been found to DNA content and gene number and therefore studies in the field are now focusing on post-transcriptional processes and the impact of the dynamic transcriptome on gene expression. We are focussing on the questions , 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.
In plants, the significance of alternative splicing was long underestimated, but we and others have shown that it greatly impacts on development and response to the environment. We therefore are using high through-put RNAseq techniques 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. To elucidate their mechanisms of action some of the plant SR proteins and cyclophilins are currently characterized in greater detail in terms of their RNA targets, interacting proteins and their impact on alternative splicing and gene expression, 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.
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.
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
Localization and dynamics of plant splicing regulators
A.S.N. Reddy,Irene S. Day, Janett Göhring and Andrea Barta
Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis.
Kalyna, Maria; Simpson, Craig G; Syed, Naeem H; Lewandowska, Dominika; Marquez, Yamile; Kusenda, Branislav; Marshall, Jacqueline; Fuller, John; Cardle, Linda; McNicol, Jim; Dihn, Huy Q; Barta, Andrea; Brown, John W S
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.