Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
J Mol Biol. 2015 Jan 30;427(2):521-36. doi: 10.1016/j.jmb.2014.11.008. Epub 2014 Nov 15.
Bidirectional promoters are widespread in insect genomes. By analyzing 23 insect genomes we show that the frequency of bidirectional gene pairs varies according to genome compactness and density of genes among the species. The density of bidirectional genes expected based on number of genes per megabase of genome explains the observed density suggesting that bidirectional pairing of genes may be due to random event. We identified specific transcription factor binding motifs that are enriched in bidirectional promoters across insect species. Furthermore, we observed that bidirectional promoters may act as transcriptional hotspots in insect genomes where protein coding genes tend to aggregate in significantly biased (p < 0.001) manner compared to unidirectional promoters. Natural selection seems to have an association with the extent of bidirectionality of genes among the species. The rate of non-synonymous-to-synonymous changes (dN/dS) shows a second-order polynomial distribution with bidirectionality between species indicating that bidirectionality is dependent upon evolutionary pressure acting on the genomes. Analysis of genome-wide microarray expression data of multiple insect species suggested that bidirectionality has a similar association with transcriptome variation across species. Furthermore, bidirectional promoters show significant association with correlated expression of the divergent gene pairs depending upon their motif composition. Analysis of gene ontology showed that bidirectional genes tend to have a common association with functions related to "binding" (including ion binding, nucleotide binding and protein binding) across genomes. Such functional constraint of bidirectional genes may explain their widespread persistence in genome of diverse insect species.
双向启动子在昆虫基因组中广泛存在。通过分析 23 种昆虫基因组，我们表明双向基因对的频率根据物种之间的基因组紧凑度和基因密度而变化。根据每个基因组百万碱基的基因数量预测的双向基因密度解释了观察到的密度，表明基因的双向配对可能是由于随机事件。我们鉴定了特定的转录因子结合基序，这些基序在昆虫物种中的双向启动子中富集。此外，我们观察到双向启动子可能在昆虫基因组中充当转录热点，与单向启动子相比，蛋白质编码基因倾向于以显著偏向（p < 0.001）的方式聚集。自然选择似乎与物种之间基因的双向性程度有关。非同义到同义变化的速率（dN/dS）与物种之间的双向性呈二阶多项式分布，表明双向性取决于作用于基因组的进化压力。对多个昆虫物种的全基因组微阵列表达数据的分析表明，双向性与物种之间的转录组变异具有相似的关联。此外，双向启动子与不同基因对的相关表达具有显著的关联，这取决于它们的基序组成。基因本体分析表明，双向基因往往与与“结合”（包括离子结合、核苷酸结合和蛋白质结合）相关的功能具有共同的关联。这种双向基因的功能约束可能解释了它们在不同昆虫物种基因组中的广泛存在。
