A Brief Review of Current 3D Genomics Research

Over the past few decades, scientists have completed genome sequencing of many species, including humans, ushering in a new era of genomics research. However, we still cannot fully explain the mechanism of gene regulation by analyzing and annotating DNA sequences because both the linear structure (sequences) and the spatial structure of the genome have an important impact on gene regulation and expression. With the advent of chromosome conformation capture technology and its derivatives, as well as the continuous development of computer technologies and sequencing technology, we finally have the ability to observe and study the spatial structure of the genome, which has made great progress in three-dimensional genomics research in recent years. Furthermore, whole-genome 3D chromatin conformation data analysis has become a hot topic in research. The first two sections of this article provide a brief review of the history of 3D genomics research, introducing chromosome conformation capture technology and its derivative technologies. Then, the most popular Hi-C data analysis workflows are introduced in Section “The Process and Main Components of Thermodynamics-Based 3D Genomic Data Analysis,” and the features of current analytic tools are listed in Section “Introduction to Popular 3D Genomic Data Analysis Tools,” with some classic methods and new research results being highlighted. In addition, we discuss related problems in the last section. The author hopes that researchers will be able to quickly understand the current status and relevant aspects of three-dimensional genomics research by reading this article, thus providing valuable support for research in this field.