Department of Chemical Engineering, Stanford University, Stanford, California.
Department of Developmental Biology, Stanford University, Stanford, California.
Biophys J. 2023 Sep 5;122(17):3532-3540. doi: 10.1016/j.bpj.2023.08.001. Epub 2023 Aug 4.
Chromosomal dynamics plays a central role in a number of critical biological processes, such as transcriptional regulation, genetic recombination, and DNA replication. However, visualization of chromatin is generally limited to live imaging of a few fluorescently labeled chromosomal loci or high-resolution reconstruction of multiple loci from a single time frame. To aid in mapping the underlying chromosomal structure based on parsimonious experimental measurements, we present an exact analytical expression for the evolution of the polymer configuration based on a flexible-polymer model, and we propose an algorithm that tracks the polymer configuration from live images of chromatin marked with several fluorescent marks. Our theory identifies the resolution of microscopy needed to achieve high-accuracy tracking for a given spacing of markers, establishing the statistical confidence in the assignment of genome identity to the visualized marks. We then leverage experimental data of locus-tracking measurements to demonstrate the validity of our modeling approach and to establish a basis for the design of experiments with a desired resolution. Altogether, this work provides a computational approach founded on polymer physics that vastly improves the interpretation of in vivo measurements of biopolymer dynamics.
染色体动力学在许多关键的生物学过程中起着核心作用，例如转录调控、遗传重组和 DNA 复制。然而，通常只能对少数荧光标记的染色体位点进行活细胞成像，或者对单个时间帧内的多个位点进行高分辨率重构，来可视化染色质。为了根据精简的实验测量来帮助绘制潜在的染色体结构，我们提出了一个基于柔性聚合物模型的聚合物构象演变的精确解析表达式，并提出了一种从用几个荧光标记标记的染色质的活细胞图像中跟踪聚合物构象的算法。我们的理论确定了在给定标记间距下实现高精度跟踪所需的显微镜分辨率，从而确定了将基因组身份分配给可视化标记的统计置信度。然后，我们利用轨迹测量的实验数据来验证我们的建模方法的有效性，并为具有所需分辨率的实验设计奠定基础。总之，这项工作提供了一种基于聚合物物理的计算方法，极大地提高了对生物聚合物动力学的体内测量的解释能力。
