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CMTR1 regulates hippocampus-dependent memory consolidation and long-term synaptic plasticity by promoting NMDA-receptor signaling

ABSTRACT: Eukaryotic mRNA is 5'-end capped with m7 guanosine, forming the cap0 (m7GpppNpNp, N: any nucleotide). Cap methyltransferase (CMTR1) further catalyzes 2'-O-ribose methylation of the first transcribed nucleotide (N1 2'-O-Me) to produce the cap1 (m7GpppNmNp) structure in all eukaryotes except yeasts. To elucidate the molecular changes in the hippocampus caused by the deletion of CMTR1 in Emx1-lineage cells, hippocampal tissues from CMTR1-cWT and cKOEmx1 mice were processed for RNA-sequencing analysis.

ORGANISM(S): Mus musculus

PROVIDER: GSE279686 | GEO | 2025/08/06

REPOSITORIES: GEO

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Project description:CMTR1 (cap methyltransferase 1), a key nuclear mRNA cap methyltransferase, catalyzes 2'-O-methylation of the first transcribed nucleotide, a critical step in mRNA cap formation. Previous studies have implicated CMTR1 in embryonic stem cell differentiation and immune responses during viral infection; however, its role in cancer biology remains largely unexplored. In this study, we conducted a comprehensive multi-omics analysis of CMTR1 across various human cancers using TCGA and CPTAC datasets. Functional studies were performed using CRISPR-mediated knockout and siRNA knockdown in human and mouse basal-like breast cancer models. Transcriptomic and pathway enrichment analyses were carried out in CMTR1 knockout/knockdown models to identify CMTR1-regulated genes. In silico screening and biochemical assays were employed to identify novel CMTR1 inhibitors.We found that CMTR1 is significantly upregulated at the mRNA, protein, and phosphoprotein levels across multiple cancer types. Functional studies demonstrated that CMTR1 depletion significantly inhibits tumor growth both in vitro and in vivo. Transcriptomic analysis of CMTR1 knockout cells revealed that CMTR1 primarily regulates ribosomal protein genes and other transcripts containing 5' Terminal Oligopyrimidine (TOP) motifs. Additionally, CMTR1 affects the expression of snoRNA host genes and snoRNAs, suggesting a broader role in RNA metabolism. Mechanistic studies indicated that CMTR1's target specificity is partly determined by mRNA structure, particularly the presence of 5'TOP motifs. Finally, through in silico screening and biochemical assays, we identified several novel CMTR1 inhibitors, including N97911, which demonstrated in vitro growth inhibition activity in breast cancer cells. In conclusion, our findings establish CMTR1 as a key player in cancer biology, regulating critical aspects of RNA metabolism and ribosome biogenesis. The study highlights CMTR1's potential as a therapeutic target across multiple cancer types and provides a foundation for developing novel cancer treatments targeting mRNA cap methylation.

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CMTR1 regulates hippocampus-dependent memory consolidation and long-term synaptic plasticity by promoting NMDA-receptor signaling

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