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Detecting Spatial Chromatin Organization by Chromosome Conformation Capture II: Genome-Wide Profiling by Hi-C

  • Matteo Vietri Rudan
  • Suzana HadjurEmail author
  • Tom SextonEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1589)

Abstract

The chromosome conformation capture (3C) method has been invaluable in studying chromatin interactions in a population of cells at a resolution surpassing that of light microscopy, for example in the detection of functional contacts between enhancers and promoters. Recent developments in sequencing-based chromosomal contact mapping (Hi-C, 5C and 4C-Seq) have allowed researchers to interrogate pairwise chromatin interactions on a wider scale, shedding light on the three-dimensional organization of chromosomes. These methods present significant technical and bioinformatic challenges to consider at the start of the project. Here, we describe two alternative methods for Hi-C, depending on the size of the genome, and discuss the major computational approaches to convert the raw sequencing data into meaningful models of how genomes are organized.

Keywords:

Hi-C 3C (chromosome conformation capture) Chromatin interactions Chromosome topology High-throughput sequencing 

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Research Department of Cancer Biology, Cancer InstituteUniversity College LondonLondonUK
  2. 2.Institute of Genetics and Molecular and Cellular BiologyCNRS UMR7104/INSERM U964IllkirchFrance
  3. 3.University of StrasbourgIllkirchFrance

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