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

本数据集为秀丽隐杆线虫（C. elegans）L1至L2期线虫的基因表达谱数据，涵盖野生型及四种突变体（alg-1、zfp-1、rde-4、lin-35）。
近期，科研人员在秀丽隐杆线虫中发现了对应数千个基因的大量内源短RNA。这一发现提示，这类小干扰RNA除可沉默病毒与转座子外，还可能参与调控众多发育及其他信号通路。本研究基于对RNA干扰（RNA interference, RNAi）相关突变体rde-4、zfp-1、alg-1以及视网膜母细胞瘤（Retinoblastoma, Rb）突变体lin-35的基因表达微阵列分析，发现Dicer复合物组分RDE-4与染色质相关锌指蛋白ZFP-1（此前未被证实参与内源RNAi过程）可调控存在重叠的基因集合。值得注意的是，在rde-4与zfp-1突变体中上调的基因，以及在lin-35(Rb)突变体中上调的基因（而非下调基因），在带有对应内源小干扰RNA（endo-siRNAs）的基因集合中占比极高。
关键词：野生型-突变体比较、RNAi、Rb、内源小干扰RNA
整体设计：线虫于L1期同步化以制备RNA样品。所有实验组（野生型与4种突变体）均设置三次生物学重复。重复样本均为生物学重复（即独立培养的线虫种群），仅存在两处例外：因lin-35(n745) unc-13(e1091) I与zfp-1(ok554) III品系的生物材料有限，我们将两份生物学样本中的一份进行了两次微阵列杂交，以确保整个数据集维持一致的三次重复结构。