Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
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DOI：
10.1038/ng1473
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发表时间：
2004-12-01
期刊：
影响因子：
30.8
通讯作者：
Bulyk, ML
中科院分区：
文献类型：
--
作者：
Mukherjee, S;Berger, MF;Bulyk, ML
我们开发了一种基于DNA微阵列的新技术，称为蛋白质结合微阵列(PBMS)，可以在一天内快速、高通量地表征转录因子的体外DNA结合位点序列特异性。利用PBMS，我们鉴定了酵母转录因子Abf1、Rap1和Mig1的DNA结合位点序列特异性。对这些蛋白质的体外结合位点和体内结合位点的比较表明，PBM衍生的序列特异性可以准确地反映体内DNA序列的特异性。除了先前已确定的靶点外，Abf1、Rap1和Mig1分别与107、90和75个假定的新靶标间隔区结合，其中许多位于先前未确定的开放阅读框的上游。比较序列分析表明，这些新发现的许多位点在五个测序的正义酵母物种中高度保守，因此很可能是体内的功能性结合位点，可能以特定条件的方式使用。类似的PBM实验在识别各种基因组中新的顺式调控元件和转录调控网络方面应该是有用的。
We developed a new DNA microarray-based technology, called protein binding microarrays (PBMs), that allows rapid, high-throughput characterization of the in vitro DNA binding site sequence specificities of transcription factors in a single day. Using PBMs, we identified the DNA binding-site sequence specificities of the yeast transcription factors Abf1, Rap1 and Mig1. Comparison of these proteins' in vitro binding sites with their in vivo binding sites indicates that PBM-derived sequence specificities can accurately reflect in vivo DNA sequence specificities. In addition to previously identified targets, Abf1, Rap1 and Mig1 bound to 107, 90 and 75 putative new target intergenic regions, respectively, many of which were upstream of previously uncharacterized open reading frames. Comparative sequence analysis indicated that many of these newly identified sites are highly conserved across five sequenced sensu stricto yeast species and, therefore, are probably functional in vivo binding sites that may be used in a condition-specific manner. Similar PBM experiments should be useful in identifying new cis regulatory elements and transcriptional regulatory networks in various genomes.