Fungal gene expression levels do not display a common mode of distribution.
RNA-seq studies in metazoa have revealed a distinct, double-peaked (bimodal) distribution of gene expression independent of species and cell type. However, two studies in filamentous fungi yielded conflicting results, with a bimodal distribution in Pyronema confluens and varying distributions in Sordaria macrospora. To obtain a broader overview of global gene expression distributions in fungi, an additional 60 publicly available RNA-seq data sets from six ascomycetes and one basidiomycete were analyzed with respect to gene expression distributions.
Clustering of normalized, log2-transformed gene expression levels for each RNA-seq data set yielded distributions with one to five peaks. When only major peaks comprising at least 15% of all analyzed genes were considered, distributions ranged from one to three major peaks, suggesting that fungal gene expression is not generally bimodal. The number of peaks was not correlated with the phylogenetic position of a species; however, higher filamentous asco- and basidiomycetes showed up to three major peaks, whereas gene expression levels in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe had only one to two major peaks, with one predominant peak containing at least 70% of all expressed genes. In several species, the number of peaks varied even within a single species, e.g. depending on the growth conditions as evidenced in the one to three major peaks in different samples from Neurospora crassa. Earlier studies based on microarray and SAGE data revealed distributions of gene expression level that followed Zipf's law, i.e. log-transformed gene expression levels were inversely proportional to the log-transformed expression rank of a gene. However, analyses of the fungal RNA-seq data sets could not identify any that confirmed to Zipf's law.
Fungal gene expression patterns cannot generally be described by a single type of distribution (bimodal or Zipf's law). One hypothesis to explain this finding might be that gene expression in fungi is highly dynamic, and fine-tuned at the level of transcription not only for individual genes, but also at a global level.
Nowrousian M