Abstract

In animals, small RNA molecules termed PIWI-interacting RNAs (piRNAs) silence transposable elements (TEs), protecting the germline from genomic instability and mutation. piRNAs have been detected in the soma in a few animals, but these are believed to be specific adaptations of individual species. Here, we report that somatic piRNAs were probably present in the ancestral arthropod more than 500 million years ago. Analysis of 20 species across the arthropod phylum suggests that somatic piRNAs targeting TEs and messenger RNAs are common among arthropods. The presence of an RNA-dependent RNA polymerase in chelicerates (horseshoe crabs, spiders and scorpions) suggests that arthropods originally used a plant-like RNA interference mechanism to silence TEs. Our results call into question the view that the ancestral role of the piRNA pathway was to protect the germline and demonstrate that small RNA silencing pathways have been repurposed for both somatic and germline functions throughout arthropod evolution.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

References

  1. 1.

    Aravin, A. A. et al. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr. Biol. 11, 1017–1027 (2001).

  2. 2.

    Aravin, A., Lagos-Quintana, M. & Yalcin, A. The small RNA profile during Drosophila melanogaster development. Dev. Cell 5, 337–350 (2003).

  3. 3.

    Czech, B. & Hannon, G. J. One loop to rule them all: the ping-pong cycle and piRNA-guided silencing. Trends Biochem. Sci. 41, 324–337 (2016).

  4. 4.

    Li, C. et al. Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 137, 509–521 (2009).

  5. 5.

    Malone, C. D. et al. Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary. Cell 137, 522–535 (2009).

  6. 6.

    Morazzani, E. M., Wiley, M. R., Murreddu, M. G., Adelman, Z. N. & Myles, K. M. Production of virus-derived ping-pong-dependent piRNA-like small RNAs in the mosquito soma. PLoS Pathog. 8, e1002470 (2012).

  7. 7.

    Miesen, P., Girardi, E. & van Rij, R. P. Distinct sets of piwi proteins produce arbovirus and transposon-derived piRNAs in Aedes aegypti mosquito cells. Nucleic Acids Res. 43, 6545–6556 (2015).

  8. 8.

    Jones, B. C. et al. A somatic piRNA pathway in the Drosophila fat body suppresses transposable elements ensuring metabolic homeostasis and normal lifespan. Nat. Commun. 7, 13856 (2016).

  9. 9.

    Ghildiyal, M. et al. Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science 320, 1077–1081 (2008).

  10. 10.

    Perrat, P. N. et al. Transposition-driven genomic heterogeneity in the Drosophila brain. Science 340, 91–95 (2013).

  11. 11.

    Palakodeti, D., Smielewska, M., Lu, Y.-C., Yeo, G. W. & Graveley, B. R. The piwi proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians. RNA 14, 1174–1186 (2008).

  12. 12.

    Reddien, P. W., Oviedo, N. J., Jennings, J. R., Jenkin, J. C. & Sánchez Alvarado, A. SMEDWI-2 is a piwi-like protein that regulates planarian stem cells. Science 310, 1327–1330 (2005).

  13. 13.

    Rajasethupathy, P. et al. A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell 149, 693–707 (2012).

  14. 14.

    Obbard, D. J., Gordon, K. H. J., Buck, A. H. & Jiggins, F. M. The evolution of RNAi as a defence against viruses and transposable elements. Phil. Trans. R. Soc. B 364, 99–115 (2009).

  15. 15.

    Kolaczkowski, B., Hupalo, D. N. & Kern, A. D. Recurrent adaptation in RNA interference genes across the Drosophila phylogeny. Mol. Biol. Evol. 28, 1033–1042 (2011).

  16. 16.

    Skinner, D. E., Rinaldi, G., Koziol, U., Brehm, K. & Brindley, P. J. How might flukes and tapeworms maintain genome integrity without a canonical piRNA pathway? Trends Parasitol. 30, 123–129 (2014).

  17. 17.

    Buck, A. H. & Blaxter, M. Functional diversification of Argonautes in nematodes: an expanding universe. Biochem. Soc. Trans. 41, 881–886 (2013).

  18. 18.

    Dowling, D. et al. Phylogenetic origin and diversification of RNAi pathway genes in insects. Genome Biol. Evol. 8, 3784–3793 (2017).

  19. 19.

