In a study published in Genome Biology on March 26th, a team led by Prof. WU Ligang from the Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, reported on the diverse compositions and functions of small RNAs in mammalian oocytes. This research lays an important foundation for future studies on the functions and mechanisms of small RNAs in mammalian oocyte development.
Small RNAs play a broad role in gene expression regulation. In germ cells, the primary types of small RNAs are microRNA (miRNA), endogenous small interfering RNA (endo-siRNA), and PIWI-interacting RNA (piRNA). Among these, miRNA and endo-siRNA are typically 22 nucleotides (nt) in length and form RNA-induced silencing complexes (RISC) with Argonaute (AGO) proteins. The piRNA forms complexes with PIWI proteins to form piRNA-induced silencing complexes (piRISCs), which primary function is to suppress active transposable elements (TEs) by post-transcriptional gene silencing (PTGS) through piRISC-mediated slicer activity, as well as transcriptional gene silencing (TGS) through guiding DNA methylation or histone modification. Studies have shown significant functional differences among miRNA, endo-siRNA, and piRNA during oocyte development across various species. In Drosophila and Zebrafish, disruption of any of the PIWI paralogs severely impairs the fertility of both males and females. In mammals, the piRNA pathway has been primarily studied in mice. However, female mice remain fertile in the absence of PIWIs. In contrast, endo-siRNA is necessary in mouse oocyte development. However, in early work by Ligang' s research group revealed the expression of a novel, unmodified short piRNA that binds to PIWIL3 in human oocytes, distinct from the long piRNA that binds to PIWIL1, whereas endo-siRNA is undatable in the oocytes of monkey, and human (2019, Nature Communications). Subsequent collaboration between Ligang's research group and Jianmin Li's group from Nanjing Medical University showed that the piRNA pathway is essential for normal oocyte development and female fertility in golden hamsters, in which oocyte the small RNA and PIWI transcriptional profiles has more closely resemble of humans than mice (2021, Nature Cell Biology; 2023, Nature Communications). These studies indicate that the composition and functions of small RNAs might be vary among different mammalian oocytes.
To comprehensively analyze and systematically compare the composition, characteristics, and potential functions of small non-coding RNAs in different mammalian oocytes, researchers conducted deep sequencing and analysis of transcriptome and small RNAs from oocytes of 12 species, including humans, crab-eating monkeys, mice, rats, golden hamsters, Chinese hamsters, rabbits, guinea pigs, beagles, pigs, goats, and zebrafish. Based on the distribution and sequence characteristics of small RNAs in the genome, piRNAs were identified in all 12 species, with higher abundances than other types of small RNAs in all species except mice. This result indicates a generally high abundance of piRNAs in mammalian oocytes, with species-specific length distributions. Additionally, researchers found that endo-siRNAs were only expressed in mouse oocytes and were not detected in the oocytes of the other ten mammalian species. Therefore, it can be inferred that most mammals (including closely related rats) may not express endo-siRNAs, suggesting that mice is an exception and may not serve as an appropriate model for studying the function of small RNAs in female reproductive regulation.
Furthermore, researchers conducted PIWI protein immunoprecipitation experiments and sodium periodate oxidation experiments on mammalian oocytes. They discovered that os-piRNAs bound to PIWIL3 were widely present in mammalian oocytes, and their 3' ends were not modified with 2'-O-methyl groups. By analyzing the conservation of piRNA sequences and piRNA clusters across species, researchers found that the sequence conservation of piRNA clusters was much lower than that of flanking coding genes and intergenic sequences. The sequence identity of piRNAs was also very low among different species. Further analysis of the composition of transposable elements distributed in piRNA clusters revealed significant differences between species. Analysis of the sequence divergence rate of transposable elements showed that those with low divergence rate typically corresponded to higher abundances of piRNAs, and such elements were usually potentially active transposable elements. Consequently, researchers proposed that the sequence and abundance of piRNAs might evolve rapidly between different species to counteract the threat of active transposable elements.
In summary, these findings have far-reaching implications in expanding our understanding of small RNA evolution in mammalian oocytes and the mechanisms by which small RNAs may affect female infertility.
Contact: lgwu@sibcb.ac.cn
Reference: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03214-w
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