RNA Biology

Overview

Overview

gene expression regulation, alternative splicing, exitron, splicing factors, Ser/Arg-rich proteins, evolution of splicing, nonsense-mediated mRNA decay, microRNA and artificial microRNA, plant stress response, DNA damage response, RNA-seq, transcript assembly, Arabidopsis thaliana, Physcomitrella patiens, human

Leader: Dr. Maria Kalyna

Projects

Publications

Selected publications:

(2017)

Zhang R, Calixto CP, 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 JW. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Res. 2017 Apr 11. doi: 10.1093/nar/gkx267.

(2016)

Maronova M, Kalyna M. Generating targeted gene knockout lines in Physcomitrella patens to study evolution of stress-responsive mechanisms. Methods Mol Biol.1398:221-34, 2016. doi: 10.1007/978-1-4939-3356-3_18.

(2015)

Brown JW, Simpson CG, Marquez M, Gadd GM, Barta A, Kalyna M. Lost in translation: pitfalls in deciphering plant alternative splicing transcripts. Plant Cell 27:2083-2087, 2015. doi: 10.1105/tpc.15.00572.

Marquez Y, Hopfler M, Ayatollahi Z, Barta A, Kalyna M. Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity. Genome Res 25: 995-1007, 2015. doi: 10.1101/gr.186585.

(2014)

Petrillo E, Godoy Herz MA, Fuchs A, Reifer D, Fuller J, Yanovsky MJ, Simpson C, Brown JW, Barta A, Kalyna M, Kornblihtt AR. A chloroplast retrograde signal regulates nuclear alternative splicing. Science 344: 427-430, 2014. doi: 10.1126/science.1250322.

(2013)

Reddy AS, Marquez Y, Kalyna M, and Barta A. Complexity of the alternative splicing landscape in plants. Plant Cell 25:3657-3683, 2013. doi: 10.1105/tpc.113.117523.

Bielewicz D, Kalak M, Kalyna M, Windels D, Barta A, Vazquez F, Szweykowska-Kulinska Z, Jarmolowski A. Introns of plant pri-miRNAs enhance miRNA biogenesisEMBO Rep 14: 622-628, 2013. doi: 10.1038/embor.2013.62.

Bannikova O, Zywicki M, Marquez Y, Skrahina T, Kalyna M, Barta A. Identification of RNA targets for the nuclear multidomain cyclophilin atCyp59 and their effect on PPIase activity. Nucleic Acids Res 41: 1783-1796, 2013. doi: 10.1093/nar/gks1252.

(2012)

Kalyna M, Simpson CG, Syed NH, Lewandowska D, Marquez Y, Kusenda B, Marshall J, Fuller J, Cardle L, McNicol J, Dinh HQ, Barta A, Brown JW. Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res 40: 2454-2469, 2012. doi: 10.1093/nar/gkr932.

Marquez Y, Brown JW, Simpson C, Barta A, Kalyna M. Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res 22:1184-1195, 2012. doi: 10.1101/gr.134106.111.

Syed NH, Kalyna M, Marquez Y, Barta A, Brown JWS. Alternative splicing in plants – coming of age. Trends in Plant Science 17: 616-623, 2012. doi: 10.1016/j.tplants.2012.06.001

(2010)

Barta A, Kalyna M, Reddy AS. Implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants. Plant Cell 22:2926-2929, 2010. doi: 10.1105/tpc.110.078352.

(2006)

Kalyna M, Lopato S, Voronin V, Barta A. Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins. Nucleic Acids Res. 34:4395-4405, 2006. doi: 10.1093/nar/gkl570.


Funding Agencies

Collaborations

Collaborations (last five years):

  • Andrea Barta, Max F. Perutz Laboratories, Medical University of Vienna, Vienna, Austria
  • John WS Brown, University of Dundee, Dundee, Scotland, UK
  • Artur Jarmolowski, Adam Mickiewicz University, Poznan, Poland
  • Heribert Hirt, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
  • Jürgen Kleine-Vehn, University of Natural Resources and Life Sciences, Vienna, Austria
  • Alberto Kornblihtt, Universidad de Buenos Aires, Buenos Aires, Argentina
  • Marjori Matzke, Institute of Plant and Microbial Biology, Taipei, Taiwan
  • Akila Mayeda, Fujita Health University, Toyoake, Japan
  • Ezequiel Petrillo, Universidad de Buenos Aires, Buenos Aires, Argentina
  • Andreas Sommer, Next Generation Sequencing (NGS) Unit, Vienna Biocenter Core Facilities GmbH, Vienna, Austria 
  • Dorothee Staiger, Universität Bielefeld, Germany
  • Zofia Szweykowska-Kulinska, Adam Mickiewicz University, Poznan, Poland