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Nature Biotechnology:CHIP-nexus助力转录因子结合位点检测

来源:生物谷 2015-03-15 13:59

2015年3月15日讯 /生物谷BIOON/ --近日,著名国际期刊Nature Biotechnology在线发表了美国科学家的一项最新研究进展,他们开发了一种叫做CHIP-nexus的染色质免疫沉淀技术,高效检测基因组内的转录因子结合位点,这项研究为转录因子结合位点图谱绘制和基因的转录调控研究提供了很大助力。
 
研究人员指出了解转录因子如何特异性结合并调节真核细胞基因组中的增强子目前仍存在很大困难。为更好地绘制基因组范围内转录因子的结合图谱,他们开发了一种强大的CHIP-exo实验流程,并将其命名为CHIP-nexus(chromatin immunoprecipitation experiments with nucleotide resolution through exonuclease, unique barcode and single ligation),这一方法高效地利用了文库制备过程中的DNA自环化过程。
 
研究人员通过CHIP-nexus方法检测了四种蛋白(人类TBP和果蝇NFkB,Twist,Max)的基因组结合位点,结果发现这种方法在分辨率和特异性方面远胜现在普遍使用的CHIP技术,并且能够对包含多个结合基序的增强子的转录因子结合位点进行准确定位,同时能够在体内条件下对结合位点特异性进行分析。研究人员还发现Max经常与其结合基序临近的DNA序列发生相互作用,并且这种结合模式与局部DNA序列特征如DNA形状具有相关性。
 
综上所述,CHIP-nexus技术会在转录因子结合特异性的体内研究方面以及研究转录因子与人类和其他模式生物顺势调控元件变化的关系方面得到广泛应用。(生物谷Bioon.com)
 
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ChIP-nexus enables improved detection of in vivo transcription factor binding footprints
 
Qiye He,Jeff Johnston&Julia Zeitlinger
 
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-nexus (chromatin immunoprecipitation experiments with nucleotide resolution through exonuclease, unique barcode and single ligation), 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-shows that it outperforms existing ChIP protocols in resolution and specificity, pinpoints relevant binding sites within enhancers containing multiple binding motifs, and allows for 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 the study of in vivotranscription factor binding specificity and its relationship to cis-regulatory changes in humans and model organisms.
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