m3C32 tRNA modification controls serine codon-biased mRNA translation, cell cycle, and DNA-damage response

Jia Cui; Erdem Sendinc; Qi Liu; Sujin Kim; Jaden Y Fang; Richard I Gregory

doi:10.1038/s41467-024-50161-y

m³C32 tRNA modification controls serine codon-biased mRNA translation, cell cycle, and DNA-damage response

Nat Commun. 2024 Jul 10;15(1):5775. doi: 10.1038/s41467-024-50161-y.

Authors

Jia Cui^#^{1

2}, Erdem Sendinc^#^{1

2}, Qi Liu^{1

2

3

4}, Sujin Kim^{1

2}, Jaden Y Fang^{1

2}, Richard I Gregory^{5

6

7

8

9}

Affiliations

¹ Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA.
² Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
³ Rice Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong Province, China.
⁴ Guangdong Key Laboratory of New Technology in Rice Breeding, 510640, Guangzhou, Guangdong Province, China.
⁵ Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, 02115, USA. [email protected].
⁶ Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA. [email protected].
⁷ Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA. [email protected].
⁸ Harvard Initiative for RNA Medicine, Boston, MA, 02115, USA. [email protected].
⁹ Harvard Stem Cell Institute, Cambridge, MA, 02138, USA. [email protected].

^# Contributed equally.

Abstract

The epitranscriptome includes a diversity of RNA modifications that influence gene expression. N3-methylcytidine (m³C) mainly occurs in the anticodon loop (position C32) of certain tRNAs yet its role is poorly understood. Here, using HAC-Seq, we report comprehensive METTL2A/2B-, METTL6-, and METTL2A/2B/6-dependent m³C profiles in human cells. METTL2A/2B modifies tRNA-arginine and tRNA-threonine members, whereas METTL6 modifies the tRNA-serine family. However, decreased m³C32 on tRNA-Ser-GCT isodecoders is only observed with combined METTL2A/2B/6 deletion. Ribo-Seq reveals altered translation of genes related to cell cycle and DNA repair pathways in METTL2A/2B/6-deficient cells, and these mRNAs are enriched in AGU codons that require tRNA-Ser-GCT for translation. These results, supported by reporter assays, help explain the observed altered cell cycle, slowed proliferation, and increased cisplatin sensitivity phenotypes of METTL2A/2B/6-deficient cells. Thus, we define METTL2A/2B/6-dependent methylomes and uncover a particular requirement of m³C32 tRNA modification for serine codon-biased mRNA translation of cell cycle, and DNA repair genes.

MeSH terms

Anticodon / genetics
Cell Cycle* / genetics
Codon* / genetics
Cytidine / analogs & derivatives
Cytidine / genetics
Cytidine / metabolism
DNA Damage*
DNA Repair
HEK293 Cells
Humans
Methyltransferases / genetics
Methyltransferases / metabolism
Protein Biosynthesis*
RNA, Messenger* / genetics
RNA, Messenger* / metabolism
RNA, Transfer* / genetics
RNA, Transfer* / metabolism
Serine* / metabolism

Substances

Codon
RNA, Messenger
RNA, Transfer
Serine
Methyltransferases
Cytidine
Anticodon

Abstract

MeSH terms

Substances

Grants and funding