RNA-based Gene Regulation

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. Coding RNAs serve as templates for protein synthesis and are tightly regulated through control of RNA synthesis, processing, and degradation. Noncoding RNAs (ncRNAs) are a diverse group of non-translated transcripts with a wide variety of functions. For example, certain ncRNAs directly repress the transcription machinery. Some RNAs have even been shown to be bifunctional, having both coding and noncoding potential. The cellular activities of all types of RNA can be further fine-tuned through subcellular localization and RNA editing.

Our group aims to understand the molecular mechanisms by which RNA controls human gene regulation. We are particularly interested in understanding how ncRNAs regulate transcription, and how RNA activity can be regulated through post-transcriptional processes. We employ a variety of biochemical and structural methods, including X-ray crystallography and cryo-electron microscopy (cryo-EM). Cryo-EM has emerged as a particularly powerful tool for the determination of near-atomic structures while simultaneously providing insight into their dynamics. Through these studies, we work to unravel the regulatory networks that employ RNA as an intermediate.

Carrie Bernecky

Institute of Science and Technology Austria (IST Austria)
Am Campus 1
A – 3400 Klosterneuburg

Phone: +43 (0)2243 9000-2082
E-mail: carrie.bernecky@remove-this.ist.ac.at

»CV and publication list

Lena Marr

Phone: +43 2243 9000-1073
E-mail: lena.marr@remove-this.ist.ac.at


  • Narkhyun Bae, Postdoc (ISTFellow, jointly with Novarino Group)
  • Edwine Lehner, Scientific Intern
  • Anita Testa Salmazo, Laboratory Technician
  • Katarina Tluckova, Postdoc

Selected Publications

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

2018 Assistant Professor, IST Austria
2011–2017 Postdoc, LMU Munich and MPI for Biophysical Chemistry, Göttingen
2010–2011 Postdoc, UC Boulder
2004–2010 PhD, UC Boulder
2001–2004 Undergrad research assistant, Cornell University

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

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