A piece of the pi(e): The diverse roles of animal piRNAs and their PIWI partners

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Abstract

Small non-coding RNAs are indispensable to many biological processes. A class of endogenous small RNAs, termed PIWI-interacting RNAs (piRNAs) because of their association with PIWI proteins, has known roles in safeguarding the genome against inordinate transposon mobilization, embryonic development, and stem cell regulation, among others. This review discusses the biogenesis of animal piRNAs and their diverse functions together with their PIWI protein partners, both in the germline and in somatic cells, and highlights the evolutionarily conserved aspects of these molecular players in animal biology.

Introduction

Three broad classes of endogenous small RNAs, microRNAs (miRNAs), endogenous small interfering RNAs (esiRNAs), and PIWI-interacting RNAs (piRNAs), are well known for their roles in cellular processes. These small RNAs act in concert with Argonaute proteins, which are found in many organisms [1], [2]. miRNAs and esiRNAs associate with a subset of Argonaute proteins that is collectively referred to as the AGO clade [3], [4], [5], [6]. Mature miRNAs and esiRNAs are approximately 21–24 nucleotides (nt) in length and are canonically generated from double-stranded regions (dsRNA) of RNA precursors [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19]. The dsRNA-slicing enzyme Dicer is required for the maturation of AGO-bound small RNAs [4], [10], [15], [20], [21], [22], [23]. These small RNAs operate by guiding their AGO effector molecule partners to targets through base pairing, and they predominantly function in gene silencing [4], [5], [6], [12], [13], [14], [15], [16], [17], [18], [19], [24], [25], [26], [27], [28], [29], [30], [31], [32], although there are several exceptions [33], [34], [35], [36], [37], [38]. Other details of the miRNA and esiRNA pathways and their functions have been reviewed elsewhere [39], [40], [41], [42], [43], [44], [45], [46], [47], [48].

The objective of this review is to provide a broad overview of the third class of small RNAs that associate with Argonaute proteins, the PIWI-interacting RNAs (piRNAs), and their protein partners. We cover the biogenesis of piRNAs and highlight their diverse features and functions in both the germline and in somatic cells of various animals. Unlike miRNAs and esiRNAs, piRNAs are typically longer, with a length of 24–31 nt, originate from single-stranded RNA (ssRNA) precursors, and do not require Dicer for maturation [49], [50], [51], [52]. First identified in the fruit fly, Drosophila melanogaster, piRNAs were initially designated as repeat-associated small interfering RNAs (rasiRNAs) because they were found to map to repetitive elements and transposons and to participate in their suppression [49], [50], [53], [54]. Subsequently, because rasiRNAs were found to bind to effector Argonaute proteins of the PIWI clade but not to those of the AGO clade, they were renamed as piRNAs [50], [51], [52], [54], [55], [56], [57]. The PIWI clade of Argonaute proteins was named after its founding member, the Drosophila piwi gene, abbreviated from P-element-induced wimpy testis (for clarity, PIWI refers to a protein of the PIWI clade, whereas Piwi refers to the individual Drosophila protein) [58]. The members of this clade, the PIWI proteins (PIWIs), are phylogenetically distinct from AGO proteins and, apart from their presence in some protists, have not been observed beyond the animal kingdom, unlike AGO proteins [1], [59].

Because many of the initial functional and mechanistic insights into these molecules were derived from work in fly ovaries, in which the majority of piRNAs map to transposable elements (TEs), the most well-studied role of the piRNA pathway is in TE silencing [53], [54], [56], [60], [61]. The piRNA pathway primarily targets class I TEs, the retrotransposons, which propagate through an RNA intermediate (reviewed in [62], [63]). piRNAs and PIWIs are mainly expressed in the gonads of many of the animals that have been studied, and they predominantly appear to negatively regulate their targets; however, exceptions do exist (discussed later) (Fig. 1). Although PIWIs are also known to participate in genome rearrangement in ciliates [64], [65], [66], [67] (reviewed in [68], [69], [70]), these non-metazoan PIWIs associate with small RNAs, termed scan RNAs (scnRNAs), which are generated from dsRNA precursors in a Dicer-dependent manner [71], [72]. Thus, ciliate PIWIs and scnRNAs might have evolved separately from metazoan PIWIs and piRNAs. In this review, we will focus on piRNAs and PIWIs in animals and will not cover them in protists.

Throughout the review, we also present a recurrent perspective: the evolutionary conservation of piRNAs and PIWIs, highlighting the known conserved features and functions of these molecules. Although there are differences between the species, many attributes appear to be conserved across metazoans, emphasizing the utility of piRNAs and PIWIs in animal biology.

Section snippets

The germline piRNA pathway

The piRNA pathway is required for protecting the germline genome against damaging levels of TE activity and for normal gametogenesis. Its importance in the germline is highlighted by the observation that mutations in piRNA pathway components often result in DNA damage caused by excessive TE mobility and sterility [60], [61], [73], [74], [75], [76], [77], [78], [79], [80], [81], [82], [83], [84], [85]. Within germline cells, many evolutionarily conserved components of the piRNA pathway,

piRNAs and PIWIs beyond the gonads

Apart from the gonads, piRNAs and PIWIs may be expressed in various somatic cell types, albeit typically at lower levels than those observed in the germline (Fig. 1). Although the direct involvement of piRNAs was not assessed in many of the studies on somatic PIWIs, it is not difficult to imagine that, as in the gonads, piRNAs function in concert with PIWIs, likely by conferring target specificity in many, if not all, biological contexts. However, as many piRNA biogenesis factors are often not

Concluding remarks and perspectives

We have reviewed many aspects of piRNAs and PIWIs, from their biogenesis to their roles in the germline and somatic cells, as well as in disease. Nonetheless, many additional characteristics of these molecules remain to be identified and examined. For example, it is unclear how piRNAs originating from piRNA precursors become predominantly antisense to TEs, despite the apparent random orientation of TEs in piRNA clusters [56]. The precise mechanisms underlying many piRNA pathway components have

Acknowledgments

We thank Amit Anand for critical reading of the manuscript and for suggestions. This work was supported by the Temasek Life Sciences Laboratory and the Singapore Millennium Foundation.

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