2. Academic Validation
  3. MapID-based quantitative mapping of chemical modifications and expression of human transfer RNA

MapID-based quantitative mapping of chemical modifications and expression of human transfer RNA

  • Cell Chem Biol. 2025 May 15;32(5):752-766.e7. doi: 10.1016/j.chembiol.2025.04.003.
Mitchel L Tepe 1,  Yitan Chen 1,  Allison Carso 1,  Huiqing Zhou 2
Affiliations

Affiliations

  • 1 Chemistry Department, Boston College, Chestnut Hill, MA 02467, USA.
  • 2 Chemistry Department, Boston College, Chestnut Hill, MA 02467, USA. Electronic address: huiqing.zhou@bc.edu.
PMID: 40318625 DOI: 10.1016/j.chembiol.2025.04.003
Abstract

Detection and quantification of tRNA chemical modifications are critical for understanding their regulatory functions in biology and diseases. However, tRNA-seq-based methods for modification mapping encountered challenges both experimentally (poor processivity of heavily modified tRNAs during reverse transcription or RT) and bioinformatically (frequent reads misalignment to highly similar tRNA genes). Here, we report "MapID-tRNA-seq" where we deployed an evolved Reverse Transcriptase (RT-1306) into tRNA-seq and developed "MapIDs" that reduce redundancy of the human tRNA genome and explicitly annotate genetic variances. RT-1306 generated robust mutations against m1A and m3C, and RT stops against multiple bulky roadblock modifications. MapID-assisted data processing enabled systematic exclusion of false-positive discoveries of modifications which arise from reads misalignment onto similar genes. We applied MapID-tRNA-seq into mapping m1A, m3C and expression levels of tRNAs in three mammary cell lines, which revealed cell-type dependent modification sites and potential translational regulation of the reduced mitochondrial activities in breast Cancer.

Keywords

human tRNA genetic variance; mammary cells; tRNA chemical modifications; tRNA-seq.

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