Spec-seq: determining protein-DNA-binding specificity by sequencing
Spec-seq: determining protein-DNA-binding specificity by sequencing
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DOI：
10.1093/bfgp/elu043
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发表时间：
2015-01-01
影响因子：
4
通讯作者：
Chang，Yiming Kenny
中科院分区：
文献类型：
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作者：
Stormo，Gary D.;Zuo，Zheng;Chang，Yiming Kenny
蛋白质-DNA相互作用的特异性可以通过在标准结合反应中对结合和未结合的部分进行测序来直接确定。该方法简单、廉价，并且对于平行测定的数千个序列的准确性可以很高。根据测量结果，可以评估简单的特异性模型（如位置权重矩阵）的准确性，并在有用时开发更复杂的模型。这些可以提供更准确的预测活体结合位点，并可以帮助我们了解识别的细节。作为一个例子，我们展示了新的信息获得的结合乳糖阻遏物。人们可以将相同的方法应用于同时与单个DNA结合的因子的组合，并确定单个因子的特异性和它们之间的协同性。
The specificity of protein–DNA interactions can be determined directly by sequencing the bound and unbound fractions in a standard binding reaction. The procedure is easy and inexpensive, and the accuracy can be high for thousands of sequences assayed in parallel. From the measurements, simple models of specificity, such as position weight matrices, can be assessed for their accuracy and more complex models developed if useful. Those may provide more accurate predictions ofin vivobinding sites and can help us to understand the details of recognition. As an example, we demonstrate new information gained about the binding of lac repressor. One can apply the same method to combinations of factors that bind simultaneously to a single DNA and determine both the specificity of the individual factors and the cooperativity between them.