On April 26th, the paper “Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture” was published in Nature Genetics. Its first authors are PhD. candidates Lin Da and Hong Ping from Prof. Cao Gang’s research group at College of Animal Sciences and Technology| College of Veterinary Medicine and Prof. Li Guoliang’s research group at College of Informatics of HZAU, and the corresponding authors are Prof. Cao and Prof. Li. The research group has developed the digestion-ligation-only Hi-C (DLO Hi-C) technology, a new chromosome conformation capture (3C) method, for the delineation of 3D genomic structures in an efficient and cost-effective way.
The gene coding regions take a minimal proportion in the genome sequence. Recent studies have shown that other “junk genome sequences” play an important role in the regulation of gene transcription. The study on chromosome conformation capture and 3D genomic structures can better correlate the distantly-distributed elements on the genome with their specific regulatory regions. It also shows great promise for uncovering transcriptional regulation, interaction between enhancers and promoters, disease susceptibility loci, DNA damage repair, and genomic structure variation and epigenetics.
Although Hi-C technologies are mainly used to investigate 3D genomic structures, there are such shortcomings as high costs, high background noise, and sophisticated and laborious experimental procedures in these methods. To tackle the problems, this article developed a new method for chromosome conformation capture-- digestion-ligation-only Hi-C (DLO Hi-C) technology. Based on simultaneous enzyme digestion and ligation steps, DNA linkers are ligated to the ends of the chromosomal enzyme, followed by the process of In-gel proximity ligation. With MmeI digestion, the recovery of fix-sized interacting DNA fragments is realized. Thereby the background data noise is greatly reduced while the high quality Hi-C data are acquired. Besides, this technology can also be applied to screen chromosomal translocations.
The DLO Hi-C technology could greatly reduce the costs for whole-genome chromosome conformation capture and simplify the experimental procedures with a significant increase in experimental success rate. Moreover, this method can be used to study genome assembly, long-distance gene regulation, disease susceptibility loci, and chromosomal translocation. A review article published in the same period in Nature Genetics said, “Lin et al. introduce an elegant dual-linker strategy that allows for noise filtering and early quality control”, which set a high value on this research.
Article: https://www.nature.com/articles/s41588-018-0111-2
Review of the article: https://www.nature.com/articles/s41588-018-0112-1
Original text: http://news.hzau.edu.cn/2018/0427/51839.shtml
Translator: Zeng Pengling
Proofreader: Guo Haiyan
