N6-Methyladenosine modification of lincRNA 1281 is critically required for mESC differentiation potential

Previous studies have revealed the critical roles of N-6-methyladenosine (m(6)A) modification of mRNA in embryonic stem cells (ESCs), but the biological function of m(6)A in large intergenic noncoding RNA (lincRNA) is unknown. Here, we showed that the internal m(6)A modification of linc1281 mediates a competing endogenous RNA (ceRNA) model to regulate mouse ESC (mESC) differentiation. We demonstrated that loss of linc1281 compromises mESC differentiation and that m(6)A is highly enriched within linc1281 transcripts. Linc1281 with RRACU m(6)A sequence motifs, but not an m(6)A-deficient mutant, restored the phenotype in linc1281-depleted mESCs. Mechanistic analyses revealed that linc1281 ensures mESC identity by sequestering pluripotency-related let-7 family microRNAs (miRNAs), and this RNA-RNA interaction is m(6)A dependent. Collectively, these findings elucidated the functional roles of linc1281 and its m(6)A modification in mESCs and identified a novel RNA regulatory mechanism, providing a basis for further exploration of broad RNA epigenetic regulatory patterns.