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

Expession data from L1-L2 stage nematodes (C. elegans), wild type and four mutants (alg-1, zfp-1, rde-4, lin-35). In C. 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 may contribute to regulation of many developmental and other signaling pathways in addition to silencing viruses and transposons. Based on this 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 previously in endogenous RNAi, regulate overlapping sets of genes. Notably, genes a) upregulated in the rde-4 and zfp-1 mutants and b) upregulated in the lin-35(Rb) mutant, but not the downregulated genes are highly represented in the set of genes with corresponding endogenous short interfering RNAs (endo-siRNAs). Keywords: wildtype-mutant comparison, RNAi, Rb, endo-siRNA Nematodes were synchronized at L1 stage for RNA preparations. All conditions (WT and 4 mutants) were profiled in triplicate. Replicates were biological replicates (separately grown worm populations), with two exceptions: due to shortage of biological material available for the lin-35(n745) unc-13(e1091) I and zfp-1(ok554) III strains, one of the two biological samples was hybridized twice in order to set up a consistent triplicate structure across the dataset.