Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
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DOI：
10.1038/nbt1246
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发表时间：
2006-11-01
影响因子：
46.9
通讯作者：
Bulyk, Martha L.
中科院分区：
文献类型：
--
作者：
Berger, Michael F.;Philippakis, Anthony A.;Bulyk, Martha L.
转录因子（TFS）与特定的DNA调节序列相互作用，以控制多个细胞过程中的基因表达。但是，只有一小部分TF的DNA结合特异性足够表征以预测它们可以和不能结合的序列。我们提出了蛋白质结合微阵列（PBM）实验（1）的最大紧凑，合成的DNA序列设计，该实验代表给定长度k的所有可能的DNA序列变体（即所有“ k-mers”） 。我们通过将高密度的单链寡核苷酸阵列转换为双链（DS）DNA阵列，构建了覆盖所有10个碱基对（BP）结合位点的所有K-MER微阵列。使用这些微阵列，我们全面确定了来自酵母，蠕虫，小鼠和人类的五个不同结构类别的五个TF的完整亲和力的结合特异性。所有K-MER的无偏覆盖范围允许以前所未有的分辨率对结合位点偏好（包括核苷酸相互依赖的）的高吞吐量询问。
Transcription factors ( TFs) interact with specific DNA regulatory sequences to control gene expression throughout myriad cellular processes. However, the DNA binding specificities of only a small fraction of TFs are sufficiently characterized to predict the sequences that they can and cannot bind. We present a maximally compact, synthetic DNA sequence design for protein binding microarray ( PBM) experiments(1) that represents all possible DNA sequence variants of a given length k ( that is, all 'k- mers') on a single, universal microarray. We constructed such all k- mer microarrays covering all 10 - base pair ( bp) binding sites by converting high- density single- stranded oligonucleotide arrays to double- stranded ( ds) DNA arrays. Using these microarrays we comprehensively determined the binding specificities over a full range of affinities for five TFs of different structural classes from yeast, worm, mouse and human. The unbiased coverage of all k-mers permits high- throughput interrogation of binding site preferences, including nucleotide interdependencies, at unprecedented resolution.