FAIRE-Seq

FAIRE-Seq (Formaldehyde-Assisted Isolation of Regulatory Elements) is a method in molecular biology used for determining the sequences of those DNA regions in the genome associated with regulatory activity.[1] In contrast to DNase-seq, the FAIRE-Seq protocol doesn't require the permeabilization of cells or isolation of nuclei, and can analyse any cell types. In a study of seven diverse human cell types, DNase-seq and FAIRE-seq produced strong cross-validation, with each cell type having 1-2% of the human genome as open chromatin[2] .

References

  1. ^ Giresi, PG; Kim, J, McDaniell, RM, Iyer, VR, Lieb, JD (2007 Jun). "FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.". Genome research 17 (6): 877–85. doi:10.1101/gr.5533506. PMC 1891346. PMID 17179217. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1891346. 
  2. ^ Song, L; Zhang, Z, Grasfeder, LL, Boyle, AP, Giresi, PG, Lee, BK, Sheffield, NC, Gräf, S, Huss, M, Keefe, D, Liu, Z, London, D, McDaniell, RM, Shibata, Y, Showers, KA, Simon, JM, Vales, T, Wang, T, Winter, D, Zhang, Z, Clarke, ND, Birney, E, Iyer, VR, Crawford, GE, Lieb, JD, Furey, TS (2011 July 12). "Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.". Genome Research. doi:10.1101/gr.121541.111. PMID 21750106.