dsRNA binding properties of RDE-4 and TRBP reflect their distinct roles in RNAi

J Mol Biol. 2008 Dec 26;384(4):967-79. doi: 10.1016/j.jmb.2008.10.002. Epub 2008 Oct 11.


Double-stranded RNA (dsRNA)-binding proteins facilitate Dicer functions in RNA interference. Caenorhabditis elegans RDE-4 facilitates cleavage of long dsRNA to small interfering RNA (siRNA), while human trans-activation response RNA-binding protein (TRBP) functions downstream to pass siRNA to the RNA-induced silencing complex. We show that these distinct in vivo roles are reflected in in vitro binding properties. RDE-4 preferentially binds long dsRNA, while TRBP binds siRNA with an affinity that is independent of dsRNA length. These properties are mechanistically based on the fact that RDE-4 binds cooperatively, via contributions from multiple domains, while TRBP binds noncooperatively. Our studies offer a paradigm for how dsRNA-binding proteins, which are not sequence specific, discern dsRNA length. Additionally, analyses of the ability of RDE-4 deletion constructs and RDE-4/TRBP chimeras to reconstitute Dicer activity suggest RDE-4 promotes activity using its dsRNA-binding motif 2 to bind dsRNA, its linker region to interact with Dicer, and its C-terminus for Dicer activation.

Publication types

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

MeSH terms

  • Animals
  • Caenorhabditis elegans / physiology*
  • Caenorhabditis elegans Proteins / metabolism*
  • Humans
  • Protein Binding
  • RNA Interference*
  • RNA, Double-Stranded / metabolism
  • RNA, Small Interfering / metabolism
  • RNA-Binding Proteins / metabolism*


  • Caenorhabditis elegans Proteins
  • RDE-4 protein, C elegans
  • RNA, Double-Stranded
  • RNA, Small Interfering
  • RNA-Binding Proteins
  • trans-activation responsive RNA-binding protein