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

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去转录标记，以细胞历史和环境依赖的方式调节基因组DNA和RNA转录本的功能，并影响RNA结构的稳定性。TRNA中的修饰特别普遍，而且在进化中似乎很保守。尽管如此，它们几乎没有得到系统的关注。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相结合来阐明tRNA中化学修饰核苷酸的进化和调节的可变性。进化问题将主要通过重新调查过多的可公开获得的小RNA-SEQ数据来解决。我们将利用芽孢杆菌和酵母菌的温度适应来示范研究其功能。作为拟议研究的一部分，我们将改进相关的计算工具，从阅读映射和变异调用到对特定修改的对齐阅读特征模式进行分类。

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.