The MID-PIWI module of Piwi proteins specifies nucleotide- and strand-biases of piRNAs

RNA. 2014 Jun;20(6):773-81. doi: 10.1261/rna.044701.114. Epub 2014 Apr 22.


Piwi-interacting RNAs (piRNAs) guide Piwi Argonautes to suppress transposon activity in animal gonads. Known piRNA populations are extremely complex, with millions of individual sequences present in a single organism. Despite this complexity, specific Piwi proteins incorporate piRNAs with distinct nucleotide- and transposon strand-biases (antisense or sense) of unknown origin. Here, we examined the contribution of structural domains in Piwi proteins toward defining these biases. We report the first crystal structure of the MID domain from a Piwi Argonaute and use docking experiments to show its ability to specify recognition of 5' uridine (1U-bias) of piRNAs. Mutational analyses reveal the importance of 5' end-recognition within the MID domain for piRNA biogenesis in vivo. Finally, domain-swapping experiments uncover an unexpected role for the MID-PIWI module of a Piwi protein in dictating the transposon strand-orientation of its bound piRNAs. Our work identifies structural features that allow distinguishing individual Piwi members during piRNA biogenesis.

Keywords: MID; Piwi; U1-bias; piRNA; strand-bias.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Argonaute Proteins / chemistry*
  • Argonaute Proteins / genetics*
  • Bombyx / genetics
  • Cell Line
  • Crystallography, X-Ray
  • Escherichia coli / genetics
  • Humans
  • Interspersed Repetitive Sequences / genetics*
  • Mice
  • Nucleotides / genetics
  • RNA, Small Interfering / chemistry*
  • RNA, Small Interfering / genetics*


  • Argonaute Proteins
  • Nucleotides
  • RNA, Small Interfering

Associated data

  • GEO/GSE55451
  • PDB/4P1Z