RNA m6A methylome in human oocytes and preimplantation embryos

RNA N6-methyladenosine (m6A) modification is a critical regulator for a range of physiological and pathological processes. Despite its significance, the dynamic m6A profiles within human preimplantation embryos remain uncharacterized, primarily due to technical challenges and the scarcity of material. Here we present the first transcriptome-wide m6A landscape of single human oocytes and early embryos, utilizing the ultrasensitive m6A mapping approach picoMeRIP-seq that we have recently developed. Comparative analyses with mouse data reveal a conserved m6A methylome between humans and mice, with intriguing divergences during the window of zygotic genome activation. m6A-modified genes, including maternally-inherited RNAs and zygotically-activated transcripts, are involved in regulation of gene transcription, while unmodified genes are mainly associated with basic metabolic processes. Maternal RNAs destined for degradation after fertilization exhibit a propensity for m6A modifications, and m6A-modified genes are more likely to be targeted by miRNAs. Genes that are constantly-expressed across all developmental stages demonstrate higher translation efficiency for m6A-modified genes, intensified when m6A resides within coding regions. Moreover, we observe frequent m6A enrichment on stage-specifically expressed retrotransposons, particularly within young subfamilies such as HERVH, L1HS, and SVA_D. We also show a diminution of m6A levels both transcriptome-wide and on retrotransposons following inhibition of m6A writer activity in human embryonic stem cells. Our study provides a valuable resource for future investigations into the regulatory mechanisms of m6A in the human oocyte-to-embryo transition, and delivers epitranscriptomomic insights into human reproductive health. Overall design: Using picoMeRIP-seq we have developed, the transcriptome-wide m6A maps are generated in human oocytes at germinal vesicle (GV) and metaphase II (MII) stages, and human embryos at zygote (1C), 2-cell (2C), 8-cell (8C) and blastocyst (BLT) stages, with 2-4 biological replicates for each stage; and in human embryonic stem cells (ESC) starting with 1000 cells, 100 cells and 10 cells; and human embryonic stem cells treated by STM2457 inhibotor and DMSO control. ***Please note that raw sequencing data of human oocytes and early embryos, which were generated in Norway, are not provided as per Norway data policy.