The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, People's Republic of China.
J Endocrinol. 2011 Jul;210(1):15-27. doi: 10.1530/JOE-11-0010. Epub 2011 Mar 9.
The DNA-binding specificity of transcription factors (TFs) has broad impacts on cell physiology, cell development and in evolution. However, the DNA-binding specificity of most known TFs still remains unknown. The specificity of a TF protein is determined by its relative affinity to all possible binding sites. In recent years, the development of several in vitro techniques permits high-throughput determination of relative binding affinity of a TF to all possible k bp-long DNA sequences, thus greatly promoting the characterization of DNA-binding specificity of many known TFs. All DNA sequences that can be bound by a TF with various binding affinities form their DNA-binding profile (DBP). The DBP is important to generate an accurate DNA-binding model, identify all DNA-binding sites and target genes of TFs in the whole genome, and build transcription regulatory network. This study reviewed these techniques, especially two master techniques: double-stranded DNA microarray and systematic evolution of ligands by exponential enrichment in combination with parallel DNA sequencing techniques (SELEX-seq).
转录因子 (TFs) 的 DNA 结合特异性对细胞生理学、细胞发育和进化都有广泛的影响。然而，大多数已知 TF 的 DNA 结合特异性仍然未知。TF 蛋白的特异性由其对所有可能结合位点的相对亲和力决定。近年来，几种体外技术的发展允许高通量测定 TF 对所有可能的 k bp 长 DNA 序列的相对结合亲和力，从而极大地促进了许多已知 TF 的 DNA 结合特异性的表征。所有可以与 TF 以各种结合亲和力结合的 DNA 序列构成其 DNA 结合谱 (DBP)。DBP 对于生成准确的 DNA 结合模型、识别整个基因组中 TF 的所有 DNA 结合位点和靶基因以及构建转录调控网络非常重要。本研究综述了这些技术，特别是两种主要技术：双链 DNA 微阵列和指数富集的配体系统进化与平行 DNA 测序技术 (SELEX-seq) 的结合。
