Alternative Splicing; Circadian Clocks; Gene Expression Profiling; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Light Signal Transduction; RNA Processing, Post-Transcriptional; RNA Splicing; Spliceosomes; Transcriptome
My research focus is on RNA Biology how the fate and function of RNAs influences gene expression. In particular, in the past years our focus has been on alternative splicing as one of the posttranscriptional events to expand the repertoire of proteins and how this has been exploited for various differentiation processes and for the responses to environmental cues. In plants, the significance of alternative splicing was long underestimated, but we and others have shown that it greatly impacts development and coordinates responses to the environment. We are investigating how alternative splicing factors, in particular the family of SR proteins, influence specific sets of transcripts and how epigenetic factors (DNA and histone modifications) shape the splicing decisions. More specifically, we are determining how light changes alternative splicing as well as alternative splicing modulates the circadian clock. Transcriptome analysis of plant and human tissues have uncovered an unusal splicing event Exitron (exonic intron) splicing where under certain regulated conditions a part of the coding region is spliced out. As many of these Exitron splicing events affect oncogenes and are deregulated in breast cancer we are currently investigating the impact of exitrons in cancer tissues.
Techniques, methods & infrastructure
The lab has access to all infrastructure needed for molecular biology and plant work, an excellent plant facility on campus, Confocal Microscopy, next generation sequencing (Solexa), and Bioinformatics (Center of Integrated Bioinformatics Vienna, CIBIV). The know –how includes Molecular Biology techniques for bacteria, agrobacteria , yeast and plants; techniques for structural characterization of RNAs and determination of binding constants of RNA-protein complexes.
- A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Zhang R, Calixto CPG, Marquez Y, Venhuizen P, Tzioutziou NA, Guo W, Spensley M, Entizne JC, Lewandowska D, Ten Have S, Frei Dit Frey N, Hirt H, James AB, Nimmo HG, Barta A, Kalyna M, Brown JWS. Nucleic Acids Res. 2017 May 19;45(9):5061-5073. doi: 10.1093/nar/gkx267.
- Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity. Marquez Y, Höpfler M, Ayatollahi Z, Barta A, Kalyna M.Genome Res. 2015 Jul;25(7):995-1007.
- RNA in Disease and Development. Barta A, Jantsch MF. RNA Biol. 2017 May 4;14(5):457-459.
- Identification of RNA targets for the nuclear multidomain cyclophilin atCyp59 and their effect on PPIase activity. Bannikova O, Zywicki M, Marquez Y, Skrahina T, Kalyna M, Barta A. Nucleic Acids Res. 2013 Feb 1;41(3):1783-96.
- Gohring, J., Jacak, J. & Barta, A., 2014. Imaging of Endogenous Messenger RNA Splice Variants in Living Cells Reveals Nuclear Retention of Transcripts Inaccessible to Nonsense-Mediated Decay in Arabidopsis. The Plant Cell, 26(2), pp.754-764. Available at: http://dx.doi.org/10.1105/tpc.113.118075.