Title

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation

UMMS Affiliation

Program in Systems Biology; Department of Biochemistry and Molecular Pharmacology

Date

7-1-2017

Document Type

Article

Disciplines

Biochemistry, Biophysics, and Structural Biology | Computational Biology | Systems Biology

Abstract

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.

Rights and Permissions

Citation: Methods. 2017 Jul 1;123:56-65. doi: 10.1016/j.ymeth.2017.04.004. Epub 2017 Apr 18. Link to article on publisher's site

Related Resources

Link to Article in PubMed

Keywords

Chromosome conformation capture, Hi-C, Paired-end sequencing

Journal Title

Methods (San Diego, Calif.)

PubMed ID

28435001