Accurate mapping of tRNA reads

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Repetitive DNA elements, including transfer RNAs (tRNAs), are transcribed at significant levels.
• Mapping RNA sequencing (RNA-seq) reads to repetitive elements is challenging due to systematic mismatches from chemical modifications and locus similarity.

Purpose of the Study:

• To develop a specialized mapping strategy for accurately analyzing RNA-seq reads originating from tRNAs.
• To overcome the difficulties in mapping RNA-seq data to tRNA loci, especially in the presence of chemical modifications.

Main Methods:

• A novel mapping strategy was implemented using a modified reference genome.
• Known tRNA loci were masked, and intronless tRNA precursor sequences were added as artificial chromosomes.
• A two-pass mapping approach was employed: first, reads overlapping mature tRNA boundaries were extracted, and second, remaining reads were mapped to a tRNA-masked genome augmented with mature tRNA sequences.

Main Results:

• The developed workflow significantly reduces mapping artifacts compared to simpler methods.
• The strategy enables reliable identification of numerous chemical tRNA modifications in generic small RNA-seq data.
• Analysis of simulated data achieved a false discovery rate (FDR) of only 2%.

Conclusions:

• The new mapping strategy provides a robust method for analyzing tRNA-related RNA-seq data.
• The approach facilitates the discovery of tissue-specific tRNA modification patterns.
• The workflow is publicly available as a bash script and a Galaxy workflow.