    Lewis, S. H., Salmela, H. & Obbard, D. J. Duplication and diversification of Dipteran Argonaute genes, and the evolutionary divergence of Piwi and Aubergine. Genome Biol. Evol. 8, 507–518 (2016).

  20. 20.

    Palmer, W. J. & Jiggins, F. M. Comparative genomics reveals the origins and diversity of arthropod immune systems. Mol. Biol. Evol. 32, 2111–2129 (2015).

  21. 21.

    Sarkar, A., Volff, J. N. & Vaury, C. piRNAs and their diverse roles: a transposable element-driven tactic for gene regulation? FASEB J. 31, 436–446 (2017).

  22. 22.

    Sarkies, P. et al. Ancient and novel small RNA pathways compensate for the loss of piRNAs in multiple independent nematode lineages. PLoS Biol. 13, e1002061 (2015).

  23. 23.

    Tomoyasu, Y. et al. Exploring systemic RNA interference in insects: a genome-wide survey for RNAi genes in Tribolium. Genome Biol. 9, R10 (2008).

  24. 24.

    Campbell, C. L., Black, W. C., Hess, A. M. & Foy, B. D. Comparative genomics of small RNA regulatory pathway components in vector mosquitoes. BMC Genomics 9, 425 (2008).

  25. 25.

    Schiebel, W. et al. Isolation of an RNA-directed RNA polymerase-specific cDNA clone from tomato. Plant Cell 10, 2087–2102 (1998).

  26. 26.

    Zong, J., Yao, X., Yin, J., Zhang, D. & Ma, H. Evolution of the RNA-dependent RNA polymerase (RdRP) genes: duplications and possible losses before and after the divergence of major eukaryotic groups. Gene 447, 29–39 (2009).

  27. 27.

    Bull, J. J. Advantage for the evolution of male. Heredity 43, 361–381 (1979).

  28. 28.

    Robine, N. et al. A broadly conserved pathway generates 3′UTR-directed primary piRNAs. Curr. Biol. 19, 2066–2076 (2009).

  29. 29.

    Palatini, U. et al. Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus. BMC Genomics 18, 512 (2017).

  30. 30.

    Alefelder, S., Patel, B. K. & Eckstein, F. Incorporation of terminal phosphorothioates into oligonucleotides. Nucleic Acids Res. 26, 4983–4988 (1998).

  31. 31.

    Zhang, Z., Theurkauf, W. E., Weng, Z. & Zamore, P. D. Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence 3, 9 (2012).

  32. 32.

    Han, B. W., Wang, W., Li, C. & Weng, Z. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production. Science 348, 817–821 (2015).

  33. 33.

    Wickersheim, M. L. & Blumenstiel, J. P. Terminator oligo blocking efficiently eliminates rRNA from Drosophila small RNA sequencing libraries. Biotechniques 55, 269–272 (2013).

  34. 34.

    Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).

  35. 35.

    Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014).

  36. 36.

    Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).

  37. 37.

    Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540–552 (2000).

  38. 38.

    Ronquist, F. & Huelsenbeck, J. P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574 (2003).

  39. 39.

    Smit, A. F. A., Hubley, R. & Green, P. RepeatMasker Open-4.0 (2013).

  40. 40.

    Smit, A. F. A. & Hubley, R. RepeatModeler Open-1.0 (2008).

  41. 41.

    Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011).

  42. 42.

    Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10 (2011).

  43. 43.

    Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

  44. 44.

    Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

  45. 45.

    Brennecke, J. et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128, 1089–1103 (2007).

  46. 46.

    Zhang, Z. et al. Heterotypic piRNA ping-pong requires Qin, a protein with both E3 ligase and Tudor domains. Mol. Cell 44, 572–584 (2011).

  47. 47.

    Antoniewski, C. in Animal Endo-siRNAs: Methods and Protocols (ed. Werner, A.) 135–146 (Humana, New York, 2014).

  48. 48.

    Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).

  49. 49.

    Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol. 15, 550 (2014).

  50. 50.

    Misof, B. et al. Phylogenomics resolves the timing and pattern of insect evolution. Science 346, 763–767 (2014).

  51. 51.

    Giribet, G. & Edgecombe, G. D. Reevaluating the arthropod tree of life. Annu. Rev. Entomol. 57, 167–186 (2012).

  52. 52.

    Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969–1973 (2012).

  53. 53.

