Beyond transposons: the epigenetic and somatic functions of the Piwi-piRNA mechanism
Introduction
Three major types of small RNAs, siRNAs, miRNAs, and piRNAs, associate with proteins in the Argonaute/Piwi family to execute sequence-specific gene silencing. Among the three types of small RNAs, piRNAs were discovered most recently and remain the least characterized. They are named by their exclusive association with Piwi but not Argonaute (Ago) subfamily proteins. Unlike the broad expression of siRNAs and miRNAs in most cell and tissue types, piRNAs are highly enriched in the germline. This expression pattern and the findings that mutations of piRNA biogenesis factors result in either germline stem cell loss or sterility of the mutant animals demonstrate the critical impact the Piwi-piRNA pathway exerts on germline development and functions [1, 2, 3, 4, 5, 6]. Strong hypormophic mutations of Drosophila piwi result in reduced germline stem cell division and eventual germline stem cell loss [3, 7]. Reduced level of Piwi homologs in Caenorhabditis elegans result in reduced germ cell division and reduced fertility [7, 8]. Knockout mutations of mouse Piwi proteins Mili, Miwi, and Miwi2 result in male sterility in all cases, spermatogonial stem cell arrest and eventual loss in Mili and Miwi2 mutants, and meiotic arrest in Miwi mutant [4, 5, 6, 9, 10]. Genetic analysis of Piwi functions in the germline of these model organisms reinforced the critical role of Piwi proteins in germline development.
Numerous excellent reviews have detailed piRNA biogenesis pathway and contrasted it with miRNA and siRNA biogenesis [11, 12, 13]. Here we highlight some less discussed points. First, in contrast to the ∼500 loci encoding miRNAs in most eukaryotic genomes, the number of piRNAs ranges up to 100 000's. Second, both the RNA polymerase transcribing the primary transcripts and the nuclease generating primary piRNAs from the primary transcripts are yet to be identified; an endonuclease Zucchini has been implicated in generating the 5′ end of piRNA [14, 15]. Third, the mechanism of RNA target selection by the piRNA-induced silencing complex is unclear. Fourth, the mechanism by which PIWI-piRNA complexes regulate epigenetic processes via sequence specificity remains unclear.
The questions highlighted above remain unsolved partially because studies of piRNA functions have mostly been focused on transposon silencing in the germline. Indeed, mutations of genes involved in piRNA biogenesis result in increased transposition and DNA damage in germ cells [16, 17] and because a subpopulation of piRNAs appears to suppress retrotransposon activities in the germline [18, 19]. These studies, however, often overlook substantial evidence demonstrating that the Piwi-piRNA pathway significantly influences epigenetic mechanisms. Drosophila Piwi and its homolog Aubergine have been shown to affect transcriptional silencing [20], to be required for heterochromatin formation [21], and to affect Polycomb Group-mediated transgene silencing [22]. Furthermore, molecular and biochemical analyses of Piwi and piRNAs demonstrated that Piwi protein directly associates with and recruits HP1a [23, 24], that the Piwi-piRNA complex directly binds to piRNA-complementary sequence in the genome and is required for proper histone modification of the sequence [25], and that maternally deposited piRNAs can epigenetically mediate transposon suppression in the offspring [26]. In addition, analyses of mouse Piwi homologs, Mili and Miwi2, indicated that they mediate DNA methylation in the male germline during embryogenesis [27, 28, 29]. Together, the above observations implicate epigenetic function of the Piwi-piRNA pathway and its importance for germline health and functions.
