Advances in methods for tRNA sequencing and quantification

Nigam H Padhiar; Upendra Katneni; Anton A Komar; Yuri Motorin; Chava Kimchi-Sarfaty

doi:10.1016/j.tig.2023.11.001

Advances in methods for tRNA sequencing and quantification

Trends Genet. 2024 Mar;40(3):276-290. doi: 10.1016/j.tig.2023.11.001. Epub 2023 Dec 19.

Authors

Nigam H Padhiar¹, Upendra Katneni¹, Anton A Komar², Yuri Motorin³, Chava Kimchi-Sarfaty⁴

Affiliations

¹ Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
² Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA.
³ CNRS-Université de Lorraine, UAR 2008, IBSLor UMR 7365 IMoPA, Nancy, France. Electronic address: yuri.motorin@univ-lorraine.fr.
⁴ Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA. Electronic address: Chava.kimchi-sarfaty@fda.hhs.gov.

PMID: 38123442
DOI: 10.1016/j.tig.2023.11.001

Abstract

In the past decade tRNA sequencing (tRNA-seq) has attracted considerable attention as an important tool for the development of novel approaches to quantify highly modified tRNA species and to propel tRNA research aimed at understanding the cellular physiology and disease and development of tRNA-based therapeutics. Many methods are available to quantify tRNA abundance while accounting for modifications and tRNA charging/acylation. Advances in both library preparation methods and bioinformatic workflows have enabled developments in next-generation sequencing (NGS) workflows. Other approaches forgo NGS applications in favor of hybridization-based approaches. In this review we provide a brief comparative overview of various tRNA quantification approaches, focusing on the advantages and disadvantages of these methods, which together facilitate reliable tRNA quantification.

Keywords: bioinformatics; hybridization; modifications; quantification; sequencing; tRNA.

Published by Elsevier Ltd.

Publication types

Review

MeSH terms

Computational Biology
High-Throughput Nucleotide Sequencing* / methods
RNA, Transfer* / genetics
Transfer RNA Aminoacylation

Substances

RNA, Transfer

Grants and funding

R01 HL151392/HL/NHLBI NIH HHS/United States