DNA recognition-element binding by GRHL/CP2-family and NKX2-1 transcription factors

GRHL/CP2 家族和 NKX2-1 转录因子结合 DNA 识别元件

• 批准号: 426109004
• 负责人: Professor Dr. Udo Heinemann, Ph.D.
• 金额: --
• 依托单位: Forschungsgruppe Makromolekulare Strukturen und Interaktionen
• 依托单位国家: 德国
• 项目类别: Research Units
• 财政年份: 2019
• 资助国家: 德国
• 起止时间: 2018-12-31 至 2022-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/426109004?language=en
• 关键词: DNA; recognition; element; binding; GRHL

Transcriptional gene regulation depends on the transcription factors’ (TFs) ability to faithfully recognize DNA target sequences in promoters or enhancers. These molecular recognition pro-cesses usually tolerate small variations within the target sequence with only moderate loss in binding affinity. In stark contrast to the wealth of structural data available on the binding geometries of TFs to their consensus target sequences, comparatively little is known about the structural and energetic interactions these TFs have with sequence variants of their binding sites. Data of this kind have considerable value for assessing genome-wide TF DNA binding patterns and for predicting consequences of mutational events by bioinformatics tools. We propose to study two distinct types of TFs: the Grainyhead-like proteins GRHL1 and GRHL2 and the thyroid-specific factor NKX2-1, for which we have determined initial binding data and crystal structures. GRHL1/2 and NKX2-1 are representative TFs because they employ distinct modes of DNA sequence recognition and binding, promising to yield complementary insight into the sequence variant-dependent DNA binding process. In addition, GRHL2 and NKX2-1 act cooperatively in epithelial tissue development, with recent data suggesting a pioneering TF role for GRHL2. We will determine the binding parameters of GRHL1/2 and NKX2-1 to hundreds of DNA target sequences identified in genome-wide mapping studies and analyze the crystal structures of these proteins bound to tens of target sequences. We will validate the impact of DNA sequence variation on TF-DNA binding using in vivo systems. From our structural and biophysical data we aim to derive generalizable rules for TF binding to enhancers and promoters that will help the RU’s bioinformaticians to improve their algorithms for identification and prediction of disease-causing variants in the non-coding genome. This in turn will enable clinical scientists to identify a larger number of underlying genetic causes of the rare diseases seen in their patients.

转录基因的调控依赖于转录因子（TF）忠实地识别启动子或增强子中的DNA靶序列的能力。这些分子识别过程通常容许靶序列内的小变化，仅具有结合亲和力的适度损失。与TF与其共有靶序列的结合几何结构上可用的丰富结构数据形成鲜明对比的是，关于这些TF与其结合位点的序列变体的结构和能量相互作用相对知之甚少。此类数据对于评估全基因组TF DNA结合模式以及通过生物信息学工具预测突变事件的后果具有相当大的价值。我们建议研究两种不同类型的TF：Grainyhead样蛋白GRHL 1和GRHL 2和甲状腺特异性因子NKX 2 -1，我们已经确定了初始结合数据和晶体结构。GRHL 1/2和NKX 2 -1是代表性的TF，因为它们采用不同的DNA序列识别和结合模式，有望产生互补的洞察序列变异依赖的DNA结合过程。此外，GRHL 2和NKX 2 -1在上皮组织发育中协同作用，最近的数据表明GRHL 2具有开创性的TF作用。我们将确定GRHL 1/2和NKX 2 -1与全基因组定位研究中鉴定的数百个DNA靶序列的结合参数，并分析与数十个靶序列结合的这些蛋白质的晶体结构。我们将使用体内系统验证DNA序列变异对TF-DNA结合的影响。从我们的结构和生物物理数据，我们的目标是获得TF结合增强子和启动子，这将有助于RU的生物信息学家，以提高他们的算法识别和预测的非编码基因组中的致病变异的可推广的规则。这反过来将使临床科学家能够确定患者中罕见疾病的大量潜在遗传原因。