Transcription factor-mediated gene regulatory networks in the formation of oocytes

Context The induction of oocytes from embryonic stem cells (ESCs) in vitro provides a promising tool for the treatment of female infertility. Various molecules are involved in this complex process, which requires further elucidation. Aims This study aims to screen for factors that induce the differentiation of ESCs into oocytes in vitro by constructing transcription factor (TF)-mediated gene regulatory networks (GRNs) during the formation of oocytes. Methods Based on publicly available multi-omics data, the weighted gene co-expression network analysis (WGCNA) method identified oocyte-specific TFs and key oocyte-specific genes. Additionally, chromatin immunoprecipitation (ChIP) sequencing data and ChIP-qPCR analysis were used to examine GRNs mediated by oocyte-specific TFs. Key results First, by analyzing assay for transposase-accessible chromatin sequencing (ATAC-seq) and DNase I hypersensitive site sequencing (DNase-seq) data from human and mouse ESCs, primordial germ cells (PGCs), and oocytes, we identified five and three oocyte-specific TFs, respectively. RNA sequencing and WGCNA further revealed 38 key oocyte-specific genes. Subsequently, when comparing cell-specific TFs in mouse and human oocytes, we identified three overlapping oocyte-specific TFs (NFYA, NFYB, and NFYC). Notably, NFYA exhibited significantly elevated expression levels in oocytes compared to ESCs and PGCs. Additionally, ChIP-qPCR results demonstrated that NFYA was relatively enriched at the promoter region of the key oocyte-specific gene, m6A demethylase Alkbh5. Conclusions This study provides preliminary insights into the role of cell-specific TFs and TF-mediated GRNs in oocyte formation by identifying oocyte-specific genes and key oocyte-specific TFs. Implications The findings indicate that their intricate regulatory mechanisms may significantly contribute to enhancing the efficiency of differentiating ESCs into oocytes.