Kim et al. 2021

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.

搜集汇总

背景与挑战

背景概述

该数据集聚焦于酵母中多种染色质重塑复合物（如RSC、SWI/SNF）的活细胞单分子追踪研究，提供轨迹数据和分析脚本，揭示了这些复合物在染色质上的超动力学行为，包括快速解离和ATP依赖的增强扩散特性。数据支持模拟显示多重塑复合物可在分钟时间尺度上反复占据启动子区域，暗示其对转录可及性的动态调控机制。