N⁶-Methyladenosine Landscape of Glioma Stem-Like Cells: METTL3 Is Essential for the Expression of Actively Transcribed Genes and Sustenance of the Oncogenic Signaling

Genes (Basel). 2019 Feb 13;10(2):141. doi: 10.3390/genes10020141.


Despite recent advances in N⁶-methyladenosine (m⁶A) biology, the regulation of crucial RNA processing steps by the RNA methyltransferase-like 3 (METTL3) in glioma stem-like cells (GSCs) remains obscure. An integrated analysis of m⁶A-RIP (RNA immunoprecipitation) and total RNA-Seq of METTL3-silenced GSCs identified that m⁶A modification in GSCs is principally carried out by METTL3. The m⁶A-modified transcripts showed higher abundance compared to non-modified transcripts. Further, we showed that the METTL3 is essential for the expression of GSC-specific actively transcribed genes. Silencing METTL3 resulted in the elevation of several aberrant alternative splicing events. We also found that putative m⁶A reader proteins play a key role in the RNA stabilization function of METTL3. METTL3 altered A-to-I and C-to-U RNA editing events by differentially regulating RNA editing enzymes ADAR and APOBEC3A. Similar to protein-coding genes, lincRNAs (long intergenic non-coding RNAs) with m⁶A marks showed METTL3-dependent high expression. m⁶A modification of 3'UTRs appeared to result in a conformation-dependent hindrance to miRNA binding to their targets. The integrated analysis of the m⁶A regulome in METTL3-silenced GSCs showed global disruption in tumorigenic pathways that are indispensable for GSC maintenance and glioma progression. We conclude that METTL3 plays a vital role in many steps of RNA processing and orchestrates successful execution of oncogenic pathways in GSCs.

Keywords: GSCs; METTL3; RNA editing; glioblastoma; histone activation; m6A; m6A reader; splicing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions / genetics
  • Adenosine / analogs & derivatives*
  • Adenosine / genetics
  • Adenosine Deaminase / genetics
  • Carcinogenesis / genetics
  • Cell Line, Tumor
  • Cytidine Deaminase / genetics
  • Gene Expression Regulation, Neoplastic
  • Glioma / genetics*
  • Glioma / pathology
  • Histones / genetics
  • Humans
  • Methyltransferases / genetics*
  • Neoplastic Stem Cells / metabolism
  • Neoplastic Stem Cells / pathology
  • Nucleic Acid Conformation
  • Proteins / genetics
  • RNA Editing / genetics
  • RNA Splicing / genetics
  • RNA-Binding Proteins / genetics
  • Signal Transduction / genetics
  • Transcription, Genetic*


  • 3' Untranslated Regions
  • Histones
  • Proteins
  • RNA-Binding Proteins
  • N-methyladenosine
  • Methyltransferases
  • METTL3 protein, human
  • ADAR protein, human
  • Adenosine Deaminase
  • APOBEC3A protein, human
  • Cytidine Deaminase
  • Adenosine