Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme

Mol Cancer. 2020 Feb 25;19(1):36. doi: 10.1186/s12943-020-01155-z.


Background: Literature reports that mature microRNA (miRNA) can be methylated at adenosine, guanosine and cytosine. However, the molecular mechanisms involved in cytosine methylation of miRNAs have not yet been fully elucidated. Here we investigated the biological role and underlying mechanism of cytosine methylation in miRNAs in glioblastoma multiforme (GBM).

Methods: RNA immunoprecipitation with the anti-5methylcytosine (5mC) antibody followed by Array, ELISA, dot blot, incorporation of a radio-labelled methyl group in miRNA, and miRNA bisulfite sequencing were perfomred to detect the cytosine methylation in mature miRNA. Cross-Linking immunoprecipiation qPCR, transfection with methylation/unmethylated mimic miRNA, luciferase promoter reporter plasmid, Biotin-tagged 3'UTR/mRNA or miRNA experiments and in vivo assays were used to investigate the role of methylated miRNAs. Finally, the prognostic value of methylated miRNAs was analyzed in a cohorte of GBM pateints.

Results: Our study reveals that a significant fraction of miRNAs contains 5mC. Cellular experiments show that DNMT3A/AGO4 methylated miRNAs at cytosine residues inhibit the formation of miRNA/mRNA duplex and leading to the loss of their repressive function towards gene expression. In vivo experiments show that cytosine-methylation of miRNA abolishes the tumor suppressor function of miRNA-181a-5p miRNA for example. Our study also reveals that cytosine-methylation of miRNA-181a-5p results is associated a poor prognosis in GBM patients.

Conclusion: Together, our results indicate that the DNMT3A/AGO4-mediated cytosine methylation of miRNA negatively.

Keywords: AGO4; Cytosine-methylation; DNMT3A; Epigenetics; Epitranscriptomics; Glioblastoma; miRNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Apoptosis
  • Argonaute Proteins / genetics
  • Argonaute Proteins / metabolism
  • Biomarkers, Tumor / genetics*
  • Cell Proliferation
  • Cytosine / chemistry*
  • DNA (Cytosine-5-)-Methyltransferases / genetics
  • DNA (Cytosine-5-)-Methyltransferases / metabolism
  • DNA Methylation*
  • Eukaryotic Initiation Factors / genetics
  • Eukaryotic Initiation Factors / metabolism
  • Gene Expression Regulation, Neoplastic
  • Glioblastoma / genetics
  • Glioblastoma / metabolism
  • Glioblastoma / pathology*
  • Humans
  • Mice
  • Mice, Nude
  • MicroRNAs / genetics*
  • Prognosis
  • Promoter Regions, Genetic
  • Survival Rate
  • Tumor Cells, Cultured
  • Xenograft Model Antitumor Assays


  • AGO4 protein, human
  • Argonaute Proteins
  • Biomarkers, Tumor
  • Eukaryotic Initiation Factors
  • MIrn181 microRNA, human
  • MicroRNAs
  • Cytosine
  • DNA (Cytosine-5-)-Methyltransferases
  • DNA methyltransferase 3A