Dts-seq: library preparation for a highly reproducible characterization of the tRNA epitranscriptome by deep sequencing

High-throughput sequencing of cellular tRNAs is severely hindered by the presence of base modifications that prevent a large fraction of transcripts to be converted into cDNA in conventional sequence library preparation. We present a method that takes advantage of the interference of modifications with reverse transcription enzymes to detect and identify them in RNA transcripts. This method, Dts-seq, is fully adapted to the direct characterization and quantification of mature tRNA transcripts. An analysis of the obtained read coverages from an Escherichia coli total RNA extraction enables to generate highly reproductible patterns of termination signals that can be used to assess the modification state of all tRNAs.