Department of Biology, William Paterson University, Wayne, New Jersey, USA.
Department of Chemistry, William Paterson University, Wayne, New Jersey, USA.
mSphere. 2018 Jun 13;3(3). doi: 10.1128/mSphere.00220-18. Print 2018 Jun 27.
It is essential that cells orchestrate gene expression for the specific niche that they occupy, and this often requires coordination of the expression of large sets of genes. There are multiple regulatory systems that exist for modulation of gene expression, including the adjacent-gene coregulation of the rRNA and ribosome biogenesis and ribosomal protein families. Both gene families exhibit a nonrandom genomic distribution, often clustered directly adjacent to another member of the same family, which results in a tighter transcriptional coordination among adjacent paired genes than that of the unpaired genes within each regulon and can result in a shared promoter that coordinates expression of the pairs. This nonrandom genomic distribution has been seen in a few functionally related gene families, and many of these functional pairings are conserved across divergent fungal lineages. To date, the significance of these observations has not been extended in a systematic way to characterize how prevalent the role of adjacent-gene coregulation is in transcriptional regulation. In the present study, we systematically analyzed the transcriptional coherence of the functional pairs compared to the singletons within all gene families defined by the Gene Ontology Slim designation, using as a model system, finding that clusters exhibit a tighter transcriptional correlation under specific contexts. We found that the longer a functional pairing is conserved the tighter its response to broad stress and nutritional responses, that roughly 25% of gene families exhibit a nonrandom genomic distribution, and that many of these clusters are conserved. This suggests that adjacent-gene coregulation is a widespread, yet underappreciated, transcriptional mechanism. The spatial positioning of genes throughout the genome arrangement can alter their expression in many eukaryotic organisms. Often this results in a genomic context-specific effect on transcription. One example of this is through the clustering of functionally related genes, which results in adjacent-gene coregulation in the budding yeast In the present study, we set out to systematically characterize the prevalence of this phenomenon, finding the genomic organization of functionally related genes into clusters is a characteristic of myriad gene families. These arrangements are found in many evolutionarily divergent fungi and thus represent a widespread, yet underappreciated, layer of transcriptional regulation.
细胞对于它们所占据的特定生态位进行基因表达的协调是至关重要的，这通常需要协调大量基因的表达。存在多种调节系统来调节基因表达，包括 rRNA 和核糖体生物发生以及核糖体蛋白家族的相邻基因共调节。这两个基因家族都表现出非随机的基因组分布，通常直接与同一家族的另一个成员簇集在一起，这导致相邻配对基因之间的转录协调比每个调控子内未配对基因之间的协调更紧密，并且可以导致共享启动子，从而协调对基因对的表达。这种非随机的基因组分布在少数几个功能相关的基因家族中已经看到，并且这些功能配对中的许多在不同的真菌谱系中是保守的。迄今为止，这些观察结果的意义尚未以系统的方式扩展，以描述相邻基因共调节在转录调节中的作用是多么普遍。在本研究中，我们使用酿酒酵母作为模型系统，系统地分析了功能对与基因本体论简化指定定义的所有基因家族中单基因相比的转录一致性，发现在特定情况下，簇表现出更紧密的转录相关性。我们发现，功能配对的保守性越强，对广泛的应激和营养反应的响应就越紧密，大约 25%的基因家族表现出非随机的基因组分布，并且其中许多簇是保守的。这表明相邻基因共调节是一种广泛存在但尚未被充分认识的转录机制。基因在整个基因组排列中的空间定位可以改变许多真核生物中它们的表达。通常，这会导致转录的基因组上下文特定效应。这种情况的一个例子是通过功能相关基因的聚类，这导致在酿酒酵母中相邻基因的共调节。在本研究中，我们着手系统地描述这种现象的普遍性，发现功能相关基因的基因组组织成簇是众多基因家族的特征。这些排列存在于许多进化上不同的真菌中，因此代表了一种广泛存在但尚未被充分认识的转录调控层。
