Results and publications

20. 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-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. DOI:10.1261/rna.080324.124

19. 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. DOI:10.1016/j.molcel.2024.10.033

18. 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. DOI:10.1093/nar/gkae937

17. Soltysova, M.; Güixens-Gallardo, P.; Sieglová, I.; Soldanova, A.; Krejcirikova, V.; Fábry, M.; Brynda, J.; Khoroshyy, P.; Hocek, M.; Rezacova, P. Using environment-sensitive tetramethylated thiophene-BODIPY fluorophore in DNA probes for studying effector-induced conformational changes of protein-DNA complexes. RSC Chem. Biol. 2024. DOI:10.1039/D4CB00260A

16. 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. DOI:10.7554/eLife.95846.2

15. 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. DOI:10.1016/j.xpro.2024.103454

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

13. 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. DOI:10.1038/s42004-024-01399-6

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. DOI: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. DOI: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. DOI: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. DOI: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. DOI: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. DOI: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. DOI: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. DOI: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. DOI: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. DOI: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. DOI: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. DOI:10.1016/j.celrep.2024.113976