Transcriptomic analysis of whole staged ovarian follicles reveals stage-specific folliculogenesis signatures in mice

Activation and maturation of ovarian follicles are essential for female reproduction, yet the underlying molecular and transcriptional mechanisms that govern these processes remain poorly understood. In this study, we used single follicle RNA-sequencing (RNA-seq) to identify transcriptional signatures of staged ovarian follicles, from primordial to secondary stages, to uncover the genes and pathways involved in early folliculogenesis. Our findings demonstrate that primordial follicles are transcriptionally distinct from growing follicles, with enrichment in DNA integrity and RNA processing pathways, which may play a role in preserving oocyte genomic stability and cell state during dormancy. Additionally, our analysis reveals minimal transcriptomic differences between primary and secondary follicles using traditional differential expression analysis. To better distinguish growing follicle stages, we introduce unsupervised approaches, including discrete-variable predictors of follicle stage and weighted gene co-expression analysis. We identified pathways involved in DNA integrity, meiotic arrest, and cellular metabolism that drive the transition from dormant to active follicle states, as well as pathways related to cellular growth, ECM organization, and biosynthesis in growing follicle stages. Our study offers novel insights into the molecular mechanisms governing early follicle activation and growth, providing a foundation for future research with applications in reproductive biology, contraception, and fertility preservation.