Publications

2025

• Dikunova, A; Noskova, N; Overbeck, JH; Polak, M; Stelzig, D; Zapletal, D; Kubicek, K; Novacek, J; Sprangers, R; Stefl, R, 2025: Assembly of the Xrn2/Rat1-Rai1-Rtt103 termination complexes in mesophilic and thermophilic organisms. STRUCTURE 33(2), doi: 10.1016/j.str.2024.11.010

2024

• Linhartova, K; Falginella, FL; Matl, M; Sebesta, M; Vacha, R; Stefl, R, 2024: Sequence and structural determinants of RNAPII CTD phase-separation and phosphorylation by CDK7. NATURE COMMUNICATIONS 15(1), doi: 10.1038/s41467-024-53305-2
• Ishemgulova, A; Mukhamedova, L; Trebichalská, Z; Rájecká, V; Payne, P; Smerdová, L; Moravcová, J; Hrebik, D; Buchta, D; Skubnik, K; Füzik, T; Vanácová, S; Novacek, J; Plevka, P, 2024: Endosome rupture enables enteroviruses from the family Picornaviridae to infect cells. COMMUNICATIONS BIOLOGY 7(1), doi: 10.1038/s42003-024-07147-9
• Keown, J; Baazaoui, A; Sebesta, M; Stefl, R; Carrique, L; Fodor, E; Grimes, JM, 2024: Structural and functional characterization of the interaction between the influenza A virus RNA polymerase and the CTD of host RNA polymerase II. JOURNAL OF VIROLOGY , doi: 10.1128/jvi.00138-24

2023

• Hasanova, Z; Klapstova, V; Porrua, O; Stefl, R; Sebesta, M, 2023: Human senataxin is a bona fide R-loop resolving enzyme and transcription termination factor. NUCLEIC ACIDS RESEARCH , doi: 10.1093/nar/gkad092
• Zapletal, D; Kubicek, K; Svoboda, P; Stefl, R, 2023: Dicer structure and function: conserved and evolving features. EMBO REPORTS 24(7), doi: 10.15252/embr.202357215
• Papageorgiou, AC; Pospisilova, M; Cibulka, J; Ashraf, R; Waudby, CA; Kaderávek, P; Maroz, V; Kubicek, K; Prokop, Z; Krejci, L; Tripsianes, K, 2023: Recognition and coacervation of G-quadruplexes by a multifunctional disordered region in RECQ4 helicase. NATURE COMMUNICATIONS 14(1), doi: 10.1038/s41467-023-42503-z

2022

• Zapletal, D; Taborska, E; Pasulka, J; Malik, R; Kubicek, K; Zanova, M; Much, C; Sebesta, M; Buccheri, V; Horvat, F; Jenickova, I; Prochazkova, M; Prochazka, J; Pinkas, M; Novacek, J; Joseph, DF; Sedlacek, R; Bernecky, C; O´Carroll, D; Stefl, R; Svoboda, P, 2022: Structural and functional basis of mammalian microRNA biogenesis by Dicer. MOLECULAR CELL 82(21), p. 4064 - +, doi: 10.1016/j.molcel.2022.10.010
• Kasiliauskaite, A; Kubicek, K; Klumpler, T; Zanova, M; Zapletal, D; Koutna, E; Novacek, J; Stefl, R, 2022: Cooperation between intrinsically disordered and ordered regions of Spt6 regulates nucleosome and Pol II CTD binding, and nucleosome assembly. NUCLEIC ACIDS RESEARCH 50(10), p. 5961 - 5973, doi: 10.1093/nar/gkac451

2021

• Appel, LM; Franke, V; Bruno, M; Grishkovskaya, I; Kasiliauskaite, A; Kaufmann, T; Schoeberl, UE; Puchinger, MG; Kostrhon, S; Ebenwaldner, C; Sebesta, M; Beltzung, E; Mechtler, K; Lin, G; Vlasova, A; Leeb, M; Pavri, R; Stark, A; Akalin, A; Stefl, R; Bernecky, C; Djinovic-Carugo, K; Slade, D, 2021: PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. NATURE COMMUNICATIONS 12(1), doi: 10.1038/s41467-021-26360-2

2020

• Han, Z; Jasnovidova, O; Haidara, N; Tudek, A; Kubicek, K; Libri, D; Stefl, R; Porrua, O, 2020: Termination of non-coding transcription in yeast relies on both an RNA Pol II CTD interaction domain and a CTD-mimicking region in Sen1. EMBO JOURNAL , doi: 10.15252/embj.2019101548
• Brazda, P; Krejcikova, M; Kasiliauskaite, A; Smirakova, E; Klumpler, T; Vacha, R; Kubicek, K; Stefl, R, 2020: Yeast Spt6 Reads Multiple Phosphorylation Patterns of RNA Polymerase II C-Terminal Domain In Vitro. JOURNAL OF MOLECULAR BIOLOGY 432(14), p. 4092 - 4107, doi: 10.1016/j.jmb.2020.05.007

2019

• Brazda, P; Sedo, O; Kubicek, K; Stefl, R, 2019: Efficient and robust preparation of tyrosine phosphorylated intrinsically disordered proteins. BIOTECHNIQUES 67(1), p. 16 - 22, doi: 10.2144/btn-2019-0033

