BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions

• Published in: Nature communications Vol. 8; no. 1; pp. 1622 - 7
• Main Authors: Liang, Zhengyu, Li, Guipeng, Wang, Zejun, Djekidel, Mohamed Nadhir, Li, Yanjian, Qian, Min-Ping, Zhang, Michael Q, Chen, Yang
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 20.11.2017; Nature Publishing Group UK; Nature Portfolio
• Subjects: Architecture; Cell cycle; Cell Line, Tumor; Chromatin; Chromatin - chemistry; Chromatin - genetics; Chromatin - metabolism; Chromosomes - chemistry; Chromosomes - genetics; Deoxyribonucleic acid; Developmental stages; DNA; DNA - genetics; DNA - metabolism; DNA-binding protein; Gene expression; Gene Expression Regulation; Gene regulation; Genomes; High-Throughput Screening Assays - trends; Histones; Histones - metabolism; Humans; Protein Binding; Proteins; Regulatory Sequences, Nucleic Acid
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-017-01754-3

In human cells, DNA is hierarchically organized and assembled with histones and DNA-binding proteins in three dimensions. Chromatin interactions play important roles in genome architecture and gene regulation, including robustness in the developmental stages and flexibility during the cell cycle. Here we propose in situ Hi-C method named Bridge Linker-Hi-C (BL-Hi-C) for capturing structural and regulatory chromatin interactions by restriction enzyme targeting and two-step proximity ligation. This method improves the sensitivity and specificity of active chromatin loop detection and can reveal the regulatory enhancer-promoter architecture better than conventional methods at a lower sequencing depth and with a simpler protocol. We demonstrate its utility with two well-studied developmental loci: the beta-globin and HOXC cluster regions.