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

N-6-methyladenosine (m(6)A) is the most abundant internal modification of mRNAs and is implicated in all aspects of post-transcriptional RNA metabolism. However, little is known about m(6)A modifications to circular (circ) RNAs. We developed a computational pipeline (AutoCirc) that, together with depletion of ribosomal RNA and m(6)A immunoprecipitation, defined thousands of m(6)A circRNAs with cell-type-specific expression. The presence of m(6)A circRNAs is corroborated by interaction between circRNAs and YTHDF1/YTHDF2, proteins that read m(6)A sites in mRNAs, and by reduced m(6)A levels upon depletion of METTL3, the m(6)A writer. Despite sharing m(6)A readers and writers, m(6)A circRNAs are frequently derived from exons that are not methylated in mRNAs, whereas mRNAs that are methylated on the same exons that compose m(6)A circRNAs exhibit less stability in a process regulated by YTHDF2. These results expand our understanding of the breadth of m(6)A modifications and uncover regulation of circRNAs through m(6)A modification.