Evolution of Chemical Modifications: from tRNAs to Transcriptome-Wide Surveys

化学修饰的演变：从 tRNA 到全转录组调查

• 批准号: 277447458
• 负责人: Professor Dr. Mario Mörl
• 金额: --
• 依托单位: Arbeitsgruppe Biochemie und Molekularbiologie
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 财政年份: 2015
• 资助国家: 德国
• 起止时间: 2014-12-31 至 2019-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/277447458?language=en
• 关键词: Evolution; Chemical; Modifications; tRNAs; Transcriptome

Chemically modified nucleotides are ubiquitous in RNA and DNA sequences. They act as epigenetic andepitranscriptomic marks modulating the function of genomic DNA and RNA transcripts in a cell history- andenvironment-dependent manner and they influence the stability of RNA structures. Modifications in tRNAsare particularly prevalent and appear to be well conserved in evolution. Nevertheless, they have received little systematic attention. Here we propose to use a combination of specialized deep sequencing approaches and sophisticated bioinformatics methods to elucidate both the evolution and the regulated variability of chemically modified nucleotides in tRNAs. Evolutionary questions will mostly be addressed by re-investigating the plethora of publicly available small RNA-seq data. Functional implications will be studied exemplarily using temperature adaptation in Bacillales and yeast. As part of the proposed research, we will improve the relevant computational tools, from read mapping and variation calling to classifying patterns of aligned reads characteristic for specific modifications.

化学修饰的核苷酸普遍存在于RNA和DNA序列中。它们作为表观遗传和转录组学标记，以细胞历史和增殖依赖性方式调节基因组DNA和RNA转录物的功能，并影响RNA结构的稳定性。tRNA中的修饰特别普遍，并且似乎在进化中很好地保守。然而，它们很少得到系统的关注。在这里，我们建议使用专门的深度测序方法和复杂的生物信息学方法的组合来阐明tRNA中化学修饰的核苷酸的进化和调节的变异性。进化问题将主要通过重新调查大量公开可用的小RNA-seq数据来解决。功能的影响将被研究示例性使用温度适应芽孢杆菌和酵母。作为拟议研究的一部分，我们将改进相关的计算工具，从读段映射和变异调用到特定修饰的对齐读段特征的分类模式。