转录因子和DNA序列结合机制的系统生物学研究

项目名称： 转录因子和DNA序列结合机制的系统生物学研究

项目编号： No.31471232

项目类型： 面上项目

立项/批准年度： 2015

项目学科： 遗传学与生物信息学、细胞生物学

项目作者： 谢志

作者单位： 中山大学

项目金额： 80万元

中文摘要： 转录因子在基因转录调控中起着十分重要的作用。转录因子的缺陷或与靶DNA序列的错误结合会引起基因转录失调，从而导致各种的疾病发生。我们在过去的研究中，利用高通量蛋白质芯片首次大规模地鉴定了蛋白质对DNA序列的结合谱。为了进一步揭示转录因子和DNA序列相互结合的机制，本项目拟结合高通量转录因子DNA结合数据及转录因子DNA复合体晶体结构, 采用生物信息和生物实验相结合的手段，发现并验证转录因子序列上影响DNA结合特异性的关键氨基酸位点及其对DNA结合特异性的影响。除了证实传统认为的与DNA交界面上的氨基酸位点对DNA的调控机制，需要强调的是，本项目的前期工作首次提供了共进化的氨基酸位点对DNA结合有远程调控作用的证据，我们将进一步深入研究其潜在机理。本项目的研究思路强调系统性和全面性，预期研究结果将突破传统理论认识，有助于加深基因转录调控机制的理解，为转录失控相关的疾病的发生机制提供重要线索。

中文关键词： 转录因子；DNA结合特异性；蛋白质DNA结合；转录调控；氨基酸位点共进化

英文摘要： Transcription factors play a central role in regulating gene transcription. Mutations in transcription factors or in DNA binding sequences in promoters lead to a variety of diseases. Only in recent years, high-throughput approaches enable us to identify protein-DNA interactions in a large scale. In our previous research, we systematically characterized protein-DNA interactions using high-throughput protein microarrays. To further understand the mechanism of how amino acids in transcription factors interact with DNA sequences, we propose a combined computational and experimental approach to identify key amino acids that specify DNA binding preferences of transcription factors. Our preliminary analysis showed that amino acids on the DNA contacting surface of transcription factors are important in controlling DNA binding specificity. Surprisingly, we further identified several key amino acids that are far away from the DNA contacting surface (long-range) also are important in specifying DNA binding preferences. Our preliminary analysis also, for the first time, provided evidence that this type of long-range amino acids are typically continuous on the tertiary structure and are evolutionarily coevolved. We propose to further experimentally validate the functions of long-range amino acids and to extend our analysis to all the other major transcription factor families such as HLH and bZIP. Our study will deepen our understanding in rules specifying DNA binding preferences of transcription factors and will provide important insights into transcriptional dysfunction related diseases.

英文关键词： Transcription factor;DNA binding specificity;protein-DNA interaction;transcriptional regulation;coevolution of amino acid site