Analysis of transcriptome data from gametes, embryos and reproductive bovine tissues

• Grant number: 25/01050-9
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: April 01, 2025
• End date: March 31, 2027
• Field of knowledge: Agronomical Sciences - Veterinary Medicine - Animal Reproduction
• Principal Investigator: Lawrence Charles Smith
• Grantee: Anna Carolina Fernandes
• Host Institution: Faculdade de Zootecnia e Engenharia de Alimentos (FZEA). Universidade de São Paulo (USP). Pirassununga , SP, Brazil
• Associated research grant: 21/09886-8 - Epigenetic maturation of the oocyte and totipotence: the potential of the oocyte and its relationship with the ovarian follicular niche, AP.SPEC

Abstract

The in vitro production of bovine embryos using oocytes obtained through the aspiration of antral follicles plays a prominent role in the national livestock and agricultural industries. This technology provides partially viable oocytes that, after in vitro culture to complete their nuclear and cytoplasmic maturation, can be used to derive embryos and viable progeny. Additionally, the ability to reprogram differentiated cells into a totipotent state is a recent scientific breakthrough. However, knowledge of the biological factors involved in the nuclear and cytoplasmic remodeling of oocytes during oogenesis remains limited.Therefore, our main goal is to contribute to the understanding of the epigenetic mechanisms coordinated by the various components of the follicular niche that are necessary for the full acquisition of developmental potential and the reprogramming of oocytes to totipotency. The objectives of this study are: (a) to unify sequencing data generated by this proposal with publicly available datasets to perform a systemic transcriptomic analysis of the bovine ovarian follicle (cumulus cells, granulosa cells, oocytes, and vesicles from follicular fluid) during maturation and competence acquisition; (b) to identify, in each experiment presented in the initial proposal, differentially expressed genes, the most stable endogenous genes, co-expressed genes, and key genes for each treatment; (c) to characterize gene pathways, interactions between mRNAs and lncRNAs, and predict the targets of lncRNAs associated with oocyte totipotency, identified through RNA sequencing in the different experiments of the main proposal; (d) to integrate multiple layers of transcriptomic data to generate interaction networks and identify potential molecular pathways linked to the acquisition of totipotency; and (e) to implement and test different bioinformatics methodologies for genomic data analysis.