University of Massachusetts Medical School Faculty Publications

UMMS Affiliation

Program in Systems Biology; Department of Biochemistry and Molecular Pharmacology

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Article Preprint


Biochemistry | Computational Biology | Genetic Phenomena | Genomics | Structural Biology | Systems Biology


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 TADs, as well as high-resolution conformational features such as DNA loops.


Hi-­C, chromosome conformation capture, paired-­end sequencing, genomics

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The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.

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bioRxiv 090001; doi: Link to preprint on bioRxiv service.

Related Resources

Now published in Methods; doi:10.1016/j.ymeth.2017.04.004

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Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.