The Farnung Lab is interested in molecular mechanisms at the interface of transcription and chromatin.

We employ biochemical, biophysical, machine learning, and structural biology approaches to understand how the transcription machinery, histone modifying enzymes, chromatin remodelers, and the nucleosome interact with each other to regulate gene expression. In this context, we are aiming to understand how the transcription machinery traverses through a chromatinized DNA template, how chromatin remodelers shape cell fate decisions, and how histone modifying enzymes shape the nucleosomal landscape. We are especially focused on developing a pseudo-time resolved cryo-EM approach called visual biochemistry that allows the visualization of dynamic biochemical reactions (such as transcription) at atomic resolution. Our structural findings are subsequently supported by biochemical experiments and biophysical approaches using fully in vitro reconstituted system. Recently, our lab has uncovered the molecular basis of how nucleosomes are retained during transcription through chromatin, explaining how epigenetic marks on actively transcribed genes are maintained during gene expression (Filipovski et al., Science, 2022). Earlier this year, we have additionally uncovered the structural basis of histone deacetylation by the histone deacetylase SIRT6 (Wang et al., JACS, 2023). The long-term goal of the Farnung lab is to fully reconstitute transcription and related processes in a test tube.