Kim et al. 2021

Published: 19-04-2021| Version 2 | DOI: 10.17632/ydwcx9yhpp.2
Jee Min Kim


Abstract: Conserved ATP-dependent chromatin remodelers establish and maintain genome-wide chromatin architectures of regulatory DNA during cellular lifespan, but the temporal interactions between remodelers and chromatin targets have been obscure. We performed live-cell single-molecule tracking for RSC, SWI/SNF, CHD1, ISW1, ISW2, and INO80 remodeling complexes in budding yeast and detected hyperkinetic behaviors for chromatin-bound molecules that frequently transition to the free state for all complexes. Chromatin-bound remodelers display notably higher diffusion than nucleosomal histones, and strikingly fast dissociation kinetics with 4-7 s mean residence times. These enhanced dynamics require ATP binding or hydrolysis by the catalytic ATPase, uncovering an additional function to its established role in nucleosome remodeling. Kinetic simulations show that multiple remodelers can repeatedly occupy the same promoter region on a timescale of minutes, implicating an unending ‘tug-of-war’ that controls a temporally shifting window of accessibility for the transcription initiation machinery. File Descriptions: SMT datasets: Filenames include information about: “factor name_HALO”_”biological replicate”_”laser power”_”frame rate”_”movie number” [i.e. STH1_HALO_WT_Rep1_90mW_10ms_1] .mat files are raw output files from tracking software DiaTrack 3.04, and contains trajectory information (X coordinate, Y coordinate, intensity, goodness of fit, etc.) from each movie. .csv files contain information about trajectory ID, frame number, x coordinate, and y coordinate, for all masked trajectories ≥ 3 frames (no skipping allowed) merged from all biological replicates. Matlab scripts: Analysis of HMM-classified trajectories This repo contains custom scripts for analyzing and quantifying HMM-classified trajectories by vbSPT (output file from 'Batch_vbSPT_classify.m'). Most analysis are done using MATLAB script, with the exception to 'subclassify DCoef' folder which requires running a shell script and an R Script using the 'Sojourner' package. PRISM was used for plotting the results. Each subfolder contains different analysis with its own README file and can be run independently of each other in any order.