RNA multi-omics in single cells reveal rhythmical RNA reshaping during human and mouse oocyte maturation.

Background: Omics technologies are widely applied in assisted reproductive technology (ART), such as embryo selection, investigation of infertility causes, and mechanisms underlying reproductive cell development. While RNAomics has shown great potential in investigating the physiology and pathology in female reproductive system, its applications are still not fully developed. More studies on epitranscriptomic regulation mechanisms and novel sequencing methods are needed to advance the field.

Results: Here, we developed a method named Cap to Tail sequencing application (C2T-APP) and simultaneously characterized the m⁷G cap, poly(A) tail structure, and gene expression level for the intact RNA molecules in single cells. C2T-APP distinguished the N6, 2'-O-dimethyladenosine modification (m⁶A_m) from N⁶-methyladenosine (m⁶A) modification with our published single-cell m⁶A sequencing (scm⁶A-seq) data. During oocyte maturation, we found a positive correlation of m⁷G and m⁶A_m with translation efficiency and finely dissected the step-wised maternal RNA de-capping and de-tailing of different types of genes. Strikingly, we uncovered a subtle structural mechanism regulating poly(A) tails in oocytes: maternal RNA translation is temporarily suppressed by removing the poly(A) tails without complete degradation, while the poly(A)-tail regulators themselves depend strictly on translation initiated after meiotic resumption. Furthermore, we profiled single-cell RNA-multi-omic features of human oocytes with different qualities during in vitro culture maturation (IVM). Defects of epi-transcriptome features, including m⁶A, m⁶A_m, m⁷G, and poly(A) structure of maternal RNA in the oocytes with poor quality, were detected.

Conclusions: Our results provided a valuable tool for RNAomics research and data resources provided novel insights into human oocyte maturation, which is helpful for IVM and oocyte selection for ART.