The DNA from a Coding Perspektive

从编码角度看DNA

• 批准号: 214186146
• 负责人: Professor Dr.-Ing. Werner Henkel
• 金额: --
• 依托单位: Department of Computer Science and Electrical Engineering
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 财政年份: 2012
• 资助国家: 德国
• 起止时间: 2011-12-31 至 2014-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/214186146?language=en
• 关键词: DNA; Coding; Perspektive

So far, we have found interesting relationships between mutation probabilities of codons and chemical differences in corresponding amino acids. Up to a few exceptions that need to be studied further, one can conclude that high mutational probabilities between two codons go together with rather relatedamino-acids, hence less damage. Within the coding regions, we did not find any error-correction procedure apart from the known mapping of codons to amino acids. Mutation probabilities also lead to a communication channel description and the capacity is compared to the minimum required information content given by the 20 amino acids.We modified all Lempel-Ziv source coding algorithms following the biological example of "embedded proteins", i.e., we modified them to be bi-directional making use of symmetries in the data.Using Next Generation Sequencing we found that i) the spatial organization of coding units is a determinant of coherent gene expression; ii) the divergent coding units in close proximity show optimal activity at physiological levels of DNA superhelicity; iii) we developed a novel concept of the DNA as a carrier of dual - analog and digital - information; iv) we generated datasets corresponding to patterns of analog information (DNA melting energy and supercoiling) and digital information (distinct functionalclasses of genes) and integrated the physicochemical properties of the genes with their functional content; v) we detected transient chromosomal domains mediating the conversion of the 3D DNA structures into expression patterns; vi) we showed that conversion of the DNA analog information into the digital linear code is a basic device coordinating the gene transcription.Having used multidimensional scaling as a tool to investigate distances between codons and amino-acids, sparse subspace clustering will be studied in the second project phase. However, the interpretation of the obtained results will be essential. Coding properties of promoter regions will be looked into and the comparison between Boltzmann and Shannon entropy is expected to give some more insights. We are keen to know how the physicochemical parameters of the DNA (DNA syntax) are converted into genetic function (DNA semantics). The relationship between Shannon and Boltzmann entropy is seen as the key to obtain insights into protection mechanisms and gene expression.

到目前为止，我们已经发现密码子的突变概率与相应氨基酸的化学差异之间存在有趣的关系。除了一些需要进一步研究的例外情况，我们可以得出结论，两个密码子之间的高突变概率与相当相关的氨基酸一起出现，因此损害较小。在编码区内，除了已知的密码子到氨基酸的映射之外，我们没有发现任何纠错程序。突变概率还导致通信通道描述，并将容量与 20 个氨基酸给出的最小所需信息内容进行比较。我们按照“嵌入蛋白质”的生物学示例修改了所有 Lempel-Ziv 源编码算法，即，我们利用数据中的对称性将它们修改为双向。使用下一代测序，我们发现 i) 编码单元的空间组织是 连贯基因表达的决定因素； ii) 非常接近的不同编码单元在 DNA 超螺旋的生理水平上表现出最佳活性； iii) 我们提出了 DNA 作为双重模拟和数字信息载体的新概念； iv) 我们生成了与模拟信息（DNA 熔化能和超螺旋）和数字信息（基因的不同功能类别）模式相对应的数据集，并将基因的理化特性与其功能内容相结合； v) 我们检测到介导 3D DNA 结构转化为表达模式的瞬时染色体结构域； vi) 我们表明，将DNA模拟信息转换为数字线性代码是协调基因转录的基本装置。在使用多维标度作为研究密码子和氨基酸之间距离的工具后，稀疏子空间聚类将在项目第二阶段进行研究。然而，对所得结果的解释至关重要。将研究启动子区域的编码特性，并且玻尔兹曼熵和香农熵之间的比较预计会提供更多见解。我们渴望知道DNA的理化参数（DNA语法）如何转化为遗传功能（DNA语义）。香农熵和玻尔兹曼熵之间的关系被视为深入了解保护机制和基因表达的关键。