Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster

Nat Struct Mol Biol. 2008 Jun;15(6):581-90. doi: 10.1038/nsmb.1438. Epub 2008 May 25.


Cis-natural antisense transcripts (cis-NATs) have been speculated to be substrates for endogenous RNA interference (RNAi), but little experimental evidence for such a pathway in animals has been reported. Analysis of massive Drosophila melanogaster small RNA data sets now reveals two mechanisms that yield endogenous small interfering RNAs (siRNAs) via bidirectional transcription. First, >100 cis-NATs with overlapping 3' exons generate 21-nt, and, based on previously published small RNA data [corrected] Dicer-2 (Dcr-2)-dependent, 3'-end modified siRNAs. The processing of cis-NATs by RNA interference (RNAi) seems to be actively restricted, and the selected loci are enriched for nucleic acid-based functions and include Argonaute-2 (AGO2) itself. Second, we report that extended intervals of the thickveins and klarsicht genes generate exceptionally abundant siRNAs from both strands. These siRNA clusters derive from atypical cis-NAT arrangements involving introns and 5' or internal exons, but their biogenesis is similarly Dcr-2- and AGO2-dependent. These newly recognized siRNA pathways broaden the scope of regulatory networks mediated by small RNAs.

Publication types

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

MeSH terms

  • Animals
  • Argonaute Proteins
  • Drosophila Proteins / physiology*
  • Drosophila melanogaster / genetics
  • Exons
  • Introns
  • RNA Helicases / physiology*
  • RNA Interference
  • RNA, Double-Stranded
  • RNA, Small Interfering / biosynthesis*
  • RNA-Induced Silencing Complex / physiology*
  • Ribonuclease III
  • Transcription, Genetic / genetics*


  • AGO2 protein, Drosophila
  • Argonaute Proteins
  • Drosophila Proteins
  • RNA, Double-Stranded
  • RNA, Small Interfering
  • RNA-Induced Silencing Complex
  • DCR-2 protein, Drosophila
  • Ribonuclease III
  • RNA Helicases

Associated data

  • GEO/GSM272651
  • GEO/GSM272652
  • GEO/GSM272653
  • GEO/GSM286644