m6A is the most abundant and well-studied RNA modification in mRNAs. The majority of m6A sites on mRNAs are catalyzed by METTL3/METTL14 methyltransferase complex facilitated by the axillary cofactors, including RBM15/15B, WTAP, KIAA1429, HAKAI, and ZC3H13. These modifications are removed by demethylases ALKBH5 and FTO, and recognized by specific direct or indirect ‘reader’ proteins represented by YTH family and HNRNP family proteins, which further mediate different aspects of downstream regulation of RNA processing, degradation, and translation 1, 2, 3.

It is worth noting that previous studies have shown that m6A is cotranscriptionally deposited and detected in chromatin-associated RNAs [4] and recently transcribed RNAs [5], suggesting that m6A might play specific transcriptional and cotranscriptional regulatory roles in the chromatin contexts. Consistent with this, three studies in 2017 showed that m6A methyltransferase METTL3 binds to and regulates specific chromatin loci, including promoters, 3’ untranslated regions, and DNA damage sites 6, 7, 8. From then on, more studies have aimed to clarify the underlying mechanisms of how m6A regulates specific chromatin features. While a number of these studies focused on active chromatin regions, such as promoters, enhancers, and gene bodies 9, 10, 11, 12••, 13, 14, several studies in the past 2–3 years have discovered surprising links between m6A and heterochromatin 12••, 15••, 16••, 17••, 18, 19••, 20••, 21•, 22, 23••, 24••, 25, 26••, 27, 28, 29•, 30, 31. This review will summarize and discuss the regulatory roles of m6A and its modulators in different types of heterochromatin regions, with a specific emphasis on the regulation in mammalian embryonic stem cells (ESCs), which exhibit distinct features of multiple heterochromatin marks, including histone methylation [32] and DNA methylation [33]. Previous studies have shown that m6A regulates the stage-specific transcriptome by promoting the timely degradation of mRNAs and is crucial for the proper self-renewal and differentiation of mouse ESCs 34, 35, 36. Consistently, depletion of key m6A regulators, including Mettl3 and Mettl14, is embryonic lethal in mice 35, 37. Although the post-transcriptional regulation roles of m6A in ESCs have been well characterized [38], its regulation in the chromatin context has not been revealed until recently. This review will focus on recent discoveries of m6A-mediated heterochromatin regulation in ESCs. Please also refer to other insightful reviews, which have discussed m6A’s regulatory roles in the chromatin contexts from different aspects 39, 40, 41, 42, 43.