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

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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.