Nowrousian Minou
Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, 44780 Bochum, Germany.
BMC Res Notes. 2013 Dec 28;6:559. doi: 10.1186/1756-0500-6-559.
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.
后生动物中的RNA测序研究揭示了一种独立于物种和细胞类型的独特双峰基因表达分布。然而，两项针对丝状真菌的研究得出了相互矛盾的结果，在融合盘菌中呈现双峰分布，而在大孢粪壳菌中则有不同的分布。为了更全面地了解真菌中全球基因表达分布情况，我们分析了另外60个来自6种子囊菌和1种担子菌的公开RNA测序数据集的基因表达分布。
对每个RNA测序数据集进行标准化、log2转换后的基因表达水平聚类，得到了具有1至5个峰的分布。当仅考虑包含至少15%所有分析基因的主要峰时，分布范围为1至3个主要峰，这表明真菌基因表达通常不是双峰的。峰的数量与物种的系统发育位置无关；然而，高等丝状子囊菌和担子菌显示出多达3个主要峰，而酿酒酵母和粟酒裂殖酵母中的基因表达水平只有1至2个主要峰，其中一个主峰包含至少70%的所有表达基因。在几个物种中，即使在单个物种内峰的数量也会变化，例如，粗糙脉孢菌不同样本中1至3个主要峰的情况表明其取决于生长条件。早期基于微阵列和SAGE数据的研究揭示了遵循齐普夫定律的基因表达水平分布，即log转换后的基因表达水平与基因的log转换表达排名成反比。然而，对真菌RNA测序数据集的分析未能识别出任何符合齐普夫定律的数据集。
真菌基因表达模式通常不能用单一类型的分布（双峰或齐普夫定律）来描述。解释这一发现的一个假设可能是，真菌中的基因表达高度动态，不仅在单个基因水平，而且在全局水平上在转录水平进行微调。
