RNA processing group

Research topics

RNA, or ribonucleic acid, is a key molecule involved in the synthesis of proteins. Phytohormones, on the other hand, are chemical signaling molecules that help coordinate various aspects of plant growth and development. These two worlds have been, so far, little connected. We are a small team using the expertise of the whole lab to illustrate the importance of this link.

We have previously identified the Arabidopsis factors (writers) required for the m6A methylation of mRNA (Ruzicka et al., 2017). Currently, we are investigating the molecular mechanism(s) underlying the role of m6A in auxin-dependent processes (Zemlyanskaya et al., unpublished). We have also recently uncovered how alternative splicing interferes with the major auxin transporter PIN7 (Kashkan et al., 2022c,b), currently seeking the upstream cues regulating this process. Furthermore, we also explore how AS interferes with the signaling pathways of abscisic acid (Timofeyenko et al., unpublished). We have also developed some tools. First, a box where the temporal dynamics of seedling morphology can be monitored under various light conditions or even in the dark (Kashkan et al., 2022a). Second, a machine-learning algorithm allowing for evolutional analysis of protein splice isoforms, even with a user-friendly interface (Timofeyenko et al., 2023, catsnap.cesnet.cz).


Kamil Růžička


Elena Zemlyanskaya

PhD student

Ksenia Timofeyenko

PhD student

Anastasiia Holoborodko

Master student

Key publications

Timofeyenko K, Kanavalau D, Alexiou P, Kalyna M, Růžička K. 2023. Catsnap: a user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing. New Phytologist 238(4):1722-1732. DOI: 10.1111/nph.18799

Kashkan I, García-González J, Lacek J, Müller K, Růžička K, Retzer K, Weckwerth W. 2022a. RaPiD-chamber: Easy to self-assemble live-imaging chamber with adjustable LEDs allows to track small differences in dynamic plant movement adaptation on tissue level. bioRxiv: 2022.08.13.503848. DOI: 10.1101/2022.08.13.503848

Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková Z, Simon S, Rombaut D, Jacobs TB, et al. 2022b. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist 233: 329–343. DOI: 10.1111/nph.17792

Kashkan I, Timofeyenko K, Růžička K. 2022c. How alternative splicing changes the properties of plant proteins. Quantitative Plant Biology 3. DOI: 10.1017/qpb.2022.9

Ruzicka K, Zhang M, Campilho A, Bodi Z, Kashif M, Saleh M, Eeckhout D, El-Showk S, Li H, Zhong S, et al. 2017. Identification of Factors Required for m6A mRNA Methylation in Arabidopsis Reveals a Role for the Conserved E3 Ubiquitin Ligase HAKAI. New Phytologist 215: 157–172. DOI: 10.1111/nph.14586

Hrtyan M, Šliková E, Hejátko J, Růžička K. 2015. RNA processing in auxin and cytokinin pathways. Journal of Experimental Botany 66: 4897–4912. DOI: 10.1093/jxb/erv189

Ruzicka K, Strader LC, Bailly A, Yang H, Blakeslee J, Langowski L, Nejedlá E, Fujita H, Itoh H, Syono K, et al. 2010. Arabidopsis PIS1 encodes the ABCG37 transporter of auxinic compounds including the auxin precursor indole-3-butyric acid. Proceedings of the National Academy of Sciences of the United States of America 107: 10749–10753. DOI: 10.1073/pnas.1005878107

Ruzicka K, Simásková M, Duclercq J, Petrásek J, Zazímalová E, Simon S, Friml J, Van Montagu MCE, Benková E. 2009. Cytokinin regulates root meristem activity via modulation of the polar auxin transport. Proceedings of the National Academy of Sciences of the United States of America 106: 4284–4289. DOI: 10.1073/pnas.0900060106

Ruzicka K, Ljung K, Vanneste S, Podhorská R, Beeckman T, Friml J, Benková E. 2007. Ethylene regulates root growth through effects on auxin biosynthesis and transport-dependent auxin distribution. The Plant Cell 19: 2197–2212. DOI: 10.1105/tpc.107.052126

Notable alumni

Ivan Kashkan, PhD student, Photon Systems Instruments spol. s r.o.



Catsnap released! You can check the evolutionary conservation of your plant and animal splice isoforms on catsnap.cesnet.cz. Read more on: Timofeyenko et al. (2023) 10.1111/nph.18799.


This is an exciting week. We got funding again! Three-years GACR project awarded!


We got funding! Important Ministry of Education project awarded!