Genome-Wide Maps of m6A circRNAs Identify Widespread and Cell-Type-Specific Methylation Patterns that Are Distinct from mRNAs

Summary

N⁶-methyladenosine (m⁶A) is the most abundant internal modification of mRNAs and is implicated in all aspects of post-transcriptional RNA metabolism. However, little is known about m⁶A modifications to circular (circ) RNAs. We developed a computational pipeline (AutoCirc) that, together with depletion of ribosomal RNA and m⁶A immunoprecipitation, defined thousands of m⁶A circRNAs with cell-type-specific expression. The presence of m⁶A circRNAs is corroborated by interaction between circRNAs and YTHDF1/YTHDF2, proteins that read m⁶A sites in mRNAs, and by reduced m⁶A levels upon depletion of METTL3, the m⁶A writer. Despite sharing m⁶A readers and writers, m⁶A circRNAs are frequently derived from exons that are not methylated in mRNAs, whereas mRNAs that are methylated on the same exons that compose m⁶A circRNAs exhibit less stability in a process regulated by YTHDF2. These results expand our understanding of the breadth of m⁶A modifications and uncover regulation of circRNAs through m⁶A modification.