    Hadfield, J. D. MCMC methods for multi-response generalized linear mixed models: the MCMCglmm R package. J. Stat. Softw. 33, 1–22 (2010).

  54. 54.

    Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

Download references

Acknowledgements

We thank A. McGregor, D. Leite, M. Akam, R. Jenner, R. Kilner, A. Duarte, C. Jiggins, R. Wallbank, A. Bourke, T. Dalmay, N. Moran, K. Warchol, R. Callahan, G. Farley and T. Livdahl for providing the arthropods. H. Robertson provided the D. virgifera genome sequence. This research was supported by a Leverhulme Research Project Grant (RPG-2016-210 to F.M.J., E.A.M. and P.S.), a European Research Council grant (281668 DrosophilaInfection to F.M.J.), a Medical Research Council grant (MRC MC-A652-5PZ80 to P.S.), an Imperial College Research Fellowship (to P.S.), Cancer Research UK (C13474/A18583 and C6946/A14492 to E.A.M.), the Wellcome Trust (104640/Z/14/Z and 092096/Z/10/Z to E.A.M.) and a National Institutes of Health R37 grant (GM62862 to P.D.Z.).

Author information

Author notes

  1. Phillip D. Zamore, Eric A. Miska, Peter Sarkies and Francis M. Jiggins contributed equally to this work.

Affiliations

  1. Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK

    • Samuel H. Lewis
    • , Melanie Tanguy
    • , Lise Frézal
    • , Eric A. Miska
    •  & Francis M. Jiggins
  2. Medical Research Council London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK

    • Samuel H. Lewis
    •  & Peter Sarkies
  3. Institute for Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK

    • Samuel H. Lewis
    •  & Peter Sarkies
  4. Howard Hughes Medical Institute, RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA

    • Kaycee A. Quarles
    • , Yujing Yang
    •  & Phillip D. Zamore
  5. Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, CB2 1QN, UK

    • Melanie Tanguy
    • , Lise Frézal
    •  & Eric A. Miska
  6. Institut de Biologie de l’Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Inserm, Ecole Normale Supérieure, Paris Sciences & Lettres Research University, 75005, Paris, France

    • Lise Frézal
  7. Department of Biomedical Sciences and Pathobiology, Virginia Maryland College of Veterinary Medicine, 205 Duck Pond Drive, Virginia Tech, Blacksburg, VA, 24061, USA

    • Stephen A. Smith
  8. Department of Zoology, University of Wisconsin–Madison, 352 Birge Hall, 430 Lincoln Drive, Madison, WI, 53706, USA

    • Prashant P. Sharma
  9. Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France

    • Richard Cordaux
    • , Clément Gilbert
    •  & Isabelle Giraud
  10. Laboratoire Evolution, Génomes, Comportement, Écologie, Unité Mixte de Recherche 9191 Centre National de la Recherche Scientifique and Unité Mixte de Recherche 247 Institut de Recherche pour le Développement, Université Paris-Sud, 91198, Gif-sur-Yvette, France

    • Clément Gilbert
  11. School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK

    • David H. Collins

Authors

  1. Search for Samuel H. Lewis in:

  2. Search for Kaycee A. Quarles in:

  3. Search for Yujing Yang in:

  4. Search for Melanie Tanguy in:

  5. Search for Lise Frézal in:

  6. Search for Stephen A. Smith in:

  7. Search for Prashant P. Sharma in:

  8. Search for Richard Cordaux in:

  9. Search for Clément Gilbert in:

  10. Search for Isabelle Giraud in:

  11. Search for David H. Collins in:

  12. Search for Phillip D. Zamore in:

  13. Search for Eric A. Miska in:

  14. Search for Peter Sarkies in:

  15. Search for Francis M. Jiggins in:

Contributions

S.H.L. and K.A.Q. performed the experiments with assistance from Y.Y., M.T., L.F., S.A.S., P.P.S., R.C., C.G., I.G. and D.H.C. S.H.L., K.A.Q. and P.S. carried out the computational analysis. P.D.Z., E.A.M., P.S. and F.M.J. supervised the project. S.H.L., K.A.Q., P.D.Z., E.A.M., P.S. and F.M.J. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Samuel H. Lewis or Francis M. Jiggins.

Electronic supplementary material

  1. Supplementary Information

    Supplementary Figures 1–13, Supplementary Tables 1–2

  2. Life Sciences Reporting Summary

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/s41559-017-0403-4

Further reading