SMiLE-seq identifies binding motifs of single and dimeric transcription factors
SMiLE-seq identifies binding motifs of single and dimeric transcription factors
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DOI：
10.1038/nmeth.4143
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发表时间：
2017-03-01
期刊：
影响因子：
48
通讯作者：
Deplancke, Bart
中科院分区：
文献类型：
--
作者：
Isakova, Alina;Groux, Romain;Deplancke, Bart
解决转录因子（TFS）的DNA结合特异性（TFS）对于理解基因调节具有关键价值。在这里，我们提出了一种新型的半小蛋白蛋白-DNA相互作用特征技术，基于选择性微流体的配体富集，然后进行测序（Smile-Seq）。 Smile-seq既不受DNA诱饵长度的限制，也不受偏向强亲和力粘合剂的偏见。它以快速且具有成本效益的方式探测TFS在广泛的亲和力范围内的DNNA结合特性。我们通过分析来自不同结构类别的58个全长人，小鼠和果蝇TF来验证微笑史。所有测试的TF产生的DNA结合模型的预测能力与其他体外测定法相比或更大。对所有JUN-FOS异二聚体和几种核受体TF复合物的从头序列发现，提供了对伴侣特异性异二聚体DNA结合偏好的新见解。我们还成功地分析了未表征的人C2H2锌指蛋白的DNA结合特性，并使用CHIP-EXO验证了几种。
Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand enrichment followed by sequencing (SMiLE-seq). SMiLE-seq is neither limited by DNA bait length nor biased toward strong affinity binders; it probes the DNDNA-binding properties of TFs over a wide affinity range in a fast and cost-effective fashion. We validated SMiLE-seq by analyzing 58 full-length human, mouse, and Drosophila TFs from distinct structural classes. All tested TFs yielded DNA-binding models with predictive power comparable to or greater than that of other in vitro assays. De novo motif discovery on all JUN-FOS heterodimers and several nuclear receptor-TF complexes provided novel insights into partner-specific heterodimer DNA-binding preferences. We also successfully analyzed the DNA-binding properties of uncharacterized human C2H2 zinc-finger proteins and validated several using ChIP-exo.