Tietjen Joshua R, Donato Leslie J, Bhimisaria Devesh, Ansari Aseem Z
Department of Biochemistry, The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, USA.
Methods Enzymol. 2011;497:3-30. doi: 10.1016/B978-0-12-385075-1.00001-9.
A central goal of biology is to understand how transcription factors target and regulate specific genes and networks to control cell fate and function. An equally important goal of synthetic biology, chemical biology, and personalized medicine is to devise molecules that can regulate genes and networks in a programmable manner. To achieve these goals, it is necessary to chart the sequence specificity of natural and engineered DNA-binding molecules. Cognate site identification (CSI) is now achieved via unbiased, high-throughput platforms that interrogate an entire sequence space bound by typical DNA-binding molecules. Analysis of these comprehensive specificity profiles is facilitated through the use of sequence-specificity landscapes (SSLs). SSLs reveal new modes of sequence cognition and overcome the limitations of current approaches that yield amalgamated "consensus" motifs. The landscapes also reveal the impact of nonconserved flanking sequences on binding to cognate sites. SSLs also serve as comprehensive binding energy landscapes that provide insights into the energetic thresholds at which natural and engineered molecules function within cells. Furthermore, applying the CSI binding data to genomic sequence (genomescapes) provides a powerful tool for identification of potential in vivo binding sites of a given DNA ligand, and can provide insight into differential regulation of gene networks. These tools can be directly applied to the design and development of synthetic therapeutic molecules and to expand our knowledge of the basic principles of molecular recognition.
生物学的一个核心目标是了解转录因子如何靶向并调控特定基因和网络，以控制细胞命运和功能。合成生物学、化学生物学和个性化医学的一个同样重要的目标是设计出能够以可编程方式调控基因和网络的分子。为实现这些目标，有必要绘制天然和工程化DNA结合分子的序列特异性图谱。同源位点鉴定（CSI）现在可通过无偏差的高通量平台来实现，这些平台可探究典型DNA结合分子所结合的整个序列空间。通过使用序列特异性景观（SSL），有助于对这些全面的特异性图谱进行分析。SSL揭示了新的序列识别模式，并克服了当前产生合并“共有”基序方法的局限性。这些景观还揭示了非保守侧翼序列对同源位点结合的影响。SSL还作为全面的结合能景观，为了解天然和工程化分子在细胞内发挥功能的能量阈值提供了见解。此外，将CSI结合数据应用于基因组序列（基因组景观）为识别给定DNA配体的潜在体内结合位点提供了一个强大工具，并可深入了解基因网络的差异调控。这些工具可直接应用于合成治疗分子的设计和开发，并扩展我们对分子识别基本原理的认识。
