scm⁶A-seq reveals single-cell landscapes of the dynamic m⁶A during oocyte maturation and early embryonic development

N⁶-methyladenosine (m⁶A) has been demonstrated to regulate RNA metabolism and various biological processes, including gametogenesis and embryogenesis. However, the landscape and function of m⁶A at single cell resolution have not been extensively studied in mammalian oocytes or during pre-implantation. In this study, we developed a single-cell m⁶A sequencing (scm⁶A-seq) method to simultaneously profile the m⁶A methylome and transcriptome in single oocytes/blastomeres of cleavage-stage embryos. We found that m⁶A deficiency leads to aberrant RNA clearance and consequent low quality of Mettl3^Gdf9 conditional knockout (cKO) oocytes. We further revealed that m⁶A regulates the translation and stability of modified RNAs in metaphase II (MII) oocytes and during oocyte-to-embryo transition, respectively. Moreover, we observed m⁶A-dependent asymmetries in the epi-transcriptome between the blastomeres of two-cell embryo. scm⁶A-seq thus allows in-depth investigation into m⁶A characteristics and functions, and the findings provide invaluable single-cell resolution resources for delineating the underlying mechanism for gametogenesis and early embryonic development.