Results and publications

48. Bobková, Š.; Plechatá, M.; Kovaľ, T.; Šanderová, H.; Blažková, S.; Akçin, R.; Kameník, Z.; Dohnálek, J.; Krásný, L.; Wiedermannová, J. The bacterial phosphotransferase system-mediated rifampicin phosphorylation: ancestral links to rifampicin-inactivating enzyme. Front. Microbiol. 2026, 17:1789656. https://doi.org/10.3389/fmicb.2026.1789656

47. Sudzinová, P.; Knežová Balgová, T.; Bobková, Š.; Schwarz, M.; Krásný, L. Dual-promoter control of gene expression: from transcriptional fine-tuning to antibiotic resistance. Curr. Opin. Microbiol. 2026, 91, 102747. https://doi.org/10.1016/j.mib.2026.102747

46. Sudzinová, P.; Knežová Balgová, T.; Schwarz, M.; Juříková Mikesková, K.; Hegrová, K.; Vítovská, D.; Rawat, P.; Bobková, Š.; Kočárková, V.; Natarajan, S.; Pospíšilová, D.; Křenková, A.; Hubálek, M.; Halada, P.; Barvík, I.; Kovaľ, T.; Dohnálek, J.; Wiedermannová, J.; Šanderová, H.; Krásný, L. Bacteria sense the antibiotic rifampicin through a widespread dual-promoter based alarm system. Nucleic Acids Res. 2026, 54 (2), gkaf1407. https://doi.org/10.1093/nar/gkaf1407

45. Banik, P.; Zimmann, F.; Thakur, P. K.; Dudakova, L.; Večerková, K.; Kostov, O.; Caruthers, M. H.; Kolář, M.; Krejčířová, I.; Vajter, M.; Liskova, P.; Bárta, T.; Staněk, D. Targeted antisense oligonucleotide therapy rescues PRPF31 expression in retinitis pigmentosa caused by a splicing mutation. Mol. Ther. 2026. https://doi.org/10.1016/j.ymthe.2026.05.033

44. Kráľová, Z.; Išler, L.; Volek, M.; Jandová, M.; Kurfürst, J.; Curtis, E. A. Probing the Specificity of Fluorescent Deoxyribozymes Using Single-Step Selections and Machine Learning. ACS Chem. Biol. 2026, 21 (5), 951–959. https://doi.org/10.1021/acschembio.5c00969

43. Jakubec, M.; Svoboda, M.; Kurfürst, J.; Svehlova, K.; Veverka, V.; Curtis, E. A. Chemiluminescent Deoxyribozyme Sensors for DNA-Editing Enzymes. ACS Chem. Biol. 2026, 21 (5), 941–950. https://doi.org/10.1021/acschembio.5c00927

42. Fakih, F.; Nandipati, S.; Kachale, A.; Heller, J.; Žváček, J.; Brázdovič, F.; Al-Chamy, N.; Tripathi, P.; Paris, Z.; Valášek, L. S.; Kolář, M. H.; Yurchenko, V.; Eliáš, M.; Koonin, E. V.; Lukeš, J.; Butenko, A. Frequent occurrence and predicted functions of tRNAs with 4-base-pair anticodon stems in bacteria: extended superwobble hypothesis. Nucleic Acids Res. 2026, 54 (7), gkag327. https://doi.org/10.1093/nar/gkag327

41. Zimmann, F.; Banik, P.; Kubovčiak, J.; Delattre, M.; Thakur, P. K.; Čapek, M.; Kolář, M.; Hrubá, E.; Dobrovolný, R.; Cvačková, Z.; Bárta, T.; Staněk, D. PRPF8-associated retinitis pigmentosa variant induces human neural retina-autonomous photoreceptor defects. Sci. Rep. 2026, 16 (1), 10264. https://doi.org/10.1038/s41598-026-40376-y

40. Obado, S. O.; Fridy, P. C.; Hegedűsová, E.; van Eeuwen, T.; Stein, M. E.; Zhang, W.; Jensen, B. C.; Chung, C.; Brillantes, M.; Glover, L.; Paris, Z.; Chait, B. T.; Field, M. C.; Rout, M. P. Division of labor in trypanosome RNA processing and export through expanded Mex67 paralogs. Nucleic Acids Res. 2026, 54 (1), gkaf1443. https://doi.org/10.1093/nar/gkaf1443

