Formaldehyde-Assisted Isolation of Regulatory Elements / Sonication of Crosslinked Chromatin

FAIRE-seq (Giresi et al., 2009) (Hogan et al., 2006) and Sono-Seq (Auerbach et al., 2009) are based on differences in crosslinking efficiencies between DNA and nucleosomes or sequence-specific DNA-binding proteins. In this method, DNA-protein complexes are crosslinked briefly in vivo using formaldehyde. The sample is then lysed and sonicated. After phenol/chloroform extraction, the DNA in the aqueous phase is purified and sequenced. Sequencing provides information for regions of DNA that are not occupied by histones.


  • Simple and highly reproducible protocol
  • Does not require antibodies
  • Does not require enzymes, such as DNase or MNase, avoiding the optimization and extra steps necessary for enzymatic processing
  • Does not require a single-cell suspension or nuclear isolation, so it is easily adapted for use on tissue samples (Simon et al., 2012)


  • Cannot identify regulatory proteins bound to DNA
  • DNase-Seq may be better at identifying nucleosome-depleted promoters of highly expressed genes (Song et al., 2011)


Illumina Library prep and Array Kit Selector


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