Reconstruction of Three-Dimensional Structures of Chromatin and Its Biological Implications

Chromatin is the basic element of eukaryotic chromosomes that package the genome in the nucleus, and its function is closely related to its three-dimensional (3D) structure. For example, many biological functions such as DNA replication, DNA damage, DNA repair, gene transcription and regulation, spread of long non-coding RNAs, and embryonic development, are processed in and affected by 3D chromatin architecture in nuclear space. In recent years, chromosome conformation capture (3C) and its derivative technologies combined with high-throughput sequencing such as ChIA-PET and Hi-C, have generated extensive chromatin interaction data. With these data, researchers have proposed a number of ways to reconstruct the 3D structures of chromsomal folding, which help to systematically study the chromatin 3D structures at different resolutions and to provide better understanding of chromatin functions with structural basis. In this review, we summarize recent advances in the methods for chromatin 3D structure modeling, and discuss its implications in chromatin function.