Exon junction complex shapes the m⁶A epitranscriptome.

Area of Science:

• Molecular Biology
• Epigenetics
• RNA Biology

Background:

• N6-methyladenosine (m⁶A) is the most prevalent mRNA modification, crucial for development and implicated in cancer.
• m⁶A enrichment in 3' UTRs affects mRNA stability and translation, but its precise distribution mechanism is unclear.

Purpose of the Study:

• To elucidate the mechanism governing m⁶A distribution on mRNA.
• To investigate the role of the exon junction complex (EJC) in regulating m⁶A modification patterns.

Main Methods:

• Depletion of EIF4A3, a core EJC component.
• Analysis of METTL3 binding and m⁶A modification sites.
• Reporter gene assays to assess splicing and EJC deposition effects on m⁶A.

Main Results:

• The EJC sterically blocks METTL3-mediated m⁶A modification near exon junctions within the coding sequence.
• EIF4A3 depletion leads to increased METTL3 binding and m⁶A modification on short internal exons and near exon-exon junctions.
• Reporter assays confirm splicing and EIF4A3 deposition regulate m⁶A via steric hindrance of METTL3.

Conclusions:

• The EJC actively shapes the m⁶A epitranscriptome by restricting m⁶A deposition near exon junctions.
• This mechanism explains the characteristic patterns of m⁶A modification observed across the transcriptome.