How best to identify chromosomal interactions: a comparison of approaches

Nat Methods. 2017 Jan 31;14(2):125-134. doi: 10.1038/nmeth.4146.


Chromosome conformation capture (3C) methods are central to understanding the link between nuclear structure and function, and the physical interactions between distal regulatory elements and promoters. However, no one method is appropriate to address all biological questions, as each variant differs markedly in resolution, reproducibility, throughput and biases. A thorough appreciation of the strengths and weaknesses of each technique is critical when choosing the correct method for a specific application or for gauging how best to interpret different sources of data. In addition, the analysis method must be carefully considered, as this choice can profoundly affect the output. In this Review, we describe and compare the different available 3C-based approaches, with a focus on the analysis of mammalian genomes.

Publication types

  • Review
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin / chemistry
  • Chromatin / genetics
  • Chromatin / metabolism
  • Chromosome Mapping
  • Chromosomes* / chemistry
  • Chromosomes* / genetics
  • Gene Library
  • Genetic Techniques*
  • High-Throughput Screening Assays / methods
  • Humans
  • In Situ Hybridization, Fluorescence
  • K562 Cells
  • Mice
  • Polymerase Chain Reaction / methods
  • SOXB1 Transcription Factors / genetics
  • alpha-Globins / genetics


  • Chromatin
  • SOXB1 Transcription Factors
  • Sox2 protein, mouse
  • alpha-Globins