Dynamic 1D search and processive nucleosome translocations by RSC and ISW2 chromatin remodelers

Eukaryotic gene expression is linked to chromatin structure and nucleosome positioning by ATP-dependent chromatin remodelers that establish and maintain nucleosome-depleted regions (NDRs) near transcription start-sites. Conserved yeast RSC and ISW2 remodelers exert antagonistic effects on nucleosomes flanking NDRs, but the temporal dynamics of remodeler search, engagement and directional nucleosome mobilization for promoter accessibility are unknown. Using optical tweezers and 2-color single-particle imaging, we investigated the Brownian diffusion of RSC and ISW2 on free DNA and sparse nucleosome arrays. RSC and ISW2 rapidly scan DNA by one-dimensional hopping and sliding respectively, with dynamic collisions between remodelers followed by recoil or apparent co-diffusion. Static nucleosomes block remodeler diffusion resulting in remodeler recoil or sequestration. Remarkably, both RSC and ISW2 use ATP hydrolysis to translocate mono-nucleosomes processively at ~30 bp/sec for surprising di..., Raw data of single molecule diffusion on naked DNA or on nucleosome arrays was collected on DNA stretched using dual optical tweezers and imaged for fluorescence using point scanning confocal microscopy. Initial raw data is in the form of an h5 file, which contains correlated metadata. However, due to the very large initial file sizes, we have chosen to upload images of kymographs (as tiff files) used for single particle tracking along with the respective single particle trajectories for both the red and green channel (as csv files). Frame-rates and pixel sizes are the same for all kymographs (0.0424 s and 0.1 mm respectively). Single particle tracking was performed using LUMICKS Pylake Kymotracker as described in the methods section of our associated manuscript.
Analysis of the resulting single particle trajectories (csv files) can be performed as follows, using the provided Matlab source code. The result of this analysis are parameter files for each single particle trajectory detected..., Matlab (2021 or newer), # Dynamic 1D Search and Processive Nucleosome Translocations by RSC and ISW2 Chromatin Remodelers'a0

Raw data of single molecule diffusion on naked DNA or on nucleosome arrays was collected on DNA stretched using dual optical tweezers and imaged for fluorescence using point scanning confocal microscopy. Initial raw data is in the form of an h5 file, which contains correlated metadata. However, due to the very large initial file sizes, we have chosen to upload images of kymographs (as tiff files) used for single particle tracking along with the respective single particle trajectories for both the red and green channel (as csv files). Frame-rates and pixel sizes are the same for all kymographs (0.0424 s and 0.1 um respectively). Single particle tracking was performed using LUMICKS Pylake Kymotracker as described in the methods section of our associated manuscript.

The uploaded data can be found in three parts as zip files:
(1) naked DNA data: remodeler diffusion on naked lambda DNA
(2) ...