FAIRE ((F)under-barormaldehyde-(A)under-barssisted (I)under-barsolation of (R)under-baregulatory (E)under-barlements) isolates active regulatory elements from human chromatin
FAIRE ((F)under-barormaldehyde-(A)under-barssisted (I)under-barsolation of (R)under-baregulatory (E)under-barlements) isolates active regulatory elements from human chromatin
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DOI：
10.1101/gr.5533506
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发表时间：
2007-06-01
期刊：
影响因子：
7
通讯作者：
Lieb, Jason D.
中科院分区：
文献类型：
--
作者：
Giresi, Paul G.;Kim, Jonghwan;Lieb, Jason D.
在体内主动调节转录的DNA片段通常以核小体从染色质中移除为特征，并通过对核酸酶的超敏感性在实验中被鉴定出来。在这里，我们展示了从人类染色质中分离核小体缺失DNA的简单程序，称为FAIRE（甲醛辅助分离调控元件）。为了执行FAIRE，染色质在体内与甲醛交联，通过超声剪切，并提取苯酚-氯仿。在水相中回收的DNA被荧光标记并杂交到DNA微阵列中。在人类细胞中进行的FAIRE强烈富集了与DNaseI超敏感位点、转录起始位点和活性启动子位置一致的DNA。还提出了FAIRE富集的细胞类型特异性模式的证据。FAIRE作为与调控活性相关的基因组区域的正选择，包括传统上由核酸酶超敏试验检测到的区域。
DNA segments that actively regulate transcription in vivo are typically characterized by eviction of nucleosomes from chromatin and are experimentally identified by their hypersensitivity to nucleases. Here we demonstrate a simple procedure for the isolation of nucleosome-depleted DNA from human chromatin, termed FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements). To perform FAIRE, chromatin is crosslinked with formaldehyde in vivo, sheared by sonication, and phenol-chloroform extracted. The DNA recovered in the aqueous phase is fluorescently labeled and hybridized to a DNA microarray. FAIRE performed in human cells strongly enriches DNA coincident with the location of DNaseI hypersensitive sites, transcriptional start sites, and active promoters. Evidence for cell-type-specific patterns of FAIRE enrichment is also presented. FAIRE has utility as a positive selection for genomic regions associated with regulatory activity, including regions traditionally detected by nuclease hypersensitivity assays.