Li Yi, Zou Fan, Bai Lu
Department of Biochemistry and Molecular Biology, University Park, PA 16802, USA.
Center for Eukaryotic Gene Regulation, University Park, PA 16802, USA.
bioRxiv. 2024 Dec 13:2024.12.09.627644. doi: 10.1101/2024.12.09.627644.
The genome-wide chromosome conformation capture method, Hi-C, has greatly advanced our understanding of genome organization. However, its quantitative properties, including sensitivity, bias, and linearity, remain challenging to assess. Measuring these properties is difficult due to the heterogenous and dynamic nature of chromosomal interactions. Here, using Chemically Induced Chromosomal Interaction (CICI) method, we create stable intra- and inter-chromosomal interactions in G1-phase budding yeast across a broad range of contact frequencies. Hi-C analysis of these engineered cell populations demonstrates that static intra-chromosomal loops do not generate Topologically Associated Domains (TADs) and only promote 3D proximity within ~50kb flanking regions. At moderate sequencing depth, Hi-C is sensitive enough to detect interactions occurring in 5-10% of cells. It also shows no inherent bias toward intra- versus inter-chromosomal interactions. Furthermore, we observe a linear relationship between Hi-C signal intensity and contact frequency. These findings illuminate the intrinsic properties of the Hi-C assay and provide a robust framework for its calibration.
全基因组染色体构象捕获方法Hi-C极大地推进了我们对基因组组织的理解。然而，其定量特性，包括灵敏度、偏差和线性度，仍然难以评估。由于染色体相互作用的异质性和动态性，测量这些特性很困难。在这里，我们使用化学诱导染色体相互作用（CICI）方法，在G1期芽殖酵母中跨广泛的接触频率创建稳定的染色体内和染色体间相互作用。对这些工程化细胞群体的Hi-C分析表明，静态染色体内环不会产生拓扑相关结构域（TADs），只会促进约50kb侧翼区域内的三维接近。在中等测序深度下，Hi-C灵敏度足以检测在5%-10%的细胞中发生的相互作用。它也没有对染色体内与染色体间相互作用的固有偏差。此外，我们观察到Hi-C信号强度与接触频率之间存在线性关系。这些发现揭示了Hi-C检测的内在特性，并为其校准提供了一个可靠的框架。
