title: RNA-sequencing analysis of Trichophyton rubrum transcriptome in response to sublethal doses of acriflavine.
abstract: BACKGROUND
  The dermatophyte Trichophyton rubrum is an anthropophilic filamentous fungus that infects keratinized tissues and is the most common etiologic agent isolated in human dermatophytoses. The clinical treatment of these infections is challenging because only few antifungal drugs are commercially available. To understand the mode of action of cytotoxic drugs against fungi, we evaluated the time-dependent effects of acriflavine on T. rubrum transcriptome using high-throughput RNA-sequencing (RNA-seq) technology.
  
  
  RESULTS
  RNA-seq analysis generated approximately 200 million short reads that were mapped to the Broad Institute's Dermatophyte Comparative Database before differential gene expression analysis was performed. By employing a stringent cut-off threshold of -1.5 and 1.5 log₂-fold changes in gene expression, a subset of 490 unique genes were found to be modulated in T. rubrum in response to acriflavine exposure. Among the selected genes, 69 genes were modulated at all exposure time points. Functional categorization indicated the putative involvement of these genes in various cellular processes such as oxidation-reduction reaction, transmembrane transport, and metal ion binding. Interestingly, genes putatively involved in the pathogenicity of dermatophytoses were down-regulated suggesting that this drug interferes with the virulence of T. rubrum. Moreover, we identified 159 novel putative transcripts in intergenic regions and two transcripts in intron regions of T. rubrum genome.
  
  
  CONCLUSIONS
  The results provide insights into the molecular events underlying the stress responses of T. rubrum to acriflavine, revealing that this drug interfered with important molecular events involved in the establishment and maintenance of fungal infection in the host. In addition, the identification of novel transcripts will further enable the improvement of gene annotation and open reading frame prediction of T. rubrum and other dermatophyte genomes.
authors.forename: Gabriela Felix
authors.initials: GF
authors.lastname: Persinoti
authors.forename: Nalu Teixeira
authors.initials: NT
authors.lastname: de Aguiar Peres
authors.forename: Tiago Rinaldi
authors.initials: TR
authors.lastname: Jacob
authors.forename: Antonio
authors.initials: A
authors.lastname: Rossi
authors.forename: Ricardo Zorzetto
authors.initials: RZ
authors.lastname: Vêncio
authors.forename: Nilce Maria
authors.initials: NM
authors.lastname: Martinez-Rossi
mesh_terms: D000167:Acriflavine / Q000494:pharmacology*; D000935:Antifungal Agents / Q000494:pharmacology*; D015966:Gene Expression Regulation, Fungal / Q000187:drug effects*; D012331:RNA, Fungal / Q000187:drug effects; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000187:drug effects*; D014249:Trichophyton / Q000187:drug effects* / Q000235:genetics* / Q000472:pathogenicity
chemical_list: D000935:Antifungal Agents; D012331:RNA, Fungal; D000167:Acriflavine