39. Quinodoz, M.; Rodenburg, K.; Cvackova, Z.; Kaminska, K.; de Bruijn, S. E.; Iglesias-Romero, A. B.; Boonen, E. G. M.; Ullah, M.; Zomer, N.; Folcher, M.; et al. De novo and inherited dominant variants in U4 and U6 snRNA genes cause retinitis pigmentosa. Nat. Genet. 2026, 58 (1), 169–179. https://doi.org/10.1038/s41588-025-02451-4

38. Kurfürst, J.; Volek, M.; Samusevich, R.; Pluskal, T.; Curtis, E. A. Using structured libraries, selection, and machine learning to rapidly explore the sequence space of a fluorescent deoxyribozyme. Nucleic Acids Res. 2025, 53 (22), gkaf1348. https://doi.org/10.1093/nar/gkaf1348

37. Thakur, P. K.; Butenko, A.; Karásek, F.; Svobodová, M.; Faktorová, D.; Pavlisková, H.; Varga, V.; Horák, A.; Lukeš, J.; Staněk, D. Splice site diversity and abundance of noncanonical introns in diplonemids (Diplonemea, Euglenozoa). RNA 2025, 31 (12), 1826–1840. http://www.rnajournal.org/cgi/doi/10.1261/rna.080641.125

36. Sanchez-Quirante, T.; Kužmová, E.; Riopedre-Fernandez, M.; Golojuch, S.; Vopálenský, P.; Raindlová, V.; El-Sagheer, A. H.; Brown, T.; Hocek, M. Enzymatic Synthesis of Modified RNA Containing 5-Methyl- or 5-Ethylpyrimidines or Substituted 7-Deazapurines and Influence of the Modifications on Stability, Translation, and CRISPR-Cas9 Cleavage. ACS Chem. Biol. 2025, 20 (11), 2755–2767. https://doi.org/10.1021/acschembio.5c00692

35. D'Halluin, A.; Petráčková, D.; Čurnová, I.; Držmíšek, J.; Čapek, J.; Bouquet, P.; Henin, L.; Antoine, R.; Coutte, L.; Locht, C.; Večerek, B.; Hot, D. An IS element-driven antisense RNA attenuates the expression of serotype 2 fimbriae and the cytotoxicity of Bordetella pertussis. Emerg. Microbes Infect. 2025, 14(1). https://doi.org/10.1080/22221751.2025.2451718

34. Quinodoz, M.; Rodenburg, K.; Cvackova, Z. et al. De novo and inherited dominant variants in U4 and U6 snRNAs cause retinitis pigmentosa. Preprint. medRxiv. 2025. Published 2025 Jan 6. https://doi.org/10.1101/2025.01.06.24317169

33. Chen, C.-W.; Papadopoli, D.; Szkop, K. J.; Guan, B.-J.; Alzahrani, M.; Wu, J.; Jobava, R.; Asraf, M. M.; Krokowski, D.; Vourekas, A.; Merrick, W. C.; Komar, A. A.; Koromilas, A. E.; Gorospe, M.; Payea, M. J.; Wang, F.; Clayton, B. L. L.; Tesar, P. J.; Schaffer, A.; Miron, A.; Bederman, I.; Jankowsky, E.; Vogel, C.; Valášek, L. S.; Dinman, J. D.; Zhang, Y.; Tirosh, B.; Larsson, O.; Topisirovic, I.; Hatzoglou, M. Plasticity of the Mammalian Integrated Stress Response. Nature 2025. https://doi.org/10.1038/s41586-025-08794-6

32. Loughran, G.; Andreev, D. E.; Terenin, I. M.; Olivier Namy; Mikl, M.; Yordanova, M. M.; McManus, C. J.; Firth, A. E.; Atkins, J. F.; Fraser, C. S.; Zoya Ignatova; Iwasaki, S.; Kufel, J.; Larsson, O.; Leidel, S. A.; Mankin, A. S.; Mariotti, M.; Tanenbaum, M. E.; Topisirovic, I.; Vázquez-Laslop, N. Guidelines for Minimal Reporting Requirements, Design and Interpretation of Experiments Involving the Use of Eukaryotic Dual Gene Expression Reporters (MINDR). Nat. Struct. Mol. Biol. 2025, 32, 418–430. https://doi.org/10.1038/s41594-025-01492-x

