Regulation of alternative splicing in plants The Kalyna research group at the Department of Applied Genetics and Cell Biology is looking for a highly motivated Master’s student who is interested in RNA biology, alternative splicing, and plant molecular biology. Background:
Alternative splicing results in multiple transcript variants produced from a single gene and is, therefore, a key strategy to increase the diversity of expressed information encoded by eukaryotic genomes. Our research has shown that alternative splicing is far more widespread in plants than previously thought. Deep transcriptome sequencing of the model plant Arabidopsis revealed that two-thirds of intron-containing genes undergo alternative splicing (Marquez et al., Genome Res, 2012; Zhang et al., Nucleic Acids Res. 2017). Closer examination of alternative splicing in Arabidopsis and humans led us to the discovery of an unusual type of introns that we termed exitrons (exonic introns) (Marquez et al., Genome Res, 2012; Marquez et al., Genome Res, 2015; featured in Staiger and Simpson, Genome Biol. 2015, Zlotorynski Nat Rev Mol Cell Biol., 2015, and Sibley et al., Nat Rev Genet., 2016). Exitrons are alternatively spliced internal regions of protein-coding exons and have features of both exons and introns. Many plant and human protein-coding genes contain exitrons. A large proportion of our research has been on the Ser/Arg-rich (SR) proteins, major regulators of alternative splicing. For example, together with our collaborators, we showed that chloroplasts signal the nucleus to change alternative splicing of SR genes in response to light or dark (Petrillo et al., Science 2014). Our current projects aim to find out more about the mechanisms of alternative splicing in plants, regulation of exitrons, and functions of SR proteins in plant development and stress response. Requirements and desired qualifications:
- bachelor (or equivalent) degree in molecular biology or a related area
- high accuracy and reliability
- solid written and oral communication skills in English Ansprechperson: To apply, please send a CV and cover letter to Mariya Kalyna e-mail The position will remain open until it is filled.
Global profiling of cancer-associated exitron splicing (Bioinformatics)
There is an opportunity for or a Master’s thesis in Bioinformatics in the Kalyna research group. We are looking for a highly motivated student who is interested in RNA biology, alternative splicing, and cancer research.
Background:
Alternative splicing is an essential layer of gene regulation. The majority of human and plant multi-exon genes are alternatively spliced producing from two to thousands of transcript and protein variants with different fates and functions from a single gene.
Closer examination of alternative splicing in humans and model plant Arabidopsis led us to the discovery of an unusual type of introns that we termed exitrons (exonic introns) (Marquez et al., Genome Res, 2012; Marquez et al., Genome Res, 2015; featured in Staiger and Simpson, Genome Biol. 2015, Zlotorynski Nat Rev Mol Cell Biol. 2015, and Sibley et al., Nat Rev Genet., 2016). Exitrons are alternatively spliced internal regions of protein-coding exons and have features of both exons and introns. Many human protein-coding genes, including those with reported functions in cancer, contain exitrons. Our finding brings us to the next research aim, which is to investigate mechanistic basis of exitron regulation and to elucidate a link between exitrons and cancer. To this end, together with our Viennese and Japanese collaborators, we perform large-scale bioinformatics analyses of various cancer RNA-seq and exome datasets.
The goal of the Master’s project is to identify and characterize exitrons misregulated in different cancer types. The student will be assisted by an experienced bioinformatician.
Requirements and desired qualifications:
- bachelor (or equivalent) degree in bioinformatics, computational biology or a related area
- high accuracy and reliability
- solid written and oral communication skills in English
Ansprechperson: To apply, please send a CV and cover letter to Mariya Kalyna e-mail
The position will remain open until it is filled.
Epigenetische Regulation ribosomaler RNA
Transcriptome-wide analyses have shown that RNA modifications occur on all major classes of RNA including ribosomal RNA. Recently a member of an evolutionarily conserved family of methyltransferases has been identified in the model plant Arabidopsis thaliana which is responsible to methylate the 25S rRNA of the large ribosomal subunit. With the help of genetic and molecular biological analyses the project analyses the dynamics of rRNA methylation during development and in response to abiotic stressors and aims to reveal the functional role of this epigenetic modification on the translational efficiency, growth and fecundity. Keywords: UV-B, heavy metals, protein synthesis, rRNA, RNA methylation, methyltransferases Ansprechperson: Marie-Theres Hauser e-mail
Untersuchungen über Metallionen induzierten epigenetischen Veränderungen bei Pflanzen Plants are sessile organisms and cannot escape adverse environmental conditions as for example the increase of heavy metals and trace elements in soils due to air pollution but also heavy use of fertilizers and fungicides. In this project the impact on the epigenome should be analyzed upon chronic exposure to elevated concentrations of metal ions. Quantitative gene expression analyses will be combined with experiments using epigenetically silenced reporter lines of the model plant Arabidopsis thaliana.
Keywords: cadmium, nickel, zinc, lead, copper, DNA methylation, chromatin remodeling, small RNA expression, gene silencing Ansprechperson: Marie-Theres Hauser e-mail
