Simon Jeremy M, Giresi Paul G, Davis Ian J, Lieb Jason D
Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Curr Protoc Mol Biol. 2013;Chapter 21:Unit21.26. doi: 10.1002/0471142727.mb2126s102.
Nucleosome displacement is a key event in the regulation of gene expression in the eukaryotic genome. This unit details an approach called Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) for isolating nucleosome-depleted regions. FAIRE does not rely on the use of antibodies or enzymes, and has proven successful in most eukaryotic cells and tissues. The set of regulatory elements enriched by FAIRE is similar to those identified through DNase hypersensitivity. The enriched fragments can be detected by quantitative PCR, tiling DNA microarrays, or next-generation sequencing. Although the signal-to-noise ratio is typically lower than that observed for DNase assays, FAIRE has high sample-to-sample reproducibility, requires very low amounts of input material, is inexpensive, is amenable to high-throughput adaptations, and is a relatively simple procedure with a high rate of success, even for those without extensive experience in molecular biology protocols.
核小体移位是真核生物基因组中基因表达调控的关键事件。本单元详细介绍了一种称为甲醛辅助调控元件分离法（FAIRE）的方法，用于分离核小体缺失区域。FAIRE不依赖于抗体或酶的使用，并且已在大多数真核细胞和组织中证明是成功的。通过FAIRE富集的调控元件集与通过DNA酶超敏反应鉴定的调控元件集相似。富集的片段可以通过定量PCR、平铺DNA微阵列或下一代测序进行检测。尽管信噪比通常低于DNA酶检测所观察到的信噪比，但FAIRE具有很高的样本间重复性，所需的起始材料量非常少，成本低廉，适合高通量应用，并且是一个相对简单的程序，成功率很高，即使对于那些没有分子生物学实验方案丰富经验的人也是如此。
