Trichophyton Rubrum MiRNA And Its Regulation Of Gene Expression In Spores And Hyphae

microRNA(miRNA)is a small molecule RNA,usually 18-24 nucleotides(nt),that plays essential roles in most eukaryotes and regulates a series of biological processes.Trichophyton rubrum is one of the most common fungal pathogen in the world and is considered as a model organism for the study of dermatophyte.In this study,we present a transcriptome-wide investigation of both miRNA and mRNA expression profiles by deep sequencing to investigate the roles of miRNA in regulating the expression of target genes in T.rubrum.The miRNA along with other regulators involved in suvival and development of T.rubrum were also analysized between the conidial and mycelial stages.158 conserved miRNAs and 12 novel miRNAs were identified in our study,which were predicted to be related to 5470 target genes.These conserved miRNAs were distributed in 92 families and were highly conserved in different species.In our data,of the 5470 target genes,approximately half of them were predicted to be targeted by two or more miRNAs.In addition,33 miRNAs target to more than one hundred genes and 12 genes corresponded to 8 miRNAs.This phenomenon is in accordance with the reports that a single miRNA can regulate the expression of hundreds of target genes,and multiple miRNAs can target a single mRNA.The 170 miRNAs identified in this study were also detected in other six related dermatophytes.70 miRNAs were conserved in at least one of the six other closely related dermatophytes.In particular,10 miRNAs that are conserved in all seven dermatophytes were analyzed in our study.Furthermore,most target genes for each of the conserved miRNA were homologous with the seven related dermatophytes.These results implied that miRNAs and their targets are highly conserved,and they share similar patterns in gene expression regulation in dermatophytes.GO and KEGG enrichment analyses of the target genes demonstrated that they are involved in various biosynthesis and metabolic pathways,indicating potential roles of miRNAs in the survival and development of T.rubrum.Furthermore,49 genes encoding secreted proteases were targeted by 47 miRNA s in our data.Since secreted proteases are key virulence factors during host infection,these results suggested that miRNA may be also involved in pathogenicity and play roles during T.rubrum infection.Additionally,137 target genes corresponding to 21 miRNAs were all differentially expressed between the conidial and mycelial stages.The correlation analysis between miRNAs and the target genes showed that 22 down-regulated target genes corresponded to 7 up-regulated miRNAs,while 42 up-regulated target genes corresponded to 12 down-regulated miRNAs;these potential miRNA/mRNA pairs were negatively correlated based on their expression levels.Functional analysis showed that most of the 137 differentially expressed genes were involved in the regulation of transcription,RNA processing,ribosome assembly and translation.These results indicated that,in addition to directly binding to complementary sequences of target mRNAs,miRNA also extensively affect gene expression,along with other regulators in T.rubrum.In general,this study provides the first integrated analysis of miRNA and mRNA expression profiles in T.rubrum as well as dermatophytes.Our study deepens the understanding of T.rubrum and other dermatophytes and will serve as a foundation for subsequent investigations to combat these fungi.