Emergence of 3D genomics

Abstract

It is already more than 10 years after the completion of Human Genome Project. However, the mechanism about how genomic information guides the gene expression in a particular space and time remains to be elucidated. Structure determines function is a consensus that we understand the laws of nature. In biology, this consensus is not only applicable to RNA, protein and other small-scale organic molecules; the same should also apply to macromolecules such as the entire DNA composition of the whole genome. Recent studies have shown that three-dimensional (3D) structure of the genome has an important impact on the regulation of gene transcription and other nuclear functions. Therefore, the study of the 3D structure and function of the whole genome (referred to as 3D genomics) has become a new trend of development in genomics. With the consideration of the genome sequence, gene structure and regulatory elements at the same time, 3D genomics studies the 3D structure of the genome in the nucleus, and its impact on gene transcription, replication, repair, regulation and others biological processes. With the progress of large-scale genome sequencing technology, we already have the relevant technologies such as ChIA-PET and Hi-C for the study of 3D genomics. Preliminary results showed the influence of genome 3D structures to genome functions, which provides the basis for further study of genome structure and function in the spatial nuclear space. This paper summarizes the emergence of 3D genomics, lists the issues and the current progress in this new field, and discusses possible applications of 3D genomics to human health and agriculture researches. We anticipate that 3D genomics will provide novel insights into the genome regulatory functions and provide new opportunities of improving human life qualities.