Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms
Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms
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DOI：
10.1007/s10142-007-0054-7
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发表时间：
2007-10-01
影响因子：
2.9
通讯作者：
Snyder, Michael
中科院分区：
文献类型：
--
作者：
Borneman, Anthony R.;Zhang, Zhengdong D.;Snyder, Michael
近年来，利用染色质免疫沉淀结合DNA微阵列(芯片)定位转录因子结合位点的技术已得到发展。最初，基于聚合酶链式反应(PCR)的DNA阵列用于芯片程序，然而，允许每个阵列产生数千个更多特征的高密度寡核苷酸(HDO)阵列已经成为一种竞争的阵列平台。为了比较这两个平台，比较了在相同的实验条件下使用HDO和PCR阵列对三个因素(Tec1、STE12和Sok2)进行芯片分析的数据。HDO阵列提供了更高的重复性和灵敏度，检测到的结合事件大约是PCR阵列的三倍，同时也显示出更高的准确性。HDO阵列提供的更高的分辨率还允许识别近距离的多个结合峰以及新的结合事件，例如ORF内的结合。从所有方面来看，HDO阵列平台提供的阵列系统都比基于聚合酶链式反应的阵列要强大得多，所有这些都直接归功于可用的大量探针。
In recent years, techniques have been developed to map transcription factor binding sites using chromatin immunoprecipitation combined with DNA microarrays (chIP chip). Initially, polymerase chain reaction (PCR)based DNA arrays were used for the chIP chip procedure, however, high-density oligonucleotide (HDO) arrays, which allow for the production of thousands more features per array, have emerged as a competing array platform. To compare the two platforms, data from chIP chip analysis performed for three factors (Tec1, Ste12, and Sok2) using both HDO and PCR arrays under identical experimental conditions were compared. HDO arrays provided increased reproducibility and sensitivity, detecting approximately three times more binding events than the PCR arrays while also showing increased accuracy. The increased resolution provided by the HDO arrays also allowed for the identification of multiple binding peaks in close proximity and of novel binding events such as binding within ORFs. The HDO array platform provides a far more robust array system by all measures than PCR-based arrays, all of which is directly attributable to the large number of probes available.