Publications

2025

Hlavata A, Neuditschko B, Schellhaas U, Plaschka C, Herzog F, Bernecky C. Structure of cytoplasmic RNA polymerase II. PrePrint @ bioRxiv; 2025. doi: https://doi.org/10.64898/2025.12.10.692585.

Wray-McCann G, Michalík D, McAllan AL, Gearing LJ, Liou RH, Campbell NK, Straub S, Hosseni-Far H, Matthews A, Tate MD, Davidson S, Fisher R, Bernecky C, Rehwinkel J, Hertzog PJ, Sampaio NG. Annexin A2 mediates RIG-I-like receptor responses to viral infection. PrePrint @ bioRxiv; 2025. doi: 10.1101/2025.10.28.684968.

Varada R, Leuchtenberger A, Vesely C, Kaczmarek B, Khosravi HM, Mandl T, Milanovic K, Tamizkar KH, Rajendra V, Senoner H, Steinbichl L, Borojevic M, Sombke A, Schmidt K, Eckhard M, Hofacker I, Walkley C, Heraud-Farlow J, Picardi E, Bernecky C, Jantsch M. Distinguishing self from non-self RNA by editing-specific inosine patterns. PrePrint @ Research Square; 2025. doi: 10.21203/rs.3.rs-6579710/v1.

Bernecky C. Understanding the machinery that reads the genome. Nature Reviews Molecular Cell Biology. Mar 28, 2025. doi: 10.1038/s41580-025-00844-1.

Rosani U, Altan N, Venier P, Bortoletto E, Volpi N, Bernecky C. Ancestral Origin and Functional Expression of a Hyaluronic Acid Pathway Complement in Mussels. Biology (Basel). 2025 Jul 24;14(8):930. doi: 10.3390/biology14080930.

Tlučková K, Kaczmarek B, Salmazo A, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. Nat Struct Mol Biol. 2025 Apr;32(4):607-612. doi: 10.1038/s41594-024-01448-7.

2024

Ramadhin AR, Lee SH, Zhou D, Salmazo A, Gonzalo-Hansen C, van Sluis M, Blom CMA, Janssens RC, Raams A, Dekkers D, Bezstarosti K, Slade D, Vermeulen W, Pines A, Demmers JAA, Bernecky C, Sixma TK, Marteijn JA. STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment. Mol Cell. 2024 Nov 13:S1097-2765(24)00870-0. doi: 10.1016/j.molcel.2024.10.030.

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. Structural and functional basis of mammalian microRNA biogenesis by Dicer. Mol Cell. 2022 Nov 3;82(21):4064-4079.e13. doi: 10.1016/j.molcel.2022.10.010.

Daiß JL, Pilsl M, Straub K, Bleckmann A, Höcherl M, Heiss FB, Abascal-Palacios G, Ramsay EP, Tlučková K, Mars JC, Fürtges T, Bruckmann A, Rudack T, Bernecky C, Lamour V, Panov K, Vannini A, Moss T, Engel C. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. Life Sci Alliance. 2022 Sep 1;5(11):e202201568. doi: 10.26508/lsa.202201568.

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. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nat Commun. 2021 Oct 19;12(1):6078. doi: 10.1038/s41467-021-26360-2.

Pre-ISTA

Bernecky C, Plitzko JM, Cramer P. Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp. Nat Struc Mol Biol. 2017 Sep 11. doi: 10.1038/nsmb.3465.

Xu Y, Bernecky C, Lee CT, Maier KC, Schwalb B, Tegunov D, Plitzko JM, Urlaub H, Cramer P. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nat Commun. 2017 Jun 6;8:15741. doi: 10.1038/ncomms15741.

Engel C, Gubbey T, Neyer S, Sainsbury S, Oberthuer C, Baejen C, Bernecky C, Cramer P.  Structural Basis of RNA Polymerase I Transcription Initiation. Cell. 2017 Mar 23;169(1):120-131.e22. doi: 10.1016/j.cell.2017.03.003.

Bernecky C, Herzog F, Baumeister W, Plitzko JM, Cramer P. Structure of transcribing mammalian RNA polymerase II. Nature. 2016 Jan 28;529(7587):551-4. doi: 10.1038/nature16482.

Sainsbury S*, Bernecky C*, Cramer P. Structural basis of transcription initiation by RNA polymerase II. *These authors contributed equally to this work. Nat Rev Mol Cell Biol. 2015 Mar;16(3):129-43. doi: 10.1038/nrm3952.

Bernecky C, Cramer P. Struggling to let go: a non-coding RNA directs its own extension and destruction. EMBO J. 2013 Mar 20;32(6):771-2. doi: 10.1038/emboj.2013.36.

Bernecky C, Taatjes DJ. Activator-mediator binding stabilizes RNA polymerase II orientation within the human mediator-RNA polymerase II-TFIIF assembly. J Mol Biol. 2012 Apr 13;417(5):387-94. doi: 10.1016/j.jmb.2012.02.014.

Bernecky C, Grob P, Ebmeier CC, Nogales E, Taatjes DJ. Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly. PLoS Biol. 2011 Mar;9(3):e1000603. doi: 10.1371/journal.pbio.1000603.

Meyer KD, Lin SC, Bernecky C, Gao Y, Taatjes DJ. p53 activates transcription by directing structural shifts in Mediator. Nat Struct Mol Biol. 2010 Jun;17(6):753-60. doi: 10.1038/nsmb.1816.

Knuesel MT, Meyer KD, Bernecky C, Taatjes DJ. The human CDK8 subcomplex is a molecular switch that controls Mediator coactivator function. Genes Dev. 2009 Feb 15;23(4):439-51