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

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


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.


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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