FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis

TLDR

The role of FTO and its substrate m6A in mRNA processing and adipogenesis is largely unknown, and m6A is enriched in exonic regions flanking splice sites overlapping SR protein binding sites. The authors used transcriptome analyses and m6A‑seq to show that FTO regulates gene expression and mRNA splicing of grouped genes. FTO expression and m6A levels are inversely correlated during adipogenesis; depletion blocks differentiation, reversible only by catalytically active FTO; increased m6A upon depletion enhances SRSF2 binding and exon inclusion, including in RUNX1T1, demonstrating that FTO‑dependent demethylation is a novel regulatory mechanism of RNA processing essential for adipogenesis.

Abstract

The role of Fat Mass and Obesity-associated protein (FTO) and its substrate N6-methyladenosine (m6A) in mRNA processing and adipogenesis remains largely unknown. We show that FTO expression and m6A levels are inversely correlated during adipogenesis. FTO depletion blocks differentiation and only catalytically active FTO restores adipogenesis. Transcriptome analyses in combination with m6A-seq revealed that gene expression and mRNA splicing of grouped genes are regulated by FTO. M6A is enriched in exonic regions flanking 5′- and 3′-splice sites, spatially overlapping with mRNA splicing regulatory serine/arginine-rich (SR) protein exonic splicing enhancer binding regions. Enhanced levels of m6A in response to FTO depletion promotes the RNA binding ability of SRSF2 protein, leading to increased inclusion of target exons. FTO controls exonic splicing of adipogenic regulatory factor RUNX1T1 by regulating m6A levels around splice sites and thereby modulates differentiation. These findings provide compelling evidence that FTO-dependent m6A demethylation functions as a novel regulatory mechanism of RNA processing and plays a critical role in the regulation of adipogenesis.