Identification of the hub genes involved in ATF5 mediated stress response in vitrified mouse oocytes based on WGCNA

Abstract

Activating transcription factor 5 (ATF5) is a key regulator in the stress response and plays a crucial role in cellular adaptation to the nonphysical environment. Our previous study indicated that a homeostatic state of ATF5 level could improve mitochondrial function in vitrified oocytes. However, the molecular mechanisms underlying the ATF5-mediated gene network in response to oocyte vitrification remain largely unknown. In this study, specific ATF5 siRNA was microinjected into oocytes to suppress ATF5 expression, and oocytes with ATF5 deficiency under normal and vitrification stress conditions were collected for Smart RNA-seq analysis. Weighted gene co-expression network analysis (WGCNA) was used to characterize oocyte co-expression modules involved in the ATF5 mediated response. Our results identified three key gene modules related to ATF5 knockdownRed, Green and, Yellow-using the screening criteria of |R| ≥0.5 and P ≤ 0.05 with WGCNA. Functional enrichment analysis of key gene modules showed that genes in the modules were mainly enriched in apoptosis, ubiquitin mediated proteolysis, the PI3K-Akt signaling pathway, and protein digestion and absorption. STEM and KEGG functional enrichment analysis showed that most genes were involved in protein digestion and absorption, the AMPK signaling pathway, the JAK-STAT signaling pathway, and the apoptosis signaling pathway. Importantly, Diablo, Map3k1, Spta1, and Ubqln4, obtained by sequential scanning of WGCNA and combined functional enrichment analysis, were identified as candidate genes under ATF5 regulation in response to vitrification. These findings demonstrate that the ATF5 mediated gene network exerts regulatory roles in various cellular events and provide novel insights for a deeper understanding of stress response associated impairments in vitrified oocytes.