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.

摘要：保守的ATP依赖型染色质重塑复合物在细胞生命周期中建立并维持全基因组调控DNA的染色质结构，然而此前学界对重塑复合物与染色质靶点之间的动态相互作用机制仍不甚明晰。
我们对出芽酵母中的RSC、SWI/SNF、CHD1、ISW1、ISW2及INO80染色质重塑复合物开展了活细胞单分子追踪（live-cell single-molecule tracking）实验，发现所有复合物的染色质结合分子均表现出高动态行为，且频繁从结合态转换为游离态。
相较于核小体组蛋白，结合于染色质的重塑复合物展现出显著更高的扩散速率，同时其解离动力学极快，平均驻留时间仅为4至7秒。这类增强的动态行为依赖于催化ATP酶的ATP结合或水解过程，这揭示了该ATP酶在核小体重塑之外的另一项功能。动力学模拟结果显示，多种重塑复合物可在数分钟的时间尺度上反复结合同一启动子区域，这意味着存在一场持续的“拉锯战”，以此调控转录起始复合物可及窗口的动态变化。

文件说明：
单分子追踪（SMT, single-molecule tracking）数据集：文件名包含以下信息格式：“因子名_HALO”_“生物学重复”_“激光功率”_“帧率”_“影像编号”（示例：STH1_HALO_WT_Rep1_90mW_10ms_1）。其中.mat格式文件为追踪软件DiaTrack 3.04的原始输出文件，包含每部影像的轨迹信息（X坐标、Y坐标、荧光强度、拟合优度等）。.csv格式文件整合了所有生物学重复样本中长度≥3帧（不允许跳帧）的有效掩膜轨迹信息，内容包括轨迹ID、帧编号、X坐标与Y坐标。

MATLAB脚本：隐马尔可夫模型（HMM, Hidden Markov Model）分类轨迹分析 本代码仓库包含用于分析和量化经vbSPT处理的HMM分类轨迹的自定义脚本（vbSPT的输出文件来自'Batch_vbSPT_classify.m'）。大部分分析工作通过MATLAB脚本完成，仅“subclassify DCoef”子文件夹需结合Shell脚本与使用“Sojourner”包的R脚本运行。结果绘图采用PRISM工具完成。每个子文件夹对应独立的分析任务，均配有专属的README文件，且可按任意顺序独立运行。

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。