title: Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster.
abstract: 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.
authors.affiliation: Sloan-Kettering Institute, Department of Developmental Biology, 521 Rockefeller Research Laboratories, 1275 York Avenue, Box 252, New York, New York 10065, USA.
authors.forename: Katsutomo
authors.initials: K
authors.lastname: Okamura
authors.forename: Sudha
authors.initials: S
authors.lastname: Balla
authors.forename: Raquel
authors.initials: R
authors.lastname: Martin
authors.forename: Na
authors.initials: N
authors.lastname: Liu
authors.forename: Eric C
authors.initials: EC
authors.lastname: Lai
mesh_terms: D000818:Animals; D060565:Argonaute Proteins; D029721:Drosophila Proteins / Q000502:physiology*; D004331:Drosophila melanogaster / Q000235:genetics; D005091:Exons; D007438:Introns; D020365:RNA Helicases / Q000502:physiology*; D034622:RNA Interference; D012330:RNA, Double-Stranded; D034741:RNA, Small Interfering / Q000096:biosynthesis*; D034743:RNA-Induced Silencing Complex / Q000502:physiology*; D043244:Ribonuclease III; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: C433807:AGO2 protein, Drosophila; D060565:Argonaute Proteins; D029721:Drosophila Proteins; D012330:RNA, Double-Stranded; D034741:RNA, Small Interfering; D034743:RNA-Induced Silencing Complex; C478069:DCR-2 protein, Drosophila; D043244:Ribonuclease III; D020365:RNA Helicases