The ERI-6/7 helicase acts at the first stage of an siRNA amplification pathway that targets recent gene duplications

• Published in: PLoS genetics 2011-11, Vol.7 (11), p.e1002369
• Main Authors: Fischer, Sylvia E J, Montgomery, Taiowa A, Zhang, Chi, Fahlgren, Noah, Breen, Peter C, Hwang, Alexia, Sullivan, Christopher M, Carrington, James C, Ruvkun, Gary
• Format: Article
• Language: English
• Subjects: Animals; Biology; Caenorhabditis elegans; Caenorhabditis elegans - genetics; Caenorhabditis elegans - metabolism; Caenorhabditis elegans Proteins - genetics; Caenorhabditis elegans Proteins - metabolism; DNA Helicases - genetics; DNA Helicases - metabolism; Experiments; Gene Duplication - genetics; Gene Expression Regulation; Gene Silencing; Genetic aspects; Genetic regulation; Genetics; Medical research; Mutation; Nematodes; Oocytes - metabolism; Physiological aspects; Proteins; Pseudogenes - genetics; Ribonuclease III - genetics; RNA, Double-Stranded - metabolism; RNA, Small Interfering - genetics; RNA, Small Interfering - metabolism; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1002369

Endogenous small interfering RNAs (siRNAs) are a class of naturally occuring regulatory RNAs found in fungi, plants, and animals. Some endogenous siRNAs are required to silence transposons or function in chromosome segregation; however, the specific roles of most endogenous siRNAs are unclear. The helicase gene eri-6/7 was identified in the nematode Caenorhabditis elegans by the enhanced response to exogenous double-stranded RNAs (dsRNAs) of the null mutant. eri-6/7 encodes a helicase homologous to small RNA factors Armitage in Drosophila, SDE3 in Arabidopsis, and Mov10 in humans. Here we show that eri-6/7 mutations cause the loss of 26-nucleotide (nt) endogenous siRNAs derived from genes and pseudogenes in oocytes and embryos, as well as deficiencies in somatic 22-nucleotide secondary siRNAs corresponding to the same loci. About 80 genes are eri-6/7 targets that generate the embryonic endogenous siRNAs that silence the corresponding mRNAs. These 80 genes share extensive nucleotide sequence homology and are poorly conserved, suggesting a role for these endogenous siRNAs in silencing of and thereby directing the fate of recently acquired, duplicated genes. Unlike most endogenous siRNAs in C. elegans, eri-6/7-dependent siRNAs require Dicer. We identify that the eri-6/7-dependent siRNAs have a passenger strand that is ∼19 nt and is inset by ∼3-4 nts from both ends of the 26 nt guide siRNA, suggesting non-canonical Dicer processing. Mutations in the Argonaute ERGO-1, which associates with eri-6/7-dependent 26 nt siRNAs, cause passenger strand stabilization, indicating that ERGO-1 is required to separate the siRNA duplex, presumably through endonucleolytic cleavage of the passenger strand. Thus, like several other siRNA-associated Argonautes with a conserved RNaseH motif, ERGO-1 appears to be required for siRNA maturation.