Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C

Nucleic Acids Res. 2017 Dec 15;45(22):e184. doi: 10.1093/nar/gkx1194.


Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells. This hampers the investigation of chromatin architecture in rare cell populations. We present a new low-input Capture-C approach that can generate high-quality 3C interaction profiles from 10 000-20 000 cells, depending on the resolution used for analysis. We also present a PCR-free, sequencing-free 3C technique based on NanoString technology called C-String. By comparing C-String and Capture-C interaction profiles we show that the latter are not skewed by PCR amplification. Furthermore, we demonstrate that chromatin interactions detected by Capture-C do not depend on the degree of cross-linking by performing experiments with varying formaldehyde concentrations.

MeSH terms

  • Animals
  • Cell Count
  • Cells, Cultured
  • Chromatin / chemistry
  • Chromatin / genetics
  • Chromatin / metabolism*
  • Chromosomes / chemistry
  • Chromosomes / genetics
  • Chromosomes / metabolism*
  • Female
  • Formaldehyde / chemistry
  • Gene Expression Regulation
  • Genetic Techniques*
  • Mice, Inbred C57BL
  • Molecular Conformation
  • Nanotechnology / methods*


  • Chromatin
  • Formaldehyde