Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
Nat Biotechnol. 2012 May 20;30(6):521-30. doi: 10.1038/nbt.2205.
Despite extensive research, our understanding of the rules according to which cis-regulatory sequences are converted into gene expression is limited. We devised a method for obtaining parallel, highly accurate gene expression measurements from thousands of designed promoters and applied it to measure the effect of systematic changes in the location, number, orientation, affinity and organization of transcription-factor binding sites and nucleosome-disfavoring sequences. Our analyses reveal a clear relationship between expression and binding-site multiplicity, as well as dependencies of expression on the distance between transcription-factor binding sites and gene starts which are transcription-factor specific, including a striking ∼10-bp periodic relationship between gene expression and binding-site location. We show how this approach can measure transcription-factor sequence specificities and the sensitivity of transcription-factor sites to the surrounding sequence context, and compare the activity of 75 yeast transcription factors. Our method can be used to study both cis and trans effects of genotype on transcriptional, post-transcriptional and translational control.
尽管进行了广泛的研究，但我们对顺式调控序列转化为基因表达的规则的理解仍然有限。我们设计了一种方法，从数千个设计的启动子中获得并行的、高度准确的基因表达测量值，并应用它来测量转录因子结合位点和核小体不利序列的位置、数量、方向、亲和力和组织的系统变化对基因表达的影响。我们的分析揭示了表达与结合位点多样性之间的明显关系，以及表达对转录因子结合位点与基因起始之间距离的依赖性，这种依赖性因转录因子的特异性而有所不同，包括基因表达与结合位点位置之间惊人的约 10bp 周期性关系。我们展示了这种方法如何测量转录因子的序列特异性以及转录因子结合位点对周围序列环境的敏感性，并比较了 75 个酵母转录因子的活性。我们的方法可用于研究基因型对转录、转录后和翻译控制的顺式和反式影响。
