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，我们已经发现了密码子突变概率与相应氨基酸的化学差异之间的有趣关系。除了一些需要进一步研究的例外，人们可以得出结论，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。利用下一代测序技术，我们发现：1)编码单元的空间组织是一致基因表达的决定因素；2)在DNA超螺旋的生理水平上，发散的编码单元显示出最佳的活性；3)提出了DNA作为双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熔化能量和超螺旋)和数字信息(不同功能类别的基因)模式相对应的数据集，并将基因的物理化学性质与其功能内容进行了整合；v)我们检测到了介导3D DNA结构转换为表达模式的瞬时染色体结构域；vi)我们证明了将DNA模拟信息转换为数字线性代码是协调基因转录的基本机制。然而，对所获得的结果的解释将是至关重要的。我们将研究启动子区域的编码特性，并将Boltzmann和Shannon熵进行比较，以期提供更多的见解。我们热衷于了解DNA的物理化学参数(DNA语法)如何转换为遗传功能(DNA语义)。香农和玻尔兹曼熵之间的关系被视为获得对保护机制和基因表达的洞察的关键。