RNA interference and retinoblastoma-related genes are required for repression of endogenous siRNA targets in Caenorhabditis elegans

Abstract

In Caenorhabditis elegans , a vast number of endogenous short RNAs corresponding to thousands of genes have been discovered recently. This finding suggests that these short interfering RNAs (siRNAs) may contribute to regulation of many developmental and other signaling pathways in addition to silencing viruses and transposons. Here, we present a microarray analysis of gene expression in RNA interference (RNAi)-related mutants rde-4 , zfp-1 , and alg-1 and the retinoblastoma (Rb) mutant lin-35 . We found that a component of Dicer complex RDE-4 and a chromatin-related zinc finger protein ZFP-1, not implicated in endogenous RNAi, regulate overlapping sets of genes. Notably, genes a) up-regulated in the rde-4 and zfp-1 mutants and b) up-regulated in the lin-35 (Rb) mutant, but not the down-regulated genes are highly represented in the set of genes with corresponding endogenous siRNAs (endo-siRNAs). Our study suggests that endogenous siRNAs cooperate with chromatin factors, either C. elegans ortholog of acute lymphoblastic leukemia-1 (ALL-1)-fused gene from chromosome 10 (AF10), ZFP-1, or tumor suppressor Rb, to regulate overlapping sets of genes and predicts a large role for RNAi-based chromatin silencing in control of gene expression in C. elegans .

synMuv B proteins antagonize germline fate in the intestine and ensure C. elegans survival

“…Many genes are misexpressed at low temperature in synMuv B mutants (Grishok et al, 2008;Kirienko and Fay, 2007). Our data show that elevated temperature enhances the misexpression of some of those genes.…”

“…The second largest category (27%) is genes expressed in the intestine. Genes with germline-and intestine-specific expression are highly represented in the list of genes that are misregulated in lin-35 mutants (Grishok et al, 2008;Kirienko and Fay, 2007). We found that these categories are even more highly represented in the HTA candidate set (see Fig.…”

Neuronal Migration Is Regulated by Endogenous RNAi and Chromatin-Binding Factor ZFP-1/AF10 in Caenorhabditis elegans

“…RNAi factors RDE-4, DRH-3, and CSR-1 regulate HSN migration A genome-wide expression study has revealed that ZFP-1 and RDE-4, a dsRNA-binding protein required for the initiation of exogenous RNAi (Parrish and Fire 2001;Tabara et al 2002), regulate close to 250 overlapping genes (Grishok et al 2008). Consistent with this finding, both RDE-4 and ZFP-1 have been shown to affect longevity and the stress response by negatively regulating the conserved IIS kinase pdk-1 (Mansisidor et al 2011).…”

miRNA, siRNA, piRNA and Argonautes: News in small matters

“…Thus, two major functions can be predicted for endogenous RNAi in C. elegans: regulation of stress response and longevity and repression of germ line fate in the soma in cooperation with LIN-35. 29 Enhanced RNAi 1 (ERI-1) and its homologues are 3'-5' exoribonucleases with conserved functions in RNA silencing regulation and ribosomal RNA (rRNA) processing. Jutta Helm from Kriton Kalantidis's group (IMBB, Heraklion, Greece) studied the involvement of the plant homologue of ERI-1, ERL1, in chloroplast rRNA biogenesis.…”