期刊
METHODS
卷 123, 期 -, 页码 56-65出版社
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ymeth.2017.04.004
关键词
Hi-C; Chromosome conformation capture; Paired-end sequencing
资金
- National Human Genome Research Institute [R01 HG003143, U54 HG007010, U01 HG007910]
- National Cancer Institute [U54 CA193419]
- NIH [U54 DK107980, U01 DA 040588]
- National Institute of General Medical Sciences [R01 GM 112720]
- National Institute of Allergy and Infectious Diseases [U01 R01 AI 117839]
Chromosome conformation capture-based methods such as Hi-C have become mainstream techniques for the study of the 3D organization of genomes. These methods convert chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions). Here, we describe an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (kb) resolution. It also includes steps to reduce random ligation and the generation of uninformative molecules, such as unligated ends, to improve the amount of valid intra-chromosomal read pairs. This protocol allows for obtaining information on conformational structures such as compartment and topologically associating domains, as well as high-resolution conformational features such as DNA loops. (C) 2017 Elsevier Inc. All rights reserved.
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