31. Zimmann, F.; McNicoll, F.; Thakur, P. K.; Blažíková, M.; Kubovčiak, J.; Hernández, C.; Nováková, Z.; Bařinka, C.; Kolář, M.; Staněk, D.; Müller-McNicoll, M.; Zuzana Cvačková. Retinitis Pigmentosa-Linked Mutations Impair the SnRNA Unwinding Activity of SNRNP200 and Reduce Pre-MRNA Binding of PRPF8. Cell. Mol. Life Sci. 2025, 82 (1). https://doi.org/10.1007/s00018-025-05621-z

30. Záhonová, K.; Füssy, Z.; Albanaz, A. T. S.; Butenko, A.; Kachale, A.; Kraeva, N.; Galan, A.; Zakharova, A.; Stojanova, B.; Votýpka, J.; Kostygov, A. Y.; Spodareva, V. V.; Malysheva, M. N.; Frolov, A. O.; Rogozin, I. B.; Paris, Z.; Valášek, L. S.; Yurchenko, V.; Lukeš, J. Comparative Genomic Analysis of Trypanosomatid Protists Illuminates an Extensive Change in the Nuclear Genetic Code. mBio 2025. https://doi.org/10.1128/mbio.00885-25

29. Galan, A.; Kraeva, N.; Kristína Záhonová; Butenko, A.; Alexei Yu Kostygov; Paris, Z.; Jiří Pergner; Bianchi, C.; Fakih, F.; Saura, A.; Lukeš, J.; Yurchenko, V. Converting Blastocrithidia Nonstop, a Trypanosomatid with Non‐Canonical Genetic Code, into a Genetically‐Tractable Model. Mol. Microbiol. 2025. https://doi.org/10.1111/mmi.15365

28. Šinkeviciute, U.; Sanchez-Quirante, T.; Ržánková, S.; Poštová Slavĕtínská, L.; Raindlová, V.; Hocek, M.: Synthesis of 2-Substituted Adenosine Triphosphate Derivatives and their use in Enzymatic Synthesis and Postsynthetic Labelling of RNA. ChemBioChem 2025, e202500241. https://doi.org/10.1002/cbic.202500241

27. Stejskal, S.; Rajecka, V.; Covelo-Molares, H.; Sinigaglia, K.; Brozinova, K.; Kasiarova, L.; Dohnalkova, M.; Reyes-Gutierrez, P. E.; Cahova, H.; Keegan, L. P.; O'Connell, M. A.; Vanacova, S. Global analysis by LC-MS/MS of N6-methyladenosine and inosine in mRNA reveal complex incidence. RNA 2025. https://doi.org/10.1261/rna.080324.124

26. Šoltysová, M.; Güixens-Gallardo, P.; Sieglová, I.; Soldánová, A.; Krejciříková, V.; Fábry, M.; Brynda, J.; Khoroshyy, P.; Hocek, M. and Řezáčová, P.: Using environment-sensitive tetramethylated thiophene-BODIPY fluorophore in DNA probes for studying effector-induced conformational changes of protein-DNA complexes. RSC Chem. Biol. 2025, 6, 376–386. https://doi.org/10.1039/D4CB00260A

25. Ivancová, I.; Sanchez Quirante, T.; Ondruš, M.; Pohl, R.; Vlková, M.; Žilecká, E.; Bouřa, E. and Hocek, M. Enzymatic synthesis of reactive RNA probes containing squaramate-linked cytidine or adenosine for bioconjugations and cross-linking with lysine-containing peptides and proteins. Commun. Chem. 2025, 8, 1. https://doi.org/10.1038/s42004-024-01399-6

24. Sgallová, R.; Volek, M.; Kurfürst, J.; Srb, P.; Veverka, V.; Curtis, E. NMR Screen Reveals the Diverse Structural Landscape of a G‐Quadruplex Library. Chem. Eur. J. 2024. https://doi.org/10.1002/chem.202401437

2‌3. Šoltysová, M.; Řezáčová, P. Structure and Function of Bacterial Transcription Regulators of the SorC Family. Transcription 2024, 1–22. https://doi.org/10.1080/21541264.2024.2387895

22. Spampinato, A.; Leone, D.; Pohl, R.; Tarábek, J.; Šoltysová, M.; Polák, M.; Kádek, A.; Sýkorová, V.; Řezáčová, P.; Hocek, M. ABNOH‐Linked Nucleotides and DNA for Bioconjugation and Cross‐Linking with Tryptophan‐Containing Peptides and Proteins. Chem. Eur. J. 2024, 30 (49). https://doi.org/10.1002/chem.202402151

