Integrated small and long RNA sequencing in single oocytes reveals piRNA-mediated transposon repression during human oogenesis

In this study, we simultaneously profiled small and long RNA transcriptomes in individual human oocytes across four developmental stages. piRNAs, especially PIWIL3-associated short piRNAs (short-piRNAs), are the predominant small non-coding RNAs during human oogenesis. A marked increase in short-piRNAs after the primordial follicle stage coincided with a global downregulation of TE expression, particularly LINE-1 (L1) and endogenous retroviruses (ERVs). On the other hand, PIWIL1- and PIWIL2-associated long piRNAs (long-piRNAs) were correlated with the silencing of certain specific ERV subfamilies. Genomic-context analyses revealed that highly productive piRNA clusters have evolved asymmetric antisense insertion bias toward L1 and ERVs, contributing to TE families-specific regulation. Overall design: A total of 30 human oocytes spanning four developmental stages, primordial follicle (PrF), primary follicle (PF), germinal vesicle (GV), and metaphase II (MII), were collected. Small and long RNA transcriptomes were simultaneously profiled at the single-oocyte level.