Section snippets
The Piwi-piRNA pathway in epigenetic regulation
The Piwi-piRNA pathway can regulate epigenetic processes via the following mechanisms (Figure 1):
Histone modifications: Histone modifications are the predominant means by which epigenetic information is transmitted from parents to offspring. Drosophila Piwi protein has been shown to directly influence histone modifications at a piRNA target site [25] and to functionally associate with HP1a and histone H3 lysine9 methylation (H3K9me) [23, 24]. HP1a and H3K9me are both characteristic marks of
The Piwi-piRNA pathway in canalization
Canalization was first described by Conrad Waddington in 1942 as the phenomenon in which ‘epigenetic landscape’ canalizes genotypic variations into manifesting phenotypic similarities [35]. In modern terms, canalization is recognized as a molecular mechanism that buffers the impact of genotypic and environmental variations on phenotype to ensure developmental robustness. A few molecules have been identified for their role in canalization, among which the heat-shock protein 90 kDa (Hsp90) is the
The Piwi-piRNA pathway in post-transcriptional and somatic regulation
Previous studies of the epigenetic regulatory functions of Drosophila Piwi indicated that it could influence epigenetic mechanisms outside the germline tissues [21, 22, 25, 45]. However, the findings that animals containing piwi mutations or mutations in other genes for piRNA biogenesis manifest sterility but no other observed deleterious effects led to the presumption that Piwi-piRNAs do not significantly impact tissues outside the germline. These findings, however, cannot rule out the
Concluding remark and future directions
Studies from the past few years have revealed the functions of the Piwi-piRNA pathway in regulating epigenetic and post-transcriptional gene regulation, in influencing somatic cell functions, and in mediating canalization to enhance developmental robustness. Because the Piwi-piRNA complex exerts its functions via piRNA sequence specificity, the high complexity of piRNAs allows them to act on a wide range of targets in the genome, and to generate broad impact on genome-wide gene regulation at
References and recommended reading
Papers of particular interest, published within the period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Acknowledgements
Work in the Lin lab is supported by NIH (DP1CA174418 and R37HD042012), the Connecticut Stem Cell Research Foundation, the G Harold and Leila Mathers Foundation, and the Ellison Medical Foundation. JCP is supported by an NIH Pathway to Independence (PI) Award (K99-HD071011).
References (49)
- et al.
Miwi2 is essential for spermatogenesis and repression of transposons in the mouse male germline
Dev Cell
(2007) - et al.
Miwi, a murine homolog of piwi, encodes a cytoplasmic protein essential for spermatogenesis
Dev Cell
(2002) - et al.
A C. elegans piwi, prg-1, regulates 21u-RNAs during spermatogenesis
Curr Biol
(2008) - et al.
Mili a piwi-interacting RNA-binding protein, is required for germ line stem cell self-renewal and appears to positively regulate translation
J Biol Chem
(2009) - et al.
Drosophila rasiRNA pathway mutations disrupt embryonic axis specification through activation of an atr/chk2 DNA damage response
Dev Cell
(2007) - et al.
Cutoff and aubergine mutations result in retrotransposon upregulation and checkpoint activation in Drosophila
Curr Biol
(2007) - et al.
Mighty piwis defend the germline against genome intruders
Cell
(2007) - et al.
RNAi related mechanisms affect both transcriptional and post-transcriptional transgene silencing in Drosophila
Mol Cell
(2002) - et al.
RNAi components are required for nuclear clustering of polycomb group response elements
Cell
(2006) - et al.
A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice
Mol Cell
(2008)
Transcriptional silencing of transposons by piwi and maelstrom and its impact on chromatin state and gene expression
Cell
PiRNAs can trigger a multigenerational epigenetic memory in the germline of C. elegans
Cell
Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse rasgrf1 locus
Science
Hsp90 as a capacitor for morphological evolution
Nature
Piwi encodes a nucleoplasmic factor whose activity modulates the number and division rate of germline stem cells
Development
Oocyte determination and the origin of polarity in Drosophila: the role of the spindle genes
Development
A novel group of pumilio mutations affects the asymmetric division of germline stem cells in the Drosophila ovary
Development
Mili, a mammalian member of piwi family gene, is essential for spermatogenesis
Development
A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal
Genes Dev
The biogenesis and function of piwi proteins and piRNAs: progress and prospect
Annu Rev Cell Dev Biol
Small noncoding RNAs in the germline
Cold Spring Harbor Perspect Biol
MicroRNAs key regulators of stem cells
Nat Rev Mol Cell Biol
Small RNA sorting: matchmaking for argonautes
Nat Rev Genet
The structural biochemistry of zucchini implicates it as a nuclease in piRNA biogenesis
Nature
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