Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jul 11;14(1):94.
doi: 10.1186/s40104-023-00894-5.

Whole-genome transcriptome and DNA methylation dynamics of pre-implantation embryos reveal progression of embryonic genome activation in buffaloes

Penghui Fu #  1   2 , Du Zhang #  3 , Chunyan Yang  4 , Xiang Yuan  5 , Xier Luo  6 , Haiying Zheng  4 , Yanfei Deng  1 , Qingyou Liu  1   6 , Kuiqing Cui  1   6 , Fei Gao  7   8 , Deshun Shi  9
Affiliations

Whole-genome transcriptome and DNA methylation dynamics of pre-implantation embryos reveal progression of embryonic genome activation in buffaloes

Penghui Fu et al. J Anim Sci Biotechnol. .

Abstract

Background: During mammalian pre-implantation embryonic development (PED), the process of maternal-to-zygote transition (MZT) is well orchestrated by epigenetic modification and gene sequential expression, and it is related to the embryonic genome activation (EGA). During MZT, the embryos are sensitive to the environment and easy to arrest at this stage in vitro. However, the timing and regulation mechanism of EGA in buffaloes remain obscure.

Results: Buffalo pre-implantation embryos were subjected to trace cell based RNA-seq and whole-genome bisulfite sequencing (WGBS) to draw landscapes of transcription and DNA-methylation. Four typical developmental steps were classified during buffalo PED. Buffalo major EGA was identified at the 16-cell stage by the comprehensive analysis of gene expression and DNA methylation dynamics. By weighted gene co-expression network analysis, stage-specific modules were identified during buffalo maternal-to-zygotic transition, and key signaling pathways and biological process events were further revealed. Programmed and continuous activation of these pathways was necessary for success of buffalo EGA. In addition, the hub gene, CDK1, was identified to play a critical role in buffalo EGA.

Conclusions: Our study provides a landscape of transcription and DNA methylation in buffalo PED and reveals deeply the molecular mechanism of the buffalo EGA and genetic programming during buffalo MZT. It will lay a foundation for improving the in vitro development of buffalo embryos.

Keywords: Buffalo; DNA methylome; Embryonic genome activation; Maternal-to-zygote transition; Transcriptome.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
The transcriptome landscape during buffalo PED. A Microscopy images of buffalo oocytes and embryos. The top images are the oocytes/embryos with their zona pellucida. The bottom images are the zona-free oocytes/embryos. From 1 to 9: GV oocyte, MII oocyte, Zygote, 2-cell, 4-cell, 8-cell, 16-cell, Morula, blastocyst (in the lower subfigure the ICM was isolated from the blastocyst). B Principal component analysis (PCA) of the transcripts for all developmental stages. C Unsupervised hierarchal clustering and heatmap of duplicate samples. D The numbers of DEGs in consecutive developmental stages during buffalo PED. E The number of expression suppression of maternal genes at each embryonic developmental stage. F The number of first expression genes at each embryonic developmental stage
Fig. 2
Fig. 2
The DNA methylome landscape during buffalo PED. A Global CpG methylation levels at each developmental stage. B The trend of average CpG methylation levels from 5 kb upstream to 5 kb downstream of the gene bodies. C The distribution percentage of CpG with different methylation levels at each developmental stage. D The numbers of DMRs in consecutive developmental stages during buffalo PED. E The distribution of DMRs across the global genome in several pairwise comparisons. a, GV oocyte vs. MII oocyte; b, MII oocyte vs. Zygote; c, Zygote vs. 2-cell; d, 2-cell vs. 4cell; e, 4-cell vs. 8-cell; f, 8-cell vs. 16-cell; g, 16-cell vs. Morula; h, Morula vs. ICM. F The trend of average CpG methylation levels with different expression levels (high, medium, low and no expression) using the 8-cell stage as an example
Fig. 3
Fig. 3
Gene co-expression analysis of stage-specific dynamics by WGCNA. A A cluster dendrogram showing the modules of the co-express genes identified. B A heatmap of the correlations between the co-express modules and the embryonic stage of development. C Schematic diagram of developmental steps during buffalo PED
Fig. 4
Fig. 4
The interaction network of enriched KEGG pathways before major EGA. Hexagon: 2-cell stage; Rectangle: 4-cell stage; Triangle: 8-cell stage
Fig. 5
Fig. 5
Enriched pathway at the 16-cell stage and the dynamics of the important KEGG pathways. A KEGG pathway enrichment at the 16-cell stage. B The timing genome-wide activation of key pathways during buffalo PED
Fig. 6
Fig. 6
Identification of the key hub genes during MZT. A The list of top 10 hub genes. B regulation pathways and related hub genes of CDK1 during EGA
Fig. 7
Fig. 7
Expression heatmap of enriched biological processes of CDK1
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Currin L, Baldassarre H, Bordignon V. In vitro production of embryos from prepubertal holstein cattle and mediterranean water buffalo: problems, progress and potential. Animals (Basel) 2021;11(8):2275–2295. doi: 10.3390/ani11082275. - DOI - PMC - PubMed
    1. Yang CY, Zheng HY, Abdelnour SA, Li LY, Shokrollahi B, Tang LP, et al. Molecular signatures of in vitro produced embryos derived from ovum pick up or slaughterhouse oocytes in buffalo. Theriogenology. 2021;169:14–20. doi: 10.1016/j.theriogenology.2021.03.025. - DOI - PubMed
    1. Lee MT, Bonneau AR, Giraldez AJ. Zygotic genome activation during the maternal-to-zygotic transition. Annu Rev Cell Dev Biol. 2014;30:581–613. doi: 10.1146/annurev-cellbio-100913-013027. - DOI - PMC - PubMed
    1. Sha QQ, Zheng W, Wu YW, Li S, Guo L, Zhang S, et al. Dynamics and clinical relevance of maternal mRNA clearance during the oocyte-to-embryo transition in humans. Nat Commun. 2020;11(1):4917–4933. doi: 10.1038/s41467-020-18680-6. - DOI - PMC - PubMed
    1. Xue Z, Huang K, Cai C, Cai L, Jiang CY, Feng Y, et al. Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature. 2013;500(7464):593–597. doi: 10.1038/nature12364. - DOI - PMC - PubMed

LinkOut - more resources