FAIRE-Seq/Sono-Seq

FAIRE-Seq/Sono-Seq

FAIRE-seq and Sono-Seq 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.

Pros:

  • 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 samples1

Cons:

  • Cannot identify regulatory proteins bound to DNA
  • DNase-Seq may be better at identifying nucleosome-depleted promoters of highly expressed genes2
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  10. Davie K., Jacobs J., Atkins M., et al. Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PLoS Genet. 2015;11:e1004994
  11. Naval-Sanchez M., Potier D., Hulselmans G., Christiaens V. and Aerts S. Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models. Mol Biol Evol. 2015;32:2441-2455
  12. Reschen M. E., Gaulton K. J., Lin D., et al. Lipid-induced epigenomic changes in human macrophages identify a coronary artery disease-associated variant that regulates PPAP2B Expression through Altered C/EBP-beta binding. PLoS Genet. 2015;11:e1005061