Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA.
Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA.
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DOI：
10.1038/nprot.2011.444
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发表时间：
2012-01-19
期刊：
影响因子：
14.8
通讯作者：
中科院分区：
文献类型：
--
作者：
核小体从染色质中移除或不稳定是真核生物基因组功能调控元件的一个标志。这些调节元件通常与转录因子或其他调节蛋白结合，历来被核酸酶超敏性鉴定。FAIRE（甲醛辅助分离调控元件）是鉴定这些基因组区域的另一种方法，已被证明在众多真核细胞和组织类型中是成功的。细胞或游离组织与甲醛短暂交联，裂解并超声。剪切的染色质经过苯酚-氯仿萃取，分离的DNA（通常包含人类基因组的1-3%）被纯化。我们提供PCR，微阵列或下一代测序的定量分析指南。FAIRE富集的调控元件与核酸酶超敏反应或ChIP鉴定的调控元件高度一致，整个过程可在3天内完成。FAIRE表现出较低的技术变异性，这使得它可以用于正常或病变组织的染色质的大规模研究。
Eviction or destabilization of nucleosomes from chromatin is a hallmark of functional regulatory elements of the eukaryotic genome. Historically identified by nuclease hypersensitivity, these regulatory elements are typically bound by transcription factors or other regulatory proteins. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) is an alternative approach to identify these genomic regions and has proven successful in a multitude of eukaryotic cell and tissue types. Cells or dissociated tissues are crosslinked briefly with formaldehyde, lysed, and sonicated. Sheared chromatin is subjected to phenol-chloroform extraction and the isolated DNA, typically encompassing 1–3% of the human genome, is purified. We provide guidelines for quantitative analysis by PCR, microarrays, or next-generation sequencing. Regulatory elements enriched by FAIRE display high concordance with those identified by nuclease hypersensitivity or ChIP, and the entire procedure can be completed in three days. FAIRE exhibits low technical variability, which allows its use in large-scale studies of chromatin from normal or diseased tissues.
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DOI：
10.1093/bioinformatics/btp527
发表时间：
2009-11-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Lassmann T;Hayashizaki Y;Daub CO
通讯作者：
Daub CO
影响因子：
64.8
作者：
Felsenfeld, G;Groudine, M
通讯作者：
Groudine, M
人类胰岛中的开放染色质图。
影响因子：
30.8
作者：
Gaulton, Kyle J.;Nammo, Takao;Pasquali, Lorenzo;Simon, Jeremy M.;Giresi, Paul G.;Fogarty, Marie P.;Panhuis, Tami M.;Mieczkowski, Piotr;Secchi, Antonio;Bosco, Domenico;Berney, Thierry;Montanya, Eduard;Mohlke, Karen L.;Lieb, Jason D.;Ferrer, Jorge
通讯作者：
Ferrer, Jorge
影响因子：
5.1
作者：
Haring M;Offermann S;Danker T;Horst I;Peterhansel C;Stam M
通讯作者：
Stam M
影响因子：
14.8
作者：
Lee, Tong Ihn;Johnstone, Sarah E.;Young, Richard A.
通讯作者：
Young, Richard A.