21. Hashimi, H.; Gahura, O.; Pánek, T. Bringing Together but Staying Apart: Decisive Differences in Animal and Fungal Mitochondrial Inner Membrane Fusion. Biol. Rev. Camb. Philos. Soc. 2024. https://doi.org/10.1111/brv.13168

2‌0. Ishemgulova, A.; Mukhamedova, L.; Trebichalská, Z.; Rájecká, V.; Payne, P.; Šmerdová, L.; Moravcová, J.; Hrebík, D.; Buchta, D.; Škubník, K.; Füzik, T.; Vaňáčová, Š.; Nováček, J.; Plevka, P. Endosome Rupture Enables Enteroviruses from the Family Picornaviridae to Infect Cells. Commun. Biol. 2024, 7 (1). https://doi.org/10.1038/s42003-024-07147-9

19. Dikunova, A.; Noskova, N.; Overbeck, J. H.; Polak, M.; Stelzig, D.; Zapletal, D.; Kubicek, K.; Novacek, J.; Sprangers, R.; Stefl, R. Assembly of the Xrn2/Rat1–Rai1–Rtt103 Termination Complexes in Mesophilic and Thermophilic Organisms. Structure 2024. https://doi.org/10.1016/j.str.2024.11.010

18. Vojtová, J.; Čapek, M.; Willeit, S.; Tomáš Groušl; Věra Chvalová; Kutejová, E.; Vladimír Pevala; Leoš Shivaya Valášek; Rinnerthaler, M. A Fully Automated Morphological Analysis of Yeast Mitochondria from Wide-Field Fluorescence Images. Sci. Rep. 2024, 14 (1). https://doi.org/10.1038/s41598-024-81241-0

17. Zhou, Y.; Ćorović, M.; Hoch-Kraft, P.; Meiser, N.; Mesitov, M.; Körtel, N.; Back, H.; Naarmann-de Vries, I. S.; Katti, K.; Obrdlík, A.; Busch, A.; Dieterich, C.; Vaňáčová, Š.; Hengesbach, M.; Zarnack, K.; König, J. m6A sites in the coding region trigger translation-dependent mRNA decay. Mol. Cell 2024, 84, 4576–4593.e12. https://doi.org/10.1016/j.molcel.2024.10.033

16. Long, Q.; Ajit, K.; Sedova, K.; Haluza, V.; Stefl, R.; Dokaneheifard, S.; Beckedorff, F.; Valencia, Monica G.; Sebesta, M.; Shiekhattar, R.; Gullerova, M. Tetrameric INTS6-SOSS1 complex facilitates DNA:RNA hybrid autoregulation at double-strand breaks. Nucleic Acids Res. 2024, 52, 13036–13056. https://doi.org/10.1093/nar/gkae937

15. Herrmannová, A.; Jelínek, J.; Pospíšilová, K.; Kerényi, F.; Vomastek, T.; Watt, K.; Brábek, J.; Mohammad, M. P.; Wagner, S.; Topisirovic, I.; Valášek, L. S. Perturbations in eIF3 subunit stoichiometry alter expression of ribosomal proteins and key components of the MAPK signaling pathways. eLife 2024. https://doi.org/10.7554/eLife.95846.2

14. Smirnova, A. M.; Herrmannová, A.; Valášek, L. S. Protocol for detecting and quantifying hATF4-HA in non-stress versus stress conditions using automated and quantitative Jess western blotting. STAR Protoc. 2024, 5, 103454. https://doi.org/10.1016/j.xpro.2024.103454

13. Mancini, F.; Cahova, H. The Mysterious World of Non-Canonical Caps – What We Know and Why We Need New Sequencing Techniques. ChemBioChem 2024, e202400604. https://doi.org/10.1002/cbic.202400604

12. Gracias, F.; Pohl, R.; Sýkorová, V.; Hocek, M. Bacteriophage-related epigenetic natural and non-natural pyrimidine nucleotides and their influence on transcription with T7 RNA polymerase. Commun. Chem. 2024, 7, 256. https://doi.org/10.1038/s42004-024-01354-5

