An optimized FAIRE procedure for low cell numbers in yeast

Yeast. 2018 Aug;35(8):507-512. doi: 10.1002/yea.3316. Epub 2018 May 28.


We report an optimized low-input FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements-sequencing) procedure to assay chromatin accessibility from limited amounts of yeast cells. We demonstrate that the method performs well on as little as 4 mg of cells scraped directly from a few colonies. Sensitivity, specificity and reproducibility of the scaled-down method are comparable with those of regular, higher input amounts, and allow the use of 100-fold fewer cells than existing procedures. The method enables epigenetic analysis of chromatin structure without the need for cell multiplication of exponentially growing cells in liquid culture, thus opening the possibility of studying colony cell subpopulations, or those that can be isolated directly from environmental samples.

Keywords: HTS; NGS; Saccharomyces cerevisiae; chromatin-accessibility; epigenetics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Count
  • Chromatin / chemistry
  • Chromatin / genetics*
  • Chromatin / metabolism
  • Formaldehyde / chemistry
  • Genome, Fungal / genetics
  • High-Throughput Nucleotide Sequencing / methods*
  • Regulatory Sequences, Nucleic Acid
  • Reproducibility of Results
  • Saccharomyces cerevisiae / genetics*


  • Chromatin
  • Formaldehyde