Watanabe, T. et al. Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev. 20, 1732-1743

Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
Genes & Development (Impact Factor: 10.8). 08/2006; 20(13):1732-43. DOI: 10.1101/gad.1425706
Source: PubMed


Small RNAs ranging in size between 18 and 30 nucleotides (nt) are found in many organisms including yeasts, plants, and animals. Small RNAs are involved in the regulation of gene expression through translational repression, mRNA degradation, and chromatin modification. In mammals, microRNAs (miRNAs) are the only small RNAs that have been well characterized. Here, we have identified two novel classes of small RNAs in the mouse germline. One class consists of approximately 20- to 24-nt small interfering RNAs (siRNAs) from mouse oocytes, which are derived from retroelements including LINE, SINE, and LTR retrotransposons. Addition of retrotransposon-derived sequences to the 3' untranslated region (UTR) of a reporter mRNA destabilizes the mRNA significantly when injected into full-grown oocytes. These results suggest that retrotransposons are suppressed through the RNAi pathway in mouse oocytes. The other novel class of small RNAs is 26- to 30-nt germline small RNAs (gsRNAs) from testes. gsRNAs are expressed during spermatogenesis in a developmentally regulated manner, are mapped to the genome in clusters, and have strong strand bias. These features are reminiscent of Tetrahymena approximately 23- to 24-nt small RNAs and Caenorhabditis elegans X-cluster small RNAs. A conserved novel small RNA pathway may be present in diverse animals.

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Available from: Toshiaki Watanabe, May 13, 2014
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    • "These observations suggest that retrotransposons are suppressed by piRNA pathway posttranscriptionally in vertebrate oocytes. In mouse oocytes, insertion of transposon sequences confers instability to reporter mRNAs (Watanabe et al., 2006). A recent study revealed that some transposon-driven mRNAs harboring transposon sequences in their 5 0 UTRs are upregulated in Mvh, "
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    ABSTRACT: Piwi proteins and Piwi-interacting RNAs (piRNAs) are essential for gametogenesis, embryogenesis, and stem cell maintenance in animals. Piwi proteins act on transposon RNAs by cleaving the RNAs and by interacting with factors involved in RNA regulation. Additionally, piRNAs generated from transposons and psuedogenes can be used by Piwi proteins to regulate mRNAs at the posttranscriptional level. Here we discuss piRNA biogenesis, recent findings on posttranscriptional regulation of mRNAs by the piRNA pathway, and the potential importance of this posttranscriptional regulation for a variety of biological processes such as gametogenesis, developmental transitions, and sex determination.
    Molecular Cell 10/2014; 56(1):18–27. DOI:10.1016/j.molcel.2014.09.012 · 14.02 Impact Factor
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    • "These experiments therefore provide evidence that although sperm contains a small quantity of microRNAs in comparison to the oocyte, it still delivers enough to influence preimplantation development and the phenotype of the offspring. Male germ cells express PIWI-interacting RNAs (piRNAs; Aravin et al., 2006; Girard et al., 2006; Grivna et al., 2006; Lau et al., 2006; Watanabe et al., 2006), also essential small non-coding RNAs for sperm (Deng and Lin, 2002; Kuramochi-Miyagawa et al., 2004; Reuter et al., 2011; Figure 2B). A lot remains to be understood about their function, processing and mechanism of action. "
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    ABSTRACT: Sperm is a highly differentiated cell type whose function is to deliver a haploid genome to the oocyte. The sperm "epigenomes" were traditionally considered to be insignificant – the sperm is transcriptionally inactive, its genome is packaged in sperm-specific protamine toroids instead of nucleosomes, and its DNA methylation profile is erased immediately post-fertilization. Yet, in recent years there has been an increase in the number of reported cases of apparent epigenetic inheritance through the male germline, suggesting that the sperm epigenome may transmit information between generations. At the same time, technical advances have made the genome-wide profiling of different layers of the sperm epigenome feasible. As a result, a large number of datasets have been recently generated and analyzed with the aim to better understand what non-genetic material is contained within the sperm and whether it has any function post-fertilization. Here, we provide an overview of the current knowledge of the sperm epigenomes as well as the challenges in analysing them and the opportunities in understanding the potential non-genetic carriers of information in sperm.
    Frontiers in Genetics 09/2014; 5(330). DOI:10.3389/fgene.2014.00330
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    • "The piRNAs are the largest and most heterogeneous class of the small ncRNA family, exceeding 2 million distinct piRNA species in the mouse (Lau et al., 2006). Initial identification and characterization of mammalian piRNAs were achieved by experimental approaches that combined the isolation of Piwi protein-interacting sequences and/or deep sequencing of germline-enriched short RNA sequences (Aravin et al., 2006; Girard et al., 2006; Watanabe et al., 2006). Although this methodology appeared productive, it could not exhaustively cover the entire repertoire of piRNA molecules in a specific organism. "
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    ABSTRACT: Motivation: Piwi-interacting RNA (piRNA) is the most recently discovered and the least investigated class of Argonaute/Piwi protein-interacting small non-coding RNAs. The piRNAs are mostly known to be involved in protecting the genome from invasive transposable elements. But recent discoveries suggest their involvement in the pathophysiology of diseases, such as cancer. Their identification is therefore an important task, and computational methods are needed. However, the lack of conserved piRNA sequences and structural elements makes this identification challenging and difficult.Results: In the present study, we propose a new modular and extensible machine learning method based on multiple kernels and a support vector machine (SVM) classifier for piRNA identification. Very few piRNA features are known to date. The use of a multiple kernels approach allows editing, adding or removing piRNA features that can be heterogeneous in a modular manner according to their relevance in a given species. Our algorithm is based on a combination of the previously identified features [sequence features (k-mer motifs and a uridine at the first position) and piRNAs cluster feature] and a new telomere/centromere vicinity feature. These features are heterogeneous, and the kernels allow to unify their representation. The proposed algorithm, named piRPred, gives promising results on Drosophila and Human data and outscores previously published piRNA identification algorithms.Availability and implementation: piRPred is freely available to non-commercial users on our Web server EvryRNA http://EvryRNA.ibisc.univ-evry.frContact:
    Bioinformatics 09/2014; 30(17):i364-i370. DOI:10.1093/bioinformatics/btu441 · 4.98 Impact Factor
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