Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
Nucleic Acids Res. 2020 Nov 18;48(20):11347-11369. doi: 10.1093/nar/gkaa927.
While transcription factors (TFs) are known to regulate the expression of their target genes (TGs), only a weak correlation of expression between TFs and their TGs has generally been observed. As lack of correlation could be caused by additional layers of regulation, the overall correlation distribution may hide the presence of a subset of regulatory TF-TG pairs with tight expression coupling. Using reported regulatory pairs in the plant Arabidopsis thaliana along with comprehensive gene expression information and testing a wide array of molecular features, we aimed to discern the molecular determinants of high expression correlation of TFs and their TGs. TF-family assignment, stress-response process involvement, short genomic distances of the TF-binding sites to the transcription start site of their TGs, few required protein-protein-interaction connections to establish physical interactions between the TF and polymerase-II, unambiguous TF-binding motifs, increased numbers of miRNA target-sites in TF-mRNAs, and a young evolutionary age of TGs were found particularly indicative of high TF-TG correlation. The modulating roles of post-transcriptional, post-translational processes, and epigenetic factors have been characterized as well. Our study reveals that regulatory pairs with high expression coupling are associated with specific molecular determinants.
虽然转录因子 (TFs) 被认为可以调节其靶基因 (TGs) 的表达，但通常观察到 TFs 和 TGs 之间的表达相关性较弱。由于缺乏相关性可能是由于额外的调控层造成的，因此整体相关性分布可能隐藏了具有紧密表达偶联的一组调节 TF-TG 对的存在。使用在植物拟南芥中报告的调节对，以及全面的基因表达信息，并测试了广泛的分子特征，我们旨在识别 TF 和其 TGs 的高表达相关性的分子决定因素。TF 家族分配、应激反应过程参与、TF 结合位点到其 TGs 的转录起始位点的短基因组距离、建立 TF 和聚合酶-II 之间物理相互作用所需的少数蛋白-蛋白相互作用连接、明确的 TF 结合基序、TF-mRNAs 中增加的 miRNA 靶位点数量，以及 TGs 的年轻进化年龄，都被发现特别表明 TF-TG 相关性高。还描述了转录后、翻译后过程和表观遗传因素的调节作用。我们的研究表明，具有高表达偶联的调节对与特定的分子决定因素相关。