2017

• Jasnovidova, O; Krejcikova, M; Kubicek, K; Stefl, R, 2017: Structural insight into recognition of phosphorylated threonine-4 of RNA polymerase II C-terminal domain by Rtt103p. EMBO REPORTS 18(6), p. 906 - 913, doi: 10.15252/embr.201643723
• Jasnovidova, O; Klumpler, T; Kubicek, K; Kalynych, S; Plevka, P; Stefl, R, 2017: Structure and dynamics of the RNAPII CTDsome with Rtt103. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 114(42), p. 11133 - 11138, doi: 10.1073/pnas.1712450114

2016

• Kubicek, K; Krejcikova, M; Brazda, P; Smirakova, E; Novacek, J; Cramer, P; Stefl, R, 2016: What are the key aspects of interaction between RNA polymerase II C-terminal domain phosphorylated on tyrosine-1 and the elongation factors. FEBS JOURNAL 283, p. 21 - 21
• Jasnovidova, O; Krejcikova, M; Kubicek, K; Stefl, R, 2016: Recognition of phosphorylated threonine-4 of RNA polymerase II C-terminal domain by 3 ´-end processing apparatus. FEBS JOURNAL 283, p. 208 - 209

2015

• Hrossova, D; Sikorsky, T; Potesil, D; Bartosovic, M; Pasulka, J; Zdrahal, Z; Stefl, R; Vanacova, S, 2015: RBM7 subunit of the NEXT complex binds U-rich sequences and targets 3 ´-end extended forms of snRNAs. NUCLEIC ACIDS RESEARCH 43(8), p. 4236 - 4248, doi: 10.1093/nar/gkv240
• Krepl, M; Havrila, M; Stadlbauer, P; Banas, P; Otyepka, M; Pasulka, J; Stefl, R; Sponer, J, 2015: Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?. JOURNAL OF CHEMICAL THEORY AND COMPUTATION 11(3), p. 1220 - 1243, doi: 10.1021/ct5008108

2014

• Tudek, A; Porrua, O; Kabzinski, T; Lidschreiber, M; Kubicek, K; Fortova, A; Lacroute, F; Vanacova, S; Cramer, P; Stefl, R; Libri, D, 2014: Molecular Basis for Coordinating Transcription Termination with Noncoding RNA Degradation. MOLECULAR CELL 55(3), p. 467 - 481, doi: 10.1016/j.molcel.2014.05.031
• Bacikova, V; Pasulka, J; Kubicek, K; Stefl, R, 2014: Structure and semi-sequence-specific RNA binding of Nrd1. NUCLEIC ACIDS RESEARCH 42(12), p. 8024 - 8038, doi: 10.1093/nar/gku446

2013

• Jasnovidova, O; Stefl, R, 2013: The CTD code of RNA polymerase II: a structural view. WILEY INTERDISCIPLINARY REVIEWS-RNA 4(1), p. 1 - 16, doi: 10.1002/wrna.1138

2012

• Holub, P; Lalakova, J; Cerna, H; Pasulka, J; Sarazova, M; Hrazdilova, K; Arce, MS; Hobor, F; Stefl, R; Vanacova, S, 2012: Air2p is critical for the assembly and RNA-binding of the TRAMP complex and the KOW domain of Mtr4p is crucial for exosome activation. NUCLEIC ACIDS RESEARCH 40(12), p. 5679 - 5693, doi: 10.1093/nar/gks223
• Kubicek, K; Cerna, H; Holub, P; Pasulka, J; Hrossova, D; Loehr, F; Hofr, C; Vanacova, S; Stefl, R, 2012: Serine phosphorylation and proline isomerization in RNAP II CTD control recruitment of Nrd1. GENES & DEVELOPMENT 26(17), p. 1891 - 1896, doi: 10.1101/gad.192781.112
• Sikorsky, T; Hobor, F; Krizanova, E; Pasulka, J; Kubicek, K; Stefl, R, 2012: Recognition of asymmetrically dimethylated arginine by TDRD3. NUCLEIC ACIDS RESEARCH 40(22), p. 11748 - 11755, doi: 10.1093/nar/gks929
• Porrua, O; Hobor, F; Boulay, J; Kubicek, K; D´Aubenton-Carafa, Y; Gudipati, RK; Stefl, R; Libri, D, 2012: In vivo SELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1-dependent transcription termination. EMBO JOURNAL 31(19), p. 3935 - 3948, doi: 10.1038/emboj.2012.237

2011

• Hobor, F; Pergoli, R; Kubicek, K; Hrossova, D; Bacikova, V; Zimmermann, M; Pasulka, J; Hofr, C; Vanacova, S; Stefl, R, 2011: Recognition of Transcription Termination Signal by the Nuclear Polyadenylated RNA-binding (NAB) 3 Protein. JOURNAL OF BIOLOGICAL CHEMISTRY 286(5), p. 3645 - 3657, doi: 10.1074/jbc.M110.158774

2010

• Richard Stefl, Florian C. Oberstrass, Jennifer L. Hood, Muriel Jourdan, Michal Zimmermann, Lenka Skrisovska, Christophe Maris, Li Peng, Ctirad Hofr, Ronald B. Emeson, Frédéric H.-T. Allaine, 2010: The solution structure of the ADAR2 dsRBM-RNA complex reveals a sequence-specific read out of the minor groove. CELL 143(2), p. 225 - 237, doi: 10.1016/j.cell.2010.09.026