Posttranscriptional regulation of gene expression by Piwi proteins and piRNAs

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.

Figure 1. Two biogenesis pathways generate piRNAs

(A) A model of the primary piRNA biogenesis pathway. The piRNA precursors are transcribed from piRNA clusters, and are then processed into piRNA intermediates. The piRNA intermediates with uridine at the 5’ ends are loaded onto Piwi proteins, with HSP90 facilitates the loading. Subsequently, the 3’ portions of piRNA intermediates are trimmed by unidentified nuclease(s). After the trimming, 3’ ends are 2’-O-methylated by Hen1 methyltransferase. Mitochondrial outer membrane proteins MitoPLD/Zucchini, GASZ, and GPAT2/Minotaur are probably involved in the processing of piRNA precursors or intermediates. (B) A model of the secondary biogenesis pathway. The Piwi/piRNA complexe cleaves a transposon RNA between the 10^th and 11^th position of piRNAs. The 3’ region of the cleaved RNA is incorporated into Piwi proteins. The 5’ region is ejected from Piwi proteins by chaperone machinery FKBP6/Shutdown and HSP90, and is then degraded. The 10^th position of the incorporated RNA is enriched in adenine, because it is complementary to the first position of a piRNA that is enriched in uridine. The incorporated RNA is then processed into a mature secondary piRNA by trimming and modification likely by the same mechanisms that generate a primary piRNA.

Figure 2. Regulation of mRNAs by piRNAs derived from transposons, pseudogenes, and cis-NAT

(A) Transposon sequence-derived piRNAs regulate mRNAs.. Transposon sequences in the 5’ UTRs of transposon-driven mRNAs (left) and the 3’ UTR of mRNAs (right) are targeted by the piRNAs. (B) Pseudogene-derived piRNAs regulate mRNAs. Pseudogenes are located in piRNA clusters in an antisense orientation to piRNA cluster transcription, so that piRNAs are produced that are antisense to the target genes. The piRNAs derived from pseudogenes then target the cognate mRNAs. (C) cis-NAT-derived piRNAs regulate sense mRNAs.

Figure 3. Biological functions of Piwi proteins and piRNAs

(A) Sex determination in silkworms is mediated by a single piRNA. In females, the sex determination region of the W-chromosome produces the fem piRNA that degrades Masc mRNA that encodes a CCCH-type zinc finger protein. Therefore, only males can produce the Masc protein that promotes the production of the male-specific splicing variant of Bmdsx, transcription factor. Bmdsx regulates genes responsible for the sexual phenotype of the body. In the absence of Masc mRNA, the female-specific splicing variant of Bmdsx is produced. (B) Functions of pachytene piRNAs during mouse spermatogenesis. Pachytene piRNAs are mostly bound to Miwi and expressed from the late spermatocyte to the elongating spermatid stage. Spermatogenesis in the Miwi KO mouse is arrested at the early round spermatid stage. In late spermatocytes and round spermatids, Miwi and pachytene piRNAs degrade L1 RNA in a slicer activity-dependent manner. In elongating spermatids, they promote massive mRNA elimination in a slicer-independent manner by interacting with CAF1 deadenylase. (C) Maternally transmitted I-element piRNAs are required for the repression of I-elements in ovaries. A dysgenic cross between reactive females devoid of I-elements (R strain) and inducer males carrying I-elements (I strain) produces a sterile daughter (top). This daughter lacks the expression of I-element piRNAs in ovaries. A non-dysgenic cross between R strain males and I strain females produces a fertile daughter, which expresses I-element piRNAs in ovaries (bottom). (D) piRNA-mediated RNA degradation may play an important role in the control of sporadic RNAs transcribed from open chromatin regions in the genome..

Figure 4. Mechanisms of regulation by Piwi proteins and piRNAs

The left figure shows a model of slicer-dependent target RNA degradation. The slicer activity of Piwi proteins cleaves target RNAs. For the cleavage, near-perfect complementarity is needed between a target RNA and a piRNA. The 5’ fragment of the cleaved RNA is probably degraded by 3’–>5’ exonucleases. The 3’ fragment is likely either degraded by 3’–>5’ exonucleases or processed into secondary piRNAs. The right figure shows possible mechanisms of slicer-independent regulation. For this, extensive complementarity is probably not needed. All proteins in this figure have been shown to interact or co-localize with Piwi proteins. They are involved in RNA-degradation (XRN1), de-capping (DCP1/2), translation initiation (cytoplasmic cap-binding complex), deadenylation (Caf1 and Ccr4/Caf1/Not complex), and RNA-binding (Smg).