Integrated small and long RNA sequencing reveals piRNA mediated transposon repression during human oogenesis

Abstract The piwi-interacting RNAs (piRNAs) are essential for controlling transposable elements (TEs) activity in germ cells, yet their expression dynamics and functions during human oogenesis remain poorly understood. Here, we simultaneously profile small and long RNAs in individual human oocytes across four developmental stages. piRNAs, especially PIWIL3-associated short piRNAs, are the predominant small non-coding RNAs during human oogenesis. A marked increase in short-piRNAs coincide with a global reduction of TE expression, particularly LINE-1 and endogenous retroviruses (ERVs). In contrast, PIWIL1- and PIWIL2-associated long piRNAs correlate with the downregulation of certain specific ERV subfamilies. Genomic analyses reveal that highly productive piRNA clusters have evolved asymmetric antisense insertion bias toward LINE-1 and ERVs, enabling TE families-specific regulation. Together, our study provides a valuable single-cell dataset of small and long RNA co-expression landscapes in developing human oocytes and reveals coordinated yet distinct roles of different PIWI/piRNA classes in TE repression during human oogenesis, with short-piRNAs acting as the primary and broad-spectrum suppressors, and long-piRNAs providing coordinated ERV-specific repression.