11. Kovaľ, T.; Borah, N.; Sudzinová, P.; Brezovská, B.; Šanderová, H.; Vaňková Hausnerová, V.; Křenková, A.; Hubálek, M.; Trundová, M.; Adámková, K.; Dušková, J.; Schwarz, M.; Wiedermannová, J.; Dohnálek, J.; Krásný, L.; Kouba, T. Mycobacterial HelD connects RNA polymerase recycling with transcription initiation. Nat. Commun. 2024, 15, 8740. https://doi.org/10.1038/s41467-024-52891-5

10. Linhartova, K.; Falginella, F. L.; Matl, M.; Sebesta, M.; Vácha, R.; Stefl, R. Sequence and structural determinants of RNAPII CTD phase-separation and phosphorylation by CDK7. Nat. Commun. 2024, 15, 9163. https://doi.org/10.1038/s41467-024-53305-2

9. Jendruchová, K.; Gaikwad, S.; Poncová, K.; Gunišová, S.; Valášek, L. S.; Hinnebusch, A. G. Differential effects of 40S ribosome recycling factors on reinitiation at regulatory uORFs in GCN4 mRNA are not dictated by their roles in bulk 40S recycling. Commun. Biol. 2024, 7, 1083. https://doi.org/10.1038/s42003-024-06761-x

8. Keown, J.; Baazaoui, A.; Šebesta, M.; Štefl, R.; Carrique, L.; Fodor, E.; Grimes, J. M. Structural and functional characterization of the interaction between the influenza A virus RNA polymerase and the CTD of host RNA polymerase II. J. Virol. 2024, 98, e00138-24. https://doi.org/10.1128/jvi.00138-24

7. Potužník, J. F.; Cahova, H. If the 5’ cap fits (wear it) – Non-canonical RNA capping. RNA Biol. 2024, 21, 1–13. https://doi.org/10.1080/15476286.2024.2372138

6. Volek, M.; Kurfürst, J.; Kožíšek, M.; Srb, P.; Veverka, V.; Curtis, E.A. Apollon: a deoxyribozyme that generates a yellow product. Nucleic Acids Res. 2024, gkae490. https://doi.org/10.1093/nar/gkae490

5. Volek, M.; Kurfürst, J.; Drexler, M.; Svoboda, M.; Srb, P.; Veverka, V.; Curtis, E.A. Aurora: a fluorescent deoxyribozyme for high-throughput screening. Nucleic Acids Res. 2024, gkae467. https://doi.org/10.1093/nar/gkae467

4. Šoltysová, M.; Škerlová, J.; Pachl, P.; Škubník, K.; Fábry, M.; Sieglová, I.; Farolfi, M.; Grishkovskaya, I.; Babiak, M.; Nováček, J.; Krásný, L.; Řezáčová, P. Structural characterization of two prototypical repressors of SorC family reveals tetrameric assemblies on DNA and mechanism of function. Nucleic Acids Res. 2024, gkae434. https://doi.org/10.1093/nar/gkae434

3. Benoni, B.; Potužník, J. F.; Škríba, A.; Benoni, R.; Trylcova, J.; Tulpa, M.; Spustová, K.; Grab, K.; Mititelu, M.-B.; Pačes, J.; Weber, J.; Stanek, D.; Kowalska, J.; Bednarova, L.; Keckesova, Z.; Vopalensky, P.; Gahurova, L.; Cahova, H. HIV-1 Infection Reduces NAD Capping of Host Cell snRNA and snoRNA. ACS Chem. Biol. 2024. https://doi.org/10.1021/acschembio.4c00151

2. Brunderová, M.; Havlíček, V.; Matyašovský, J.; Pohl, R.; Poštová Slavětínská, L.; Krömer, M.; Hocek, M. Expedient production of site specifically nucleobase-labelled or hypermodified RNA with engineered thermophilic DNA polymerases. Nat. Commun. 2024, 15, 3054. https://doi.org/10.1038/s41467-024-47444-9

1. Smirnova, A. M.; Hronová, V.; Mohammad, M. P.; Herrmannová, A.; Gunišová, S.; Petráčková, D.; Halada, P.; Coufal, Š.; Świrski, M.; Rendleman, J.; Jendruchová, K.; Hatzoglou, M.; Beznosková, P.; Vogel, C.; Valášek, L. S. Stem-loop-induced ribosome queuing in the uORF2/ATF4 overlap fine-tunes stress-induced human ATF4 translational control. Cell Rep. 2024, 43. https://doi.org/10.1016/j.celrep.2024.113976