Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
Confirmatory Results

Hi-C 2.0: An Optimized Hi-C Procedure for High-Resolution Genome-Wide Mapping of Chromosome Conformation

Houda Belaghzal, Job Dekker, Johan H. Gibcus
doi: https://doi.org/10.1101/090001
Houda Belaghzal
1Program in Systems Biology Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-0103, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Job Dekker
1Program in Systems Biology Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-0103, USA.
2Howard Hughes Medical Institute
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: job.dekker@umassmed.edu
Johan H. Gibcus
1Program in Systems Biology Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-0103, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

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

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted November 27, 2016.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Hi-C 2.0: An Optimized Hi-C Procedure for High-Resolution Genome-Wide Mapping of Chromosome Conformation
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Hi-C 2.0: An Optimized Hi-C Procedure for High-Resolution Genome-Wide Mapping of Chromosome Conformation
Houda Belaghzal, Job Dekker, Johan H. Gibcus
bioRxiv 090001; doi: https://doi.org/10.1101/090001
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
Hi-C 2.0: An Optimized Hi-C Procedure for High-Resolution Genome-Wide Mapping of Chromosome Conformation
Houda Belaghzal, Job Dekker, Johan H. Gibcus
bioRxiv 090001; doi: https://doi.org/10.1101/090001

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (2635)
  • Biochemistry (5224)
  • Bioengineering (3650)
  • Bioinformatics (15730)
  • Biophysics (7218)
  • Cancer Biology (5597)
  • Cell Biology (8051)
  • Clinical Trials (138)
  • Developmental Biology (4739)
  • Ecology (7472)
  • Epidemiology (2059)
  • Evolutionary Biology (10531)
  • Genetics (7704)
  • Genomics (10090)
  • Immunology (5157)
  • Microbiology (13829)
  • Molecular Biology (5354)
  • Neuroscience (30605)
  • Paleontology (212)
  • Pathology (872)
  • Pharmacology and Toxicology (1520)
  • Physiology (2235)
  • Plant Biology (4987)
  • Scientific Communication and Education (1037)
  • Synthetic Biology (1380)
  • Systems Biology (4131)
  • Zoology (804)