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Background  RNA interference (RNAi) is a conserved mechanism of genome defence that can also have a role in the regulation of endogenous functions through endogenous small RNAs (esRNAs). In fungi, knowledge of the functions regulated by esRNAs has been hampered by lack of clear phenotypes in most mutants affected in the RNAi machinery. Mutants of  Mucor circinelloides  affected in RNAi genes show defects in physiological and developmental processes, thus making  Mucor  an outstanding fungal model for studying endogenous functions regulated by RNAi. Some classes of  Mucor  esRNAs map to exons (ex-siRNAs) and regulate expression of the genes from which they derive. To have a broad picture of genes regulated by the silencing machinery during vegetative growth, we have sequenced and compared the mRNA profiles of mutants in the main RNAi genes by using RNA-seq. In addition, we have achieved a more complete phenotypic characterization of silencing mutants.    Results  Deletion of any main RNAi gene provoked a deep impact in mRNA accumulation at exponential and stationary growth. Genes showing increased mRNA levels, as expected for direct ex-siRNAs targets, but also genes with decreased expression were detected, suggesting that, most probably, the initial ex-siRNA targets regulate the expression of other genes, which can be up- or down-regulated. Expression of 50% of the genes was dependent on more than one RNAi gene in agreement with the existence of several classes of ex-siRNAs produced by different combinations of RNAi proteins. These combinations of proteins have also been involved in the regulation of different cellular processes. Besides genes regulated by the canonical RNAi pathway, this analysis identified processes, such as growth at low pH and sexual interaction that are regulated by a  dicer -independent non-canonical RNAi pathway.    Conclusion  This work shows that the RNAi pathways play a relevant role in the regulation of a significant number of endogenous genes in  M. circinelloides  during exponential and stationary growth phases and opens up an important avenue for in-depth study of genes involved in the regulation of physiological and developmental processes in this fungal model.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1443-2) contains supplementary material, which is available to authorized users.

The RNAi machinery controls distinct responses to environmental signals in the basal fungus Mucor circinelloides