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

• FAIRE-Seq: Giresi P. G. and Lieb J. D. (2009) Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods 48: 233-239
• FAIRE-Seq: Hogan G. J., Lee C. K. and Lieb J. D. (2006) Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters. PLoS Genet 2: e158
• Sono-Seq: Auerbach R. K., Euskirchen G., Rozowsky J., Lamarre-Vincent N., Moqtaderi Z., et al. (2009) Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A 106: 14926-14931
• 1. Simon J. M., Giresi P. G., Davis I. J. and Lieb J. D. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nat Protoc. 2012;7:256-267
• 2. Song L., Zhang Z., Grasfeder L. L., et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res. 2011;21:1757-1767

1. Yan H., Tian S., Slager S. L., Sun Z. and Ordog T. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol. 2016;183:96-109

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