Total RNA was isolated from chromatin-associated fraction of mESCs. Non-ribosome RNA was further enriched from total RNA by using RiboMinus transcriptome isolation kit (Invitrogen). 1 uL 1:1000 diluted m6A spike-in from EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 1 ug non-ribosome RNA, followed by fragmentation using RNA Fragmentation Reagents (Invitrogen). 5% of the fragmented RNA was saved as input. m6A immunoprecipitation was performed using the EpiMark N6-Methyladenosine Enrichment Kit (NEB) according to the manufacturer's instructions. RNA libraries were constructed using the SMARTer Stranded Total RNA-seq Kit v2 (Takara) according to the manufacturer's protocol.