FAIRE-Seq/Sono-Seq

FAIRE-Seq/Sono-Seq

Formaldehyde-assisted isolation of regulatory elements (FAIRE-Seq), or sonication of crosslinked chromatin (Sono-seq) is based on differences in crosslinking efficiencies between DNA and nucleosomes or sequence-specific DNA-binding proteins. In this method, DNA-protein complexes are briefly crosslinked 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.

• 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

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