Bernecky Group

RNA-Based Gene Regulation

The regulated expression of genetic material is one of the most basic processes of a cell, affecting everything from organism development to environmental response. Through structural studies of the involved complexes, the Bernecky group works to unravel the gene expression regulatory networks that employ RNA as an intermediate.

RNA is an important focal point for the regulation of gene expression. Both protein-coding and noncoding RNAs are integral components of diverse regulatory pathways, and often act together with protein cofactors. Despite their importance, an understanding of the mechanisms of action of the involved RNA-protein complexes is lacking. Many of these RNA-containing complexes are flexible, modular, and lowly abundant. For such challenging targets, cryo-electron microscopy (cryo-EM) has emerged as a particularly powerful tool for the determination of near-atomic structures while simultaneously providing insight into their dynamics. Using this and related methods, the Bernecky Lab aims to understand how RNA protein complexes assemble and regulate cellular RNA metabolism.

Group Leader

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Current Projects

Molecular basis of transcriptional regulation | Transcriptional inhibition by non-coding RNA | Substrate recognition by RNA modifying enzymes


Bernecky CA, Plitzko J, Cramer P. 2017. Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp. Nature Structural and Molecular Biology. 24(10), 809–815. View

Xu Y, Bernecky CA, Lee C, Maier K, Schwalb B, Tegunov D, Plitzko J, Urlaub H, Cramer P. 2017. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nature Communications. 8, 15741. View

Engel C, Gubbey T, Neyer S, Sainsbury S, Oberthuer C, Baejen C, Bernecky CA, Cramer P. 2017. Structural basis of RNA polymerase I transcription initiation. Cell. 169(1), 120–131.e22. View

Bernecky CA, Herzog F, Baumeister W, Plitzko J, Cramer P. 2016. Structure of transcribing mammalian RNA polymerase II. Nature. 529(7587), 551–554. View

Sainsbury S, Bernecky CA, Cramer P. 2015. Structural basis of transcription initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology. 16(3), 129–143. View

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since 2018 Assistant Professor, IST Austria
2011 – 2017 Postdoc, LMU Munich and MPI for Biophysical Chemistry, Göttingen, Germany
2010 – 2011 Postdoc, University of Colorado Boulder, USA
2010 PhD, University of Colorado Boulder, USA

Selected Distinctions

2012 – 2014 Humboldt Research Fellowship
2005 – 2007 NIH Molecular Biophysics Training Grant
2002 Hughes Undergraduate Research Scholar (Cornell-HHMI)

Additional Information

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