Piwi/piRNA evolution

Our research intends to throw light on the adaptations of Piwi proteins, piRNAs and genomic piRNA clusters that ensure the maintenance of a functional transposon defense over evolutionary time spans. We aim to figure out different patterns of subfunctionalization/specialization regarding single components of the Piwi/piRNA pathway in different species that may reflect the specific activity of the particular transposon repertoire. Further we want to understand which factors influence the production of piRNAs from distinct loci in different species including human and representative non-human primates resulting in observable variation (on/off states) on different phylogenetic lineages. Finally, analyses of piRNA transcriptomes in different species and tissue types will help us to understand putative Piwi/piRNA functions that are not related to transposon silencing.

Background: Jumping Genes     show Background: Small RNAs     show

Sequence evolution of piRNA clusters and piRNAs

piRNA clusters do not evolve uniformely. Instead, we can observe different conservation patterns within the same piRNA clusters: Residues that are overrepresented in tree shrew (Tupaia belangeri) testis piRNA transcriptomes show stronger sequence conservation whereas piRNA coding residues in general show only very weak sequence conservation (Figure from Rosenkranz et al. 2015, RNA 21(5):911-922). In addition, piRNA clusters exhibit conserved regions that do not code for piRNAs. Some of these conserved spots were identified as putative A-Myb and RFX4 transcription factor binding sites which gives the impression that the ability of a certain genomic locus to produce piRNAs is more important than preserving primary sequences of piRNAs over evolutionary time scales.

Different target sites for transposon related piRNAs and siRNAs

piRNAs and siRNAs target transposon transcriptsTransposable elements in the tree shrew are targeted not only by piRNAs but also by smaller RNAs resembling typical features of siRNAs. Interestingly, the two classes of small RNAs apperently differ from each other with respect to their target sites. Comprehensive bioinformatic analyses showed that piRNAs preferentially target transposon transcripts at sites that do not form strong secundary structures and thus remain accessible for guiding piRNAs. As an example, the coverage of piRNAs along the TUS element (tree shree specific SINE) displays a maximum at the site that also exhibits the lowest amount of paired bases (Figure from Rosenkranz et al. 2015, RNA 21(5):911-922, top and bottom right). In contrast, transposon transcripts with a strong secondary structure such as MariN1 elements apperently circumvent piRNA dependent processing as they do not represent adequate targets for guiding sRNAs. Instead, transcripts of these elements are processed by Dicer, an enzyme that recognizes double-stranded RNA molecules and that is also critically involved in miRNA biogenesis. As an outcome small RNA transcriptomes comprise a considerable amount of transposon derived siRNAs that corresponds to transposon sites with an increased amount of paired bases (bottom left).

Conservation of gene regulatory function

While in flys piRNAs are enriched for transposon sequences, the majority of mammalian pachytene piRNAs matches single-copy sequences. This raised the question of whether the Piwi/piRNA system is involved in functions beyond transposon silencing. Our in-deep characterization of the porcine testis piRNA transcriptome provided evidence for a processing of protein-coding transcripts within the piRNA ping-pong cycle. Remarkably, orthologous genes are targeted by piRNAs accross different mammalian species pointing towards a conserved function in post-transcriptional gene regulation in mammals (Figure from Gebert et al. 2015, PLoS ONE 10(5):e0124860).

Piwi proteins and piRNAs in oocytes and early embryos

piRNAs in oocytesGerm cells of most animals critically depend on piRNAs and Piwi proteins. Surprisingly, piRNAs in mouse oocytes are relatively rare and dispensable. We presented compelling evidence for strong Piwi and piRNA expression in oocytes of other mammals. Human fetal oocytes express PIWIL2 and transposon-enriched piRNAs. Oocytes in adult human ovary express PIWIL1 and PIWIL2, whereas those in bovine ovary only express PIWIL1. In human, macaque, and bovine ovaries, we found piRNAs that resemble testis-borne pachytene piRNAs. Isolated bovine follicular oocytes were shown to contain abundant, relatively short piRNAs that preferentially target transposable elements. Using label-free quantitative proteome analysis, we showed that these maturing oocytes strongly and specifically express the PIWIL3 protein, alongside other, known piRNA-pathway components. A piRNA pool is still present in early bovine embryos, revealing a potential impact of piRNAs on mammalian embryogenesis. Our results revealed that there are highly dynamic piRNA pathways in mammalian oocytes and early embryos (Figure from Roovers et al. 2015, Cell Reports 10:2069-2082)

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