Genome-wide discovery and phenotyping of non-coding transcripts in A. fumigatus reveals lncRNAs with a role in antifungal drug sensitivity

Recent data suggests one fungus, Aspergillus fumigatus, causes more deaths annually than HIV or malaria combined. Coupled with rapid emergence of antifungal drug resistance, the limited range of effective treatments, and mortality rates of >50%, aspergillosis represents a major challenge in infectious diseases. Recent studies have identified long-noncoding RNAs (lncRNAs) involved in drug resistance and virulence in pathogenic yeasts such as Candida spp. However, there is very limited knowledge of lncRNAs in human pathogenic moulds, including A. fumigatus. Here we exploit transcriptomics data of A. fumigatus exposed to different environments to annotate transcripts mapping to 2388 genomic loci. After manual curation we generate a database of over 1000 lncRNAs. We observe that the lncRNAs display orchestrated transcriptional profiles upon drug treatment and many are proximal to genes involved in azole sensitivity. We knock out a set of intergenic lncRNAs and perform a large-scale phenotypic analysis to identify 60 lncRNA mutants displaying condition-dependent fitness changes with 35 mutants exhibiting a positive growth phenotype under azole stress. Overall, this study generates and experimentally validates an important resource that will enable the wider research community to increase understanding of the functional importance of lncRNAs in A. fumigatus, including their involvement in drug sensitivity. Here, the authors present a bioinformatic pipeline to annotate lncRNA genes in Aspergillus fumigatus. The majority of these lncRNAs are only conserved at the species level, and their expression is highly responsive to antifungal exposure in Aspergillus fumigatus.