Mettl1/Wdr4-Mediated m7G tRNA Methylome Is Required for Normal mRNA Translation and Embryonic Stem Cell Self-Renewal and Differentiation

Shuibin Lin; Qi Liu; Victor S Lelyveld; Junho Choe; Jack W Szostak; Richard I Gregory

doi:10.1016/j.molcel.2018.06.001

Mettl1/Wdr4-Mediated m⁷G tRNA Methylome Is Required for Normal mRNA Translation and Embryonic Stem Cell Self-Renewal and Differentiation

Mol Cell. 2018 Jul 19;71(2):244-255.e5. doi: 10.1016/j.molcel.2018.06.001. Epub 2018 Jul 5.

Authors

Shuibin Lin¹, Qi Liu², Victor S Lelyveld³, Junho Choe², Jack W Szostak⁴, Richard I Gregory⁵

Affiliations

¹ Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
² Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
³ Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
⁴ Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
⁵ Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Initiative for RNA Medicine, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address: rgregory@enders.tch.harvard.edu.

Abstract

tRNAs are subject to numerous modifications, including methylation. Mutations in the human N⁷-methylguanosine (m⁷G) methyltransferase complex METTL1/WDR4 cause primordial dwarfism and brain malformation, yet the molecular and cellular function in mammals is not well understood. We developed m⁷G methylated tRNA immunoprecipitation sequencing (MeRIP-seq) and tRNA reduction and cleavage sequencing (TRAC-seq) to reveal the m⁷G tRNA methylome in mouse embryonic stem cells (mESCs). A subset of 22 tRNAs is modified at a "RAGGU" motif within the variable loop. We observe increased ribosome occupancy at the corresponding codons in Mettl1 knockout mESCs, implying widespread effects on tRNA function, ribosome pausing, and mRNA translation. Translation of cell cycle genes and those associated with brain abnormalities is particularly affected. Mettl1 or Wdr4 knockout mESCs display defective self-renewal and neural differentiation. Our study uncovers the complexity of the mammalian m⁷G tRNA methylome and highlights its essential role in ESCs with links to human disease.

Keywords: MeRIP-seq; Mettl1; N(7)-methylguanosine; RNA methylation; TRAC-seq; Wdr4; embryonic stem cells; m(7)G; neural development; tRNA; translation.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Base Sequence
Cell Differentiation / genetics
Cell Line
Cell Self Renewal / genetics
Embryonic Stem Cells
GTP-Binding Proteins / genetics*
GTP-Binding Proteins / metabolism
Guanosine / analogs & derivatives*
Guanosine / genetics
Guanosine / metabolism
Humans
Methylation
Methyltransferases / genetics*
Methyltransferases / metabolism
Mice
Mouse Embryonic Stem Cells
RNA Processing, Post-Transcriptional
RNA, Transfer / genetics*
RNA, Transfer / metabolism

Substances

8-methylguanosine
WDR4 protein, human
Guanosine
RNA, Transfer
METTL1 protein, human
Methyltransferases
GTP-Binding Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding