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Background  In metazoans, Piwi-related Argonaute proteins play important roles in maintaining germline integrity and fertility and have been linked to a class of germline-enriched small RNAs termed piRNAs.  Caenorhabditis elegans  encodes two Piwi family proteins called PRG-1 and PRG-2, and PRG-1 interacts with the  C. elegans  piRNAs (21U-RNAs). Previous studies found that mutation of  prg-1  causes a marked reduction in the expression of 21U-RNAs, temperature-sensitive defects in fertility and other phenotypic defects.    Results  In this study, we wanted to systematically demonstrate the function of PRG-1 in the regulation of small RNAs and their targets. By analyzing small RNAs and mRNAs with and without a mutation in  prg-1  during  C. elegans  development, we demonstrated that (1) mutation of  prg-1  leads to a decrease in the expression of 21U-RNAs, and causes 35 ~ 40% of miRNAs to be down-regulated; (2) in  C. elegans , approximately 3% (6% in L4) of protein-coding genes are differentially expressed after mutating  prg-1 , and 60 ~ 70% of these substantially altered protein-coding genes are up-regulated; (3) the target genes of the down-regulated miRNAs and the candidate target genes of the down-regulated 21U-RNAs are enriched in the up-regulated protein-coding genes; and (4) PRG-1 regulates protein-coding genes by down-regulating small RNAs (miRNAs and 21U-RNAs) that target genes that participate in the development of  C. elegans .    Conclusions  In  prg-1 -mutated  C. elegans , the expression of miRNAs and 21U-RNAs was reduced, and the protein-coding targets, which were associated with the development of  C. elegans , were up-regulated. This may be the mechanism underlying PRG-1 function.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-321) contains supplementary material, which is available to authorized users.

The influences of PRG-1 on the expression of small RNAs and mRNAs