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Advances in Genomic Profiling and Analysis of 3D Chromatin Structure and Interaction

Epigenetics & Function Group, School of the Internet of Things, Hohai University, Changzhou Campus, Changzhou 213022, Jiangsu, China
School of Public Health, Shanghai Jiao Tong University, Shanghai 200025, China
Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX 78229, USA
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2017, 8(9), 223;
Received: 28 July 2017 / Revised: 25 August 2017 / Accepted: 4 September 2017 / Published: 8 September 2017
(This article belongs to the Special Issue Integrative Genomics and Systems Medicine in Cancer)
Recent sequence-based profiling technologies such as high-throughput sequencing to detect fragment nucleotide sequence (Hi-C) and chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) have revolutionized the field of three-dimensional (3D) chromatin architecture. It is now recognized that human genome functions as folded 3D chromatin units and looping paradigm is the basic principle of gene regulation. To better interpret the 3D data dramatically accumulating in past five years and to gain deep biological insights, huge efforts have been made in developing novel quantitative analysis methods. However, the full understanding of genome regulation requires thorough knowledge in both genomic technologies and their related data analyses. We summarize the recent advances in genomic technologies in identifying the 3D chromatin structure and interaction, and illustrate the quantitative analysis methods to infer functional domains and chromatin interactions, and further elucidate the emerging single-cell Hi-C technique and its computational analysis, and finally discuss the future directions such as advances of 3D chromatin techniques in diseases. View Full-Text
Keywords: Hi-C; 3D chromatin; structure interaction; single cell; disease Hi-C; 3D chromatin; structure interaction; single cell; disease
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MDPI and ACS Style

Tang, B.; Cheng, X.; Xi, Y.; Chen, Z.; Zhou, Y.; Jin, V.X. Advances in Genomic Profiling and Analysis of 3D Chromatin Structure and Interaction. Genes 2017, 8, 223.

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