scm(6)A-seq reveals single-cell landscapes of the dynamic m(6)A during oocyte maturation and early embryonic development

N(6)-methyladenosine (m(6)A) has been demonstrated to regulate RNA metabolism and various biological processes, including gametogenesis and embryogenesis. However, the landscape and function of m(6)A at single cell resolution have not been extensively studied in mammalian oocytes or during pre-implantation. In this study, we developed a single-cell m(6)A sequencing (scm(6)A-seq) method to simultaneously profile the m(6)A methylome and transcriptome in single oocytes/blastomeres of cleavage-stage embryos. We found that m(6)A deficiency leads to aberrant RNA clearance and consequent low quality of Mettl3(Gdf9) conditional knockout (cKO) oocytes. We further revealed that m(6)A regulates the translation and stability of modified RNAs in metaphase II (MII) oocytes and during oocyte-to-embryo transition, respectively. Moreover, we observed m(6)A-dependent asymmetries in the epi-transcriptome between the blastomeres of two-cell embryo. scm(6)A-seq thus allows in-depth investigation into m(6)A characteristics and functions, and the findings provide invaluable single-cell resolution resources for delineating the underlying mechanism for gametogenesis and early embryonic development.