Li Hou#; Wei Liu#; Hongdao Zhang; Ronghong Li; Miao Liu; Huijuan Shi; Ligang Wu
Small RNAs are essential for germ cell development and fertilization. However, fundamental questions remain, such as the level of conservation in small RNA composition between species and whether small RNAs control transposable elements in mammalian oocytes. Here, we use high-throughput sequencing to profile small RNAs and poly(A)-bearing long RNAs in oocytes of 12 representative vertebrate species (including 11 mammals). The results show that miRNAs are generally expressed in the oocytes of each representative species (although at low levels), whereas endo-siRNAs are specific to mice. Notably, piRNAs are predominant in oocytes of all species (except mice), and vary widely in length. We find PIWIL3-associated piRNAs are widespread in mammals and generally lack 3’-2’- O -methylation. Additionally, sequence identity is low between homologous piRNAs in different species, even among those present in syntenic piRNA clusters. Despite the species-specific divergence, piRNAs retain the capacity to silence younger TE subfamilies in oocytes. Collectively, our findings illustrate a high level of diversity in the small RNA populations of mammalian oocytes. Furthermore, we identify sequence features related to conserved roles of small RNAs in silencing TEs, providing a large-scale reference for future in-depth study of small RNA functions in oocytes.
The raw data were deposited at NCBI GEO under the accession number: GSE200470 and GSE256514.
The processed data and code can also be downloaded from 
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Hou, L., Liu, W. et al. Divergent composition and transposon-silencing activity of small RNAs in mammalian oocytes. Genome Biology 25, 80 (2024). https://doi.org/10.1186/s13059-024-03214-w