Detection of short-range chromatin interactions by chromosome conformation capture (3C) in yeast

Badri Nath Singh, Michael Hampsey

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


We describe a modified 3C (“chromosome conformation capture”) protocol for detection of transient, short-range chromatin interactions in the yeast Saccharomyces cerevisiae. 3C was initially described by Job Dekker and involves formaldehyde cross-linking to stabilize transient chromatin interactions, followed by restriction digestion, ligation, and locus-specific PCR. As such, 3C reveals complex three-dimensional interactions between distal genetic elements within intact cells at high resolution. Using a modified version of Dekker’s protocol, we are able to detect gene loops that juxtapose promoter and terminator regions of yeast genes with ORFs as short as 1 kb. We are using this technique to define the cis- and trans-acting requirements for the formation and maintenance of gene loops, and to elucidate their physiological consequences. We anticipate that this method will be generally applicable to detect dynamic, short-range chromatin interactions, not limited to gene loops.

Original languageEnglish (US)
Pages (from-to)209-218
Number of pages10
JournalMethods in Molecular Biology
StatePublished - 2014

All Science Journal Classification (ASJC) codes

  • Genetics
  • Molecular Biology


  • 3C
  • Chromatin
  • Gene loop
  • Saccharomyces cerevisiae
  • Short-range interaction
  • Transcription
  • Yeast


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