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

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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Correspondence to Suzana Hadjur or Tom Sexton .

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Vietri Rudan, M., Hadjur, S., Sexton, T. (2016). Detecting Spatial Chromatin Organization by Chromosome Conformation Capture II: Genome-Wide Profiling by Hi-C. In: Haggarty, P., Harrison, K. (eds) Population Epigenetics. Methods in Molecular Biology, vol 1589. Humana Press, New York, NY. https://doi.org/10.1007/7651_2015_261

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  • DOI: https://doi.org/10.1007/7651_2015_261

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6901-2

  • Online ISBN: 978-1-4939-6903-6

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