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FAIRE實驗過程包括:細(xì)胞或組織培養(yǎng)、甲醛交聯(lián)、細(xì)胞裂解、超聲波打斷染色質(zhì)，然后進(jìn)行酚氯仿抽提制備水相DNA、檢測水相DNA。在FAIRE酚氯仿抽提過程中，蛋白未交聯(lián)的DNA溶于水相，而蛋白結(jié)合型DNA留在兩相界面，從而把全基因組DNA分為兩部分（即水相和有機(jī)相DNA）然后對水相DNA進(jìn)行檢測，常用的檢測方法有熒光定量PCR、DNA微陣列芯片、第二代測序技術(shù)等。FAIRE樣品制備及檢測過程如下圖所示：

Fig FAIRE Procedure

(A) The FAIRE procedure described in the text is shown on the left， while preparation of the reference or input sample is shown on the right. The DNA recovered from he aqueous phase of each extraction can then be used to identify sites of open chromatin using qPCR， tiling microarrays， or high-throughput sequencing applications. (B) For qPCR， a series of primers， depicted as convergent arrows， are designed to span a genomic region of interest. Sites of open chromatin are highlighted in blue， with qPCR results depicted above. Amplicons that span or are near the boundaries of open chromatin often result in lower relative enrichment due to shearing of DNA fragments， as shown by asterisks. (C) Microarrays. Typically we use highresolution microarrays that tile either regions of interest or the entire genome of an organism with 50 to 70 bp oligonucleotides. (D) High-throughput sequencing technologies can be used to map the DNA fragments back to the reference genome.【圖片來源：Giresi P G， Lieb J D. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)[J]. Methods， 2009， 48(3):233-239.】

近年來，F(xiàn)AIRE與高通量技術(shù)結(jié)合產(chǎn)生的FAIRE-Seq技術(shù)，得到了廣泛應(yīng)用。將ChIP-Seq，DNase-Seq和FAIRE-Seq三種實驗技術(shù)聯(lián)用，可用于揭示轉(zhuǎn)錄因子結(jié)合位點(diǎn)、核小體分布位置、染色質(zhì)開放區(qū)域，以及三者之間的關(guān)系。三種實驗技術(shù)的原理如下圖所示。

Fig Comparison of experimental protocols.Experiments to detect different aspects of DNA-binding proteins share many of the same steps; simplified schematics of the main steps are shown.

a | Chromatin immunoprecipitation followed by sequencing (ChIP–seq) for DNA-binding proteins such as transcription factors. Recent variations on the standard protocol include using endonuclease digestion instead of sonication (ChIP–exo) to increase the resolution of binding-site detection and to eliminate contaminating DNA， and DNA amplification after ChIP for samples with limited cells. b | ChIP–seq for histone modifications uses micrococcal nuclease (MNase) digestion to fragment DNA and can also now be run on low-quantity samples when combined with the additional post-ChIP amplification. c | DNase–seq relies on digestion by the DNaseI nuclease to identify regions of nucleosome-depleted open chromatin where there are binding sites for all types of factors， but it cannot identify what specific factors are bound. d | Formaldehyde-assisted identification of regulatory elements (FAIRE–seq) similarly identifies nucleosome-depleted regions by extracting fragmented DNA that is not crosslinked to nucleosomes. LinDA， single-tube linear DNA amplification; T7， T7 phage RNA polymerase.【圖片來源：Furey， Terrence S . ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions[J]. Nature Reviews Genetics， 2012， 13(12):840-852.】