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

Abstract

tRNAs are subject to numerous modifications, including methylation. Mutations in the human N-methylguanosine (mG) methyltransferase complex METTL1/WDR4 cause primordial dwarfism and brain malformation, yet the molecular and cellular function in mammals is not well understood. We developed mG methylated tRNA immunoprecipitation sequencing (MeRIP-seq) and tRNA reduction and cleavage sequencing (TRAC-seq) to reveal the mG 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 mG tRNA methylome and highlights its essential role in ESCs with links to human disease.

7-Methylguanosine Modifications in tRNA

“…In mESCs, the global m 7 G tRNA methylome is essential for appropriate translation of cell cycle genes and genes associated with brain malformation. Further to this observation, Mettl1 or Wdr4 knockout causes defective mESC self-renewal and neural lineage differentiation [103]. This study has clearly demonstrated the tRNA m 7 G methylome in mammals and shown the critical nature of METTL1 and WDR and m 7 G modification in regulation of stem cells and disease.…”

“…Amino acid substitution of WDR4 has been revealed as the cause mutation [101,102] The molecular mechanism of microcephaly has not been well understood. In order to profile the m 7 G tRNA methylome in mouse embryonic stem cell (mESCs), two independent methods have been developed: m 7 G methylated immunoprecipitation sequencing (MeRIP-seq) and tRNA reduction and cleavage sequencing (TRAC-seq) [103]. In mESCs, the global m 7 G tRNA methylome is essential for appropriate translation of cell cycle genes and genes associated with brain malformation.…”

“…modification have been demonstrated [81,93]. Furthermore, the physiological functions of m 7 G46 in tRNA have started to be determined over the past decade [99][100][101][102][103]. There seems to be little commonality between tRNA (m 7 G46) methyltransferase, rRNA m 7 G methyltransferase, and cap-m 7 G methyltransferase as far as the active centers are concerned.…”

Epigenetic modulations of noncoding RNA: a novel dimension of Cancer biology

“…m7G also occurs internally within human cytoplasmic tRNA and 18S-rRNA, installed by METTL1-WDR4 [87], a m7G "writer" complex, which is similar to m6A complex, and WBSCR22 [88,89], respectively. These internal m7G modifications impact RNA processing and function, especially mRNA translation [85,90]. However, its existence and distribution within miR-NAs or lncRNAs remain to be investigated.…”

Disruption of the RNA modifications that target the ribosome translation machinery in human cancer

“…m 7 G METTL1 and WDR4 are both necessary for the introduction of the 7-methylguanosine at position 46 [34]. In 2018, Lin et al have reported that METTL1 knockdown reduces the m 7 G fraction, which causes tRNA destabilization and ribosome pausing at m 7 G tRNA-dependent codons that leads to a decrease in translation [35]. Overexpression of METTL1 in hepatocellular carcinoma has been shown to promote cell proliferation and migration, and to lead to poor prognosis in HCC [36].…”