Targeted sequencing reveals expanded genetic diversity of human transfer RNAs

Abstract

Transfer RNAs are required to translate genetic information into proteins as well as regulate other cellular processes. Nucleotide changes in tRNAs can result in loss or gain of function that impact the composition and fidelity of the proteome. Despite links between tRNA variation and disease, the importance of cytoplasmic tRNA variation has been overlooked. Using a custom capture panel, we sequenced 605 human tRNA-encoding genes from 84 individuals. We developed a bioinformatic pipeline that allows more accurate tRNA read mapping and identifies multiple polymorphisms occurring within the same variant. Our analysis identified 522 unique tRNA-encoding sequences that differed from the reference genome from 84 individuals. Each individual had~66 tRNA variants including nine variants found in less than 5% of our sample group. Variants were identified throughout the tRNA structure with 17% predicted to enhance function. Eighteen anticodon mutants were identified including potentially mistranslating tRNAs; e.g., a tRNA Ser that decodes Phe codons. Similar engineered tRNA variants were previously shown to inhibit cell growth, increase apoptosis and induce the unfolded protein response in mammalian cell cultures and chick embryos. Our analysis shows that human tRNA variation has been underestimated. We conclude that the large number of tRNA genes provides a buffer enabling the emergence of variants, some of which could contribute to disease.

The amino acid substitution affects cellular response to mistranslation

“…Significance of the differing impacts of tRNA variants tRNA variants with the potential to mistranslate are found in the human population (Berg et al 2019a). Approximately 20% of all individuals have either an anticodon mutation in tRNA Ser or tRNA Ala or an acceptor stem mutation that generates a G3:U70 base pair, the major identity element for charging with alanine (Hou and Schimmel 1988;Francklyn and Schimmel 1989).…”

“…Similar tRNA variants that likely mistranslate are found in human populations. In a sample of 84 individuals, we identified six variants that create G3:U70 base pairs in non-alanine tRNAs and 14 anticodon variants that alter tRNA decoding identity (Berg et al 2019a).…”

The amino acid substitution affects cellular response to mistranslation

“…tRNA variants with the potential to mistranslate are found in the human population ( Berg et al 2019a ). Approximately 20% of all individuals have either an anticodon mutation in tRNA Ser or tRNA Ala or an acceptor stem mutation that generates a G3: U70 base pair, the major identity element for charging with alanine ( Hou and Schimmel 1988 ; Francklyn and Schimmel 1989 ).…”

“…Similar tRNA variants that likely mistranslate are found in human populations. In a sample of 84 individuals, we identified six variants that create G3: U70 base pairs in nonalanine tRNAs and 14 anticodon variants that alter tRNA decoding identity ( Berg et al 2019a ).…”

Transfer RNAs: diversity in form and function

“…Interestingly, similar mutations within tRNA encoding genes that cause mistranslation in yeast are found in human tRNA genes [381,387]. Using a DNA capture array, we sequenced the tRNA genes from 84 individuals.…”