Mammalian Genome

, Volume 19, Issue 7–8, pp 581–586

piRNA-like RNAs in the marsupial Monodelphis domestica identify transcription clusters and likely marsupial transposon targets



PIWI-interacting RNAs (piRNAs) are a recently discovered class of small noncoding RNAs that have been detected in human, mouse, rat, zebrafish, and Drosophila genomes. We have utilized a size-directed small-RNA cloning procedure to clone and map more than 300 candidate piRNA-like small RNAs in the genome of the marsupial species Monodelphis domestica. Our results are consistent with those from other species in that the piRNA-like candidate sequences range in size from 28 to 31 nucleotides, show a pronounced preference for uridine at the 5′ end, are transcribed from a few large clusters, appear to target transposons, and display virtually no sequence conservation.

Supplementary material

335_2008_9109_MOESM1_ESM.doc (926 kb)
(DOC 925 kb)
335_2008_9109_MOESM2_ESM.doc (22 kb)
(DOC 21 kb)


  1. Aravin A, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P et al (2006) A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442:203–207PubMedGoogle Scholar
  2. Aravin AA, Hannon GJ, Brennecke J (2007) The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318:761–764PubMedCrossRefGoogle Scholar
  3. Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123:1279–1291PubMedCrossRefGoogle Scholar
  4. Brennecke J, Aravin AA, Stark A, Dus M, Kellis M et al (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128:1–15CrossRefGoogle Scholar
  5. Cardazzo B, Bargelloni L, Toffolatti L, Rimessi P, Ferlini A et al (2003) Tempo and mode of evolution of a primate-specific retrotransposon belonging to the LINE1 family. J Mol Evol 57:S268–S276PubMedCrossRefGoogle Scholar
  6. Duke SE, Samollow PB, Mauceli E, Lindblad-Toh K, Breen M (2007) Integrated cytogenetic BAC map of the genome of the grey, short-tailed opossum, Monodelphis domestica. Chromosome Res 15:361–370PubMedGoogle Scholar
  7. Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA et al (2007) Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Res 17:992–1004PubMedCrossRefGoogle Scholar
  8. Girard A, Sachidanandam R, Hannon GJ, Carmell MA (2006) A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442:199–202PubMedGoogle Scholar
  9. Grivna ST, Beyret E, Wang Z, Lin H (2006) A novel class of small RNAs in mouse spermatogenic cells. Genes Dev 20:1709–1714PubMedCrossRefGoogle Scholar
  10. Houwing S, Kamminga LM, Berezikov E, Cronembold D, Girard A et al (2007) A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in zebrafish. Cell 129:69–82PubMedCrossRefGoogle Scholar
  11. Kim VN (2006) Small RNAs just got bigger, Piwi-interacting RNAs (piRNAs) in mammalian testes. Genes Dev 20:1993–1997PubMedCrossRefGoogle Scholar
  12. Kirino Y, Mourelatos Z (2007) Mouse Piwi-interacting RNAs are 2′-O-methylated at their 3′ termini. Nat Struct Mol Biol 14:347–348PubMedCrossRefGoogle Scholar
  13. Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294:858–862PubMedCrossRefGoogle Scholar
  14. Lau NC, Seto AG, Kim J, Kuramochi-Miyagawa S, Nakano T et al (2006) Characterization of the piRNA complex from rat testes. Science 313:363–367PubMedCrossRefGoogle Scholar
  15. Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843–854PubMedCrossRefGoogle Scholar
  16. Lee RC, Hammell CM, Ambros V (2006) Interacting endogenous and exogenous RNAi pathways in Caenorhabditis elegans. RNA 12:589–597PubMedCrossRefGoogle Scholar
  17. Martin SL, Voliva CF, Hardies SC, Edgell MH, Hutchinson CA (1985) Tempo and mode of concerted evolution in the L1 repeat family in mice. Mol Biol Evol 2:127–140PubMedGoogle Scholar
  18. Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL et al (2007) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447:167–178PubMedCrossRefGoogle Scholar
  19. O’Donnell KA, Boeke JD (2007) Mighty Piwis defend the germline against genome intruders. Cell 129:37–44PubMedCrossRefGoogle Scholar
  20. Ohara T, Sakaguchi Y, Suzuki T, Ueda H, Miyauchi K et al (2007) The 3′ termini of mouse Piwi-interacting RNAs are 2′-O-methylated. Nat Struct Mol Biol 14:349–350PubMedCrossRefGoogle Scholar
  21. Peragrine A, Yoshikawa M, Wu G, Albreacht HL, Poethig RS (2004) SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev 18:2368–2379CrossRefGoogle Scholar
  22. Ro S, Park C, Song R, Nguyen D, Jin J et al (2007a) Cloning and expression profiling of testis-expressed piRNA-like RNAs. RNA 13:1693–1702PubMedCrossRefGoogle Scholar
  23. Ro S, Song R, Park C, Zheng H, Sanders KM et al (2007b) Cloning and expression profiling of small RNAs expressed in the mouse ovary. RNA 13:2366–2380PubMedCrossRefGoogle Scholar
  24. Ruby JG, Jan C, Player C, Axtell MJ, Lee W et al (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C elegans. Cell 127:1193–1207PubMedCrossRefGoogle Scholar
  25. Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T et al (2006) Identification and characterization of two novel classes of small RNAs in the mouse germline, retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev 20:1732–1743PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Eric J. Devor
    • 1
  • Lingyan Huang
    • 1
  • Paul B. Samollow
    • 2
  1. 1.Molecular Genetics and BiophysicsIntegrated DNA TechnologiesCoralvilleUSA
  2. 2.Department of Veterinary Integrative BiosciencesTexas A&M UniversityTXUSA

Personalised recommendations