Small noncoding RNAs in the germline

Abstract

Small noncoding RNAs have emerged as potent regulators of gene expression, especially in the germline. We review the biogenesis and regulatory function of three major small noncoding RNA pathways in the germline: The small interfering RNA (siRNA) pathway that leads to the degradation of target mRNAs, the microRNA (miRNA) pathway that mostly represses the translation of target mRNAs, and the newly discovered Piwi-interacting RNA (piRNA) pathway that appears to have diverse functions in epigenetic programming, transposon silencing, and the regulation of mRNA translation and stability. The siRNA and miRNA pathways are present in the germline as well as many somatic tissues, whereas the piRNA pathway is predominantly confined to the germline. Investigation of the three small RNA pathways has started to reveal a new dimension of gene regulation with defining roles in germline specification and development.

Figure 1.

The PIWI/Ago family of proteins. (A) Schematic representation of the amino-terminal (N-term), PAZ, Mid, and PIWI domains of Drosophila Piwi. (B) Crystal structure of Thermus thermophilus Ago bound to a 21-bp guide RNA (red) and a 19-bp target RNA (blue). Figure created from data from Wang et al. (2009). (C) Radial cladogram of the Piwi (black branches) and Ago (gray branches) subfamilies. Human, mouse, zebrafish, and selected Caenorhabditis elegans Piwi and Ago proteins are shown.

Figure 2.

The siRNA and miRNA pathways. (A) Endogenous siRNAs are produced from inverted repeats or bidirectional transcription. The long dsRNA precursors are transported into the cytoplasm by Exportin5. Exogenous siRNAs are introduced by viral infection or transfection and are localized to the cytoplasm. In both cases, long dsRNAs are processed by Dicer to form mature siRNAs that are then incorporated into RNA-induced silencing complexes (RISCs) which mediate target cleavage. (B) miRNAs are produced by transcription of pri-miRNA precursors from miRNA genes, which are processed to pre-miRNAs by the microprocessor containing Drosha and Dgcr8. Alternatively, pre-miRNAs are also produced by splicing of intronic sequences containing miRNA sequences. Pre-miRNAs are exported from the nucleus by Exportin and processed into mature miRNAs by Dicer. miRNAs are then incorporated into RISCs that can mediate translational silencing or activation.

Figure 3.

Biogenesis of piRNAs. (A) In somatic cells of the Drosophila ovary, antisense piRNA precursors are produced from uni- and bidirectional piRNA clusters and processed into mature antisense piRNAs through an undefined mechanism. These piRNAs are them bound by Piwi and exert divergent effects including epigenetic regulation, transposon silencing, and others. A similar biogenesis mechanism utilizing Miwi and Mili may function in pachytene mouse testes. (B) Within the Drosophila germline, Aub and Ago3 function in a piRNA amplification loop. Antisense piRNAs are maternally inherited and/or produced from uni- and bidirectional piRNA clusters and bind to Aub. Aub-piRNA complexes catalyze degradation of transposon mRNAs and sense cluster transcripts, producing sense piRNAs that are then bound by Ago3. Ago3-piRNA complexes then produce additional antisense piRNAs through degradation of antisense cluster transcripts. (C) A similar mechanism functions during generation of prepachytene mouse piRNAs. Mili binds sense piRNAs, likely produced from sense piRNA precursors. The Mili-piRNA complex mediates degradation of antisense cluster transcripts, and the resulting antisense piRNAs are bound by Miwi2. Miwi2-piRNA complexes then mediate destruction of transposon mRNAs, generating additional sense piRNAs that are incorporated into Mili-piRNA complexes.