Herrera Bernardo J Zubillaga, Das Amit, Burack Linden, Wang Ailung, Di Pierro Michele
Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts 02115, United States.
Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States.
bioRxiv. 2025 May 4:2025.05.02.649190. doi: 10.1101/2025.05.02.649190.
In the last decade, DNA-DNA proximity ligation assays opened powerful new ways to study the 3D organization of genomes and have become a mainstay experimental technology. Yet many aspects of these experiments remain poorly understood. We study the inner workings of DNA-DNA proximity ligation assays through numerical experiments and theoretical modeling. Chromosomes are modeled at nucleosome resolution and evolved in time via molecular dynamics. A virtual Hi-C experiment reproduces, in-silico, the different steps of the Hi-C protocol, including: crosslinking of chromatin to an underlying proteic matrix, enzymatic digestion of DNA, and subsequent proximity ligation of DNA open ends. The protocol is simulated on ensembles of different structures as well as individual structures, enabling the construction of ligation maps and the calculation of ligation probabilities as functions of genomic and Euclidean distance. The methods help to assess the effect of the many variables of the Hi-C experiment and of subsequent data processing methods on the quality of the final results.
在过去十年中，DNA-DNA邻近连接测定法为研究基因组的三维组织开辟了强大的新途径，并已成为一项主要的实验技术。然而，这些实验的许多方面仍未得到充分理解。我们通过数值实验和理论建模来研究DNA-DNA邻近连接测定法的内部机制。染色体以核小体分辨率进行建模，并通过分子动力学随时间演化。虚拟Hi-C实验在计算机上重现了Hi-C协议的不同步骤，包括：染色质与下层蛋白质基质的交联、DNA的酶促消化以及随后DNA开放末端的邻近连接。该协议在不同结构的集合以及单个结构上进行模拟，从而能够构建连接图谱并计算连接概率作为基因组距离和欧几里得距离的函数。这些方法有助于评估Hi-C实验的众多变量以及后续数据处理方法对最终结果质量的影响。
