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

5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design

Ji Hun Kim, Katelyn R. Titus, Wanfeng Gong, Jonathan A. Beagan, Zhendong Cao, View ORCID ProfileJennifer E. Phillips-Cremins
doi: https://doi.org/10.1101/244285
Ji Hun Kim
1Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104 USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Katelyn R. Titus
1Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104 USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Wanfeng Gong
1Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104 USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jonathan A. Beagan
1Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104 USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Zhendong Cao
2Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jennifer E. Phillips-Cremins
1Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104 USA
2Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
3Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jennifer E. Phillips-Cremins
  • For correspondence: jcremins@seas.upenn.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C generates high quality, high resolution maps of looping interactions genome-wide, but is intractable for high-throughput screening of loops across conditions due to the requirement of an enormous number of reads (>6 Billion) per library. Here, we describe 5C-ID, an updated version of Chromosome-Conformation-Capture-Carbon-Copy (5C) with restriction digest and ligation performed in the nucleus (in situ Chromosome-Conformation-Capture (3C)) and ligation-mediated amplification performed with a new double alternating design. 5C-ID reduces spatial noise and enables higher resolution 3D genome folding maps than canonical 5C, allowing for a marked improvement in sensitivity and specificity of loop detection. 5C-ID enables the creation of high-resolution, high-coverage maps of chromatin loops in up to a 30 Megabase subset of the genome at a fraction of the cost of Hi-C.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted January 10, 2018.
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.
5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design
(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
5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design
Ji Hun Kim, Katelyn R. Titus, Wanfeng Gong, Jonathan A. Beagan, Zhendong Cao, Jennifer E. Phillips-Cremins
bioRxiv 244285; doi: https://doi.org/10.1101/244285
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design
Ji Hun Kim, Katelyn R. Titus, Wanfeng Gong, Jonathan A. Beagan, Zhendong Cao, Jennifer E. Phillips-Cremins
bioRxiv 244285; doi: https://doi.org/10.1101/244285

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 (4237)
  • Biochemistry (9153)
  • Bioengineering (6793)
  • Bioinformatics (24045)
  • Biophysics (12147)
  • Cancer Biology (9557)
  • Cell Biology (13811)
  • Clinical Trials (138)
  • Developmental Biology (7650)
  • Ecology (11726)
  • Epidemiology (2066)
  • Evolutionary Biology (15530)
  • Genetics (10661)
  • Genomics (14343)
  • Immunology (9499)
  • Microbiology (22873)
  • Molecular Biology (9113)
  • Neuroscience (49076)
  • Paleontology (357)
  • Pathology (1487)
  • Pharmacology and Toxicology (2573)
  • Physiology (3851)
  • Plant Biology (8343)
  • Scientific Communication and Education (1473)
  • Synthetic Biology (2299)
  • Systems Biology (6201)
  • Zoology (1302)