Oluwadare Oluwatosin, Highsmith Max, Cheng Jianlin
1Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211 USA.
2Informatics Institute, University of Missouri, Columbia, MO 65211 USA.
Biol Proced Online. 2019 Apr 24;21:7. doi: 10.1186/s12575-019-0094-0. eCollection 2019.
Over the past decade, methods for predicting three-dimensional (3-D) chromosome and genome structures have proliferated. This has been primarily due to the development of high-throughput, next-generation chromosome conformation capture (3C) technologies, which have provided next-generation sequencing data about chromosome conformations in order to map the 3-D genome structure. The introduction of the Hi-C technique-a variant of the 3C method-has allowed researchers to extract the interaction frequency (IF) for all loci of a genome at high-throughput and at a genome-wide scale. In this review we describe, categorize, and compare the various methods developed to map chromosome and genome structures from 3C data-particularly Hi-C data. We summarize the improvements introduced by these methods, describe the approach used for method evaluation, and discuss how these advancements shape the future of genome structure construction.
在过去十年中，预测三维（3-D）染色体和基因组结构的方法激增。这主要归功于高通量、新一代染色体构象捕获（3C）技术的发展，这些技术提供了有关染色体构象的新一代测序数据，以便绘制三维基因组结构。Hi-C技术（3C方法的一种变体）的引入，使研究人员能够在高通量和全基因组范围内提取基因组所有位点的相互作用频率（IF）。在本综述中，我们描述、分类并比较了从3C数据（特别是Hi-C数据）绘制染色体和基因组结构所开发的各种方法。我们总结了这些方法带来的改进，描述了方法评估所采用的方法，并讨论了这些进展如何塑造基因组结构构建的未来。
