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Single-cell multi-omics profiling reveals key regulatory mechanisms that poise germinal vesicle oocytes for maturation in pigs

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Abstract

The molecular mechanisms controlling the transition from meiotic arrest to meiotic resumption in mammalian oocytes have not been fully elucidated. Single-cell omics technology provides a new opportunity to decipher the early molecular events of oocyte growth in mammals. Here we focused on analyzing oocytes that were collected from antral follicles in different diameters of porcine pubertal ovaries, and used single-cell M&T-seq technology to analyze the nuclear DNA methylome and cytoplasmic transcriptome in parallel for 62 oocytes. 10× Genomics single-cell transcriptomic analyses were also performed to explore the bi-directional cell–cell communications within antral follicles. A new pipeline, methyConcerto, was developed to specifically and comprehensively characterize the methylation profile and allele-specific methylation events for a single-cell methylome. We characterized the gene expressions and DNA methylations of individual oocyte in porcine antral follicle, and both active and inactive gene’s bodies displayed high methylation levels, thereby enabled defining two distinct types of oocytes. Although the methylation levels of Type II were higher than that of Type I, Type II contained nearly two times more of cytoplasmic transcripts than Type I. Moreover, the imprinting methylation patterns of Type II were more dramatically divergent than Type I, and the gene expressions and DNA methylations of Type II were more similar with that of MII oocytes. The crosstalk between granulosa cells and Type II oocytes was active, and these observations revealed that Type II was more poised for maturation. We further confirmed Insulin Receptor Substrate-1 in insulin signaling pathway is a key regulator on maturation by in vitro maturation experiments. Our study provides new insights into the regulatory mechanisms between meiotic arrest and meiotic resumption in mammalian oocytes. We also provide a new analytical package for future single-cell methylomics study.

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Availability of data and materials

Sequence data and processed data are available under the Gene Expression Omnibus accessions GSE235731. The code of methyConcerto was deposited at github.com/hippo-yf/methyConcerto.

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Funding

This project was supported by the Guangdong Basic and Applied Basic Research Foundation (2023A1515030054), the earmarked fund for China Agriculture Research System (CARS-35), the National Natural Science Foundation of China (31902131, 32072694), the Key R&D Program of Guangdong Province Project (2022B0202090002) and the Agricultural Sciences and Technology Innovation Program of CAAS.

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Author notes

  1. Xiaolong Yuan, Na Chen and Yance Feng contributed equally to this work.

Authors and Affiliations

  1. Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China

    Xiaolong Yuan, Nian Li, Xiangchun Pan, Yuhan Tian & Jiaqi Li

  2. Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China

    Na Chen, Yance Feng, Yao Jiang, Dou He & Fei Gao

  3. E-GENE Co., Ltd, Shenzhen, China

    Junwen Wang

  4. Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA, Australia

    Yao Jiang

  5. Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark

    Fei Gao

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  1. Xiaolong Yuan
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Contributions

FG, XY and JL conceived the study. NC, NL, JY, XP and YT collected samples and performed in vitro experiments. JW and DH performed scM&T-seq library construction. XY and JL provided samples. NC and YF carried out bioinformatic analysis. FG, XY and YF drafted the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Fei Gao.

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Yuan, X., Chen, N., Feng, Y. et al. Single-cell multi-omics profiling reveals key regulatory mechanisms that poise germinal vesicle oocytes for maturation in pigs. Cell. Mol. Life Sci. 80, 222 (2023). https://doi.org/10.1007/s00018-023-04873-x

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