title: Nucleosomal arrangement affects single-molecule transcription dynamics.
abstract: In eukaryotes, gene expression depends on chromatin organization. However, how chromatin affects the transcription dynamics of individual RNA polymerases has remained elusive. Here, we use dual trap optical tweezers to study single yeast RNA polymerase II (Pol II) molecules transcribing along a DNA template with two nucleosomes. The slowdown and the changes in pausing behavior within the nucleosomal region allow us to determine a drift coefficient,χ, which characterizes the ability of the enzyme to recover from a nucleosomal backtrack. Notably,χcan be used to predict the probability to pass the first nucleosome. Importantly, the presence of a second nucleosome changesχin a manner that depends on the spacing between the two nucleosomes, as well as on their rotational arrangement on the helical DNA molecule. Our results indicate that the ability of Pol II to pass the first nucleosome is increased when the next nucleosome is turned away from the first one to face the opposite side of the DNA template. These findings help to rationalize how chromatin arrangement affects Pol II transcription dynamics.
authors: Biotechnology Center, Technical University Dresden, 01307 Dresden, Germany.|Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
authors: Veronika
authors: V
authors: Fitz
authors: Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.
authors: Jaeoh
authors: J
authors: Shin
authors: Biotechnology Center, Technical University Dresden, 01307 Dresden, Germany.|Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
authors: Christoph
authors: C
authors: Ehrlich
authors: Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
authors: Lucas
authors: L
authors: Farnung
authors: Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
authors: Patrick
authors: P
authors: Cramer
authors: Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.
authors: Vasily
authors: V
authors: Zaburdaev
authors: Biotechnology Center, Technical University Dresden, 01307 Dresden, Germany; stephan.grill@biotec.tu-dresden.de.|Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.|Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.
authors: Stephan W
authors: SW
authors: Grill
keywords: Pol II; internucleosomal distance; optical tweezers; single-molecule; transcription