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Clemens Plaschka

Messenger RNA (mRNA) maturation is a crucial step in gene expression, requiring the coordinated action of multiple cellular machines. These machines make dramatic changes to the mRNA, the mRNA-bound proteins, and ultimately prepare mature mRNA for export from nucleus to cytoplasm. We apply structural and functional methods to reveal the molecular basis of human mRNA biogenesis and the coordination between maturation events. Our goal is to understand how an mRNA is made.

Publications

2026

Navalayeu, T., Beer, N., Bebjaková, M., Kalis, RW., Hohmann, U., Stejskal, K., Krššáková, G., Fasching, N., Herzog, VA., Popitsch, N., Roitinger, E., Plaschka, C., Zuber, J., Ameres, SL. (2026)

Cellular assembly and functional resilience of the mammalian RNA exosome.

 EMBO J. 45(15):5423-5456
Bugai, A., Hohmann, U., Lorenzo, A., Graf, M., Fin, L., Rouvière, JO., Tirian, L., Dou, Y., Le Rest, M., Polák, P., Johnsen, D., Jakobsen, L., Andersen, JS., Brennecke, J., Plaschka, C., Jensen, TH. (2026)

Molecular basis of polyadenylated RNA fate determination in the nucleus.

 Nature. 655(8124):1070-1078
Hlavata, A., Neuditschko, B., Schellhaas, U., Plaschka, C., Herzog, F., Bernecky, C. (2026)

Structure of cytoplasmic RNA polymerase II.

 Nat Commun.

2025

Hohmann, U., Graf, M., Tirián, L., Pacheco-Fiallos, B., Schellhaas, U., Fin, L., Handler, D., Phillips, AW., Riabov-Bassat, D., Faraway, R., Pühringer, T., Szalay, MF., Roitinger, E., Brennecke, J., Plaschka, C. (2025)

An ATP-gated molecular switch orchestrates human mRNA export

 Nature. 649(8098):1042-1050
Faraway, R., Costello Heaven, N., Digby, H., Kuret Hodnik, K., Rebselj, J., Wilkins, OG., Chakrabarti, AM., Iosub, IA., Vadnjal, N., Dore, R., Knez, L., Ameres, SL., Plaschka, C., Ule, J. (2025)

Collective homeostasis of condensation-prone proteins via their mRNAs.

 Nature.
Faraway, R., Zenklusen, D., Plaschka, C. (2025)

Mechanisms of Messenger RNA Packaging and Export.

 Annu Rev Cell Dev Biol. 41(1):479-504
Portell-Montserrat, J., Tirian, L., Yu, C., Silvestri, G., Hohmann, U., Handler, D., Duchek, P., Fin, L., Plaschka, C., Brennecke, J. (2025)

Target RNA recognition drives PIWI∗ complex assembly for transposon silencing.

 Mol Cell. 85(17):3288-3305.e6

2024

Vorländer, MK., Rothe, P., Kleifeld, J., Cormack, ED., Veleti, L., Riabov-Bassat, D., Fin, L., Phillips, AW., Cochella, L., Plaschka, C. (2024)

Mechanism for the initiation of spliceosome disassembly.

 Nature. 632(8024):443-450
Riabov Bassat, D., Visanpattanasin, S., Vorländer, MK., Fin, L., Phillips, AW., Plaschka, C. (2024)

Structural basis of human U5 snRNP late biogenesis and recycling.

 Nat Struct Mol Biol.
Pre-printHohmann, U., Graf, M., Schellhaas, U., Pacheco-Fiallos, B., Fin, L., Riabov-Bassat, D., Pühringer, T., Szalay, MF., Tirián, L., Handler, D., Brennecke, J., Plaschka, C. (2024)

A molecular switch orchestrates the nuclear export of human messenger RNA

 BioRxiv.

2023

Pacheco-Fiallos, B., Vorländer, MK., Riabov-Bassat, D., Fin, L., O'Reilly, FJ., Ayala, FI., Schellhaas, U., Rappsilber, J., Plaschka, C. (2023)

mRNA recognition and packaging by the human transcription-export complex.

 Nature.

2022

Vorländer, MK., Pacheco-Fiallos, B., Plaschka, C. (2022)

Structural basis of mRNA maturation: Time to put it together.

 Curr Opin Struct Biol. 75:102431

2020

Pühringer, T., Hohmann, U., Fin, L., Pacheco-Fiallos, B., Schellhaas, U., Brennecke, J., Plaschka, C. (2020)

Structure of the human core transcription-export complex reveals a hub for multivalent interactions.

 Elife. 9

2021

Schnabl, J., Wang, J., Hohmann, U., Gehre, M., Batki, J., Andreev, VI., Purkhauser, K., Fasching, N., Duchek, P., Novatchkova, M., Mechtler, K., Plaschka, C., Patel, DJ., Brennecke, J. (2021)

Molecular principles of Piwi-mediated cotranscriptional silencing through the dimeric SFiNX complex.

 Genes Dev. 35(5-6):392-409

2019

Plaschka, C., Newman, AJ., Nagai, K. (2019)

Structural Basis of Nuclear pre-mRNA Splicing: Lessons from Yeast.

 Cold Spring Harb Perspect Biol. 11(5)

2018

Wilkinson, ME., Lin, PC., Plaschka, C., Nagai, K. (2018)

Cryo-EM Studies of Pre-mRNA Splicing: From Sample Preparation to Model Visualization.

 Annu Rev Biophys. 47:175-199
Plaschka, C., Lin, PC., Charenton, C., Nagai, K. (2018)

Prespliceosome structure provides insights into spliceosome assembly and regulation.

 Nature. 559(7714):419-422

2017

Plaschka, C., Lin, PC., Nagai, K. (2017)

Structure of a pre-catalytic spliceosome.

 Nature. 546(7660):617-621

2016

Plaschka, C., Nozawa, K., Cramer, P. (2016)

Mediator Architecture and RNA Polymerase II Interaction.

 J Mol Biol. 428(12):2569-2574
Plaschka, C., Hantsche, M., Dienemann, C., Burzinski, C., Plitzko, J., Cramer, P. (2016)

Transcription initiation complex structures elucidate DNA opening.

 Nature. 533(7603):353-8

2015

Plaschka, C., Larivière, L., Wenzeck, L., Seizl, M., Hemann, M., Tegunov, D., Petrotchenko, EV., Borchers, CH., Baumeister, W., Herzog, F., Villa, E., Cramer, P. (2015)

Architecture of the RNA polymerase II-Mediator core initiation complex.

 Nature. 518(7539):376-80

2013

Larivière, L., Plaschka, C., Seizl, M., Petrotchenko, EV., Wenzeck, L., Borchers, CH., Cramer, P. (2013)

Model of the Mediator middle module based on protein cross-linking.

 Nucleic Acids Res. 41(20):9266-73

2012

Larivière, L., Plaschka, C., Seizl, M., Wenzeck, L., Kurth, F., Cramer, P. (2012)

Structure of the Mediator head module.

 Nature. 492(7429):448-51