ChIP-nexus enables improved detection of in vivo transcription factor binding footprints.
ChIP-nexus enables improved detection of in vivo transcription factor binding footprints.
复制标题
DOI：
10.1038/nbt.3121
复制
发表时间：
2015-04
影响因子：
46.9
通讯作者：
Zeitlinger, Julia
中科院分区：
文献类型：
--
作者：
He, Qiye;Johnston, Jeff;Zeitlinger, Julia
了解真核增强子如何被转录因子的特定组合结合和调节仍然是一个重大挑战。为了更好地在体内以核苷酸分辨率绘制全基因组转录因子结合图谱，我们开发了一种强大的 ChIP-exo 方案，称为 ChIP 实验，通过核酸外切酶、独特的条形码和单连接 (ChIP-nexus) 实现核苷酸分辨率，该方案在文库制备过程中利用了高效的 DNA 自环化步骤。 ChIP-nexus 对四种蛋白质（人 TBP 和果蝇 NFkB、Twist 和 Max）的应用表明，它在分辨率和特异性方面优于现有的 ChIP 方案，精确定位包含多个结合基序的增强子内的相关结合位点，并允许分析体内结合特异性。值得注意的是，我们表明 Max 经常与其基序旁边的 DNA 序列相互作用，并且这种结合模式与局部 DNA 序列特征（例如 DNA 形状）相关。 ChIP-nexus 将广泛应用于研究体内转录因子结合特异性及其与人类和模型生物体内顺式调控变化的关系。
Understanding how eukaryotic enhancers are bound and regulated by specific combinations of transcription factors is still a major challenge. To better map transcription factor binding genome-wide at nucleotide resolution in vivo, we have developed a robust ChIP-exo protocol called ChIP experiments with nucleotide resolution through exonuclease, unique barcode and single ligation (ChIP-nexus), which utilizes an efficient DNA self-circularization step during library preparation. Application of ChIP-nexus to four proteins—human TBP and Drosophila NFkB, Twist and Max— demonstrates that it outperforms existing ChIP protocols in resolution and specificity, pinpoints relevant binding sites within enhancers containing multiple binding motifs and allows the analysis of in vivo binding specificities. Notably, we show that Max frequently interacts with DNA sequences next to its motif, and that this binding pattern correlates with local DNA sequence features such as DNA shape. ChIP-nexus will be broadly applicable to studying in vivo transcription factor binding specificity and its relationship to cis-regulatory changes in humans and model organisms.
登录
查看更多内容
影响因子：
30.8
作者：
He, Qiye;Bardet, Anais F.;Zeitlinger, Julia
通讯作者：
Zeitlinger, Julia
影响因子：
9.9
作者：
Fakhouri, Walid D.;Ay, Ahmet;Sayal, Rupinder;Dresch, Jacqueline;Dayringer, Evan;Arnosti, David N.
通讯作者：
Arnosti, David N.
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
16.8
作者：
通讯作者：
--
影响因子：
14.9
作者：
Casbon JA;Osborne RJ;Brenner S;Lichtenstein CP
通讯作者：
Lichtenstein CP