Genome-wide profiling of tRNA modifications by Induro-tRNAseq reveals coordinated changes

Yuko Nakano, Howard Gamper, Henri McGuigan, Sunita Maharjan, Jiatong Li, Zhiyi Sun, Erbay Yigit, Sebastian Grünberg, Keerthana Krishnan, Nan-Sheng Li, Joseph A. Piccirilli, Ralph Kleiner, Nicole Nichols, Brian D. Gregory and Ya-Ming Hou ()
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Yuko Nakano: Thomas Jefferson University
Howard Gamper: Thomas Jefferson University
Henri McGuigan: Thomas Jefferson University
Sunita Maharjan: Thomas Jefferson University
Jiatong Li: University of Pennsylvania
Zhiyi Sun: New England Biolabs
Erbay Yigit: New England Biolabs
Sebastian Grünberg: New England Biolabs
Keerthana Krishnan: New England Biolabs
Nan-Sheng Li: University of Chicago
Joseph A. Piccirilli: University of Chicago
Ralph Kleiner: Princeton University
Nicole Nichols: New England Biolabs
Brian D. Gregory: University of Pennsylvania
Ya-Ming Hou: Thomas Jefferson University

Nature Communications, 2025, vol. 16, issue 1, 1-19

Abstract: Abstract While all native tRNAs undergo extensive post-transcriptional modifications as a mechanism to regulate gene expression, mapping these modifications remains challenging. The critical barrier is the difficulty of readthrough of modifications by reverse transcriptases (RTs). Here we use Induro—a new group-II intron-encoded RT—to map and quantify genome-wide tRNA modifications in Induro-tRNAseq. We show that Induro progressively increases readthrough over time by selectively overcoming RT stops without altering the misincorporation frequency. In a parallel analysis of Induro vs. a related RT, we provide comparative datasets to facilitate the prediction of each modification. We assess tRNA modifications across five human cell lines and three mouse tissues and show that, while the landscape of modifications is highly variable throughout the tRNA sequence framework, it is stabilized for modifications that are required for reading of the genetic code. The coordinated changes have fundamental importance for development of tRNA modifications in protein homeostasis.

Date: 2025
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DOI: 10.1038/s41467-025-56348-1

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