Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
VIB Center for Plant Systems Biology, Ghent, Belgium.
BMC Genomics. 2022 Jan 4;23(1):18. doi: 10.1186/s12864-021-08215-8.
Transposable elements (TE) make up a large portion of many plant genomes and are playing innovative roles in genome evolution. Several TEs can contribute to gene regulation by influencing expression of nearby genes as stress-responsive regulatory motifs. To delineate TE-mediated plant stress regulatory networks, we took a 2-step computational approach consisting of identifying TEs in the proximity of stress-responsive genes, followed by searching for cis-regulatory motifs in these TE sequences and linking them to known regulatory factors. Through a systematic meta-analysis of RNA-seq expression profiles and genome annotations, we investigated the relation between the presence of TE superfamilies upstream, downstream or within introns of nearby genes and the differential expression of these genes in various stress conditions in the TE-poor Arabidopsis thaliana and the TE-rich Solanum lycopersicum.
We found that stress conditions frequently expressed genes having members of various TE superfamilies in their genomic proximity, such as SINE upon proteotoxic stress and Copia and Gypsy upon heat stress in A. thaliana, and EPRV and hAT upon infection, and Harbinger, LINE and Retrotransposon upon light stress in S. lycopersicum. These stress-specific gene-proximal TEs were mostly located within introns and more detected near upregulated than downregulated genes. Similar stress conditions were often related to the same TE superfamily. Additionally, we detected both novel and known motifs in the sequences of those TEs pointing to regulatory cooption of these TEs upon stress. Next, we constructed the regulatory network of TFs that act through binding these TEs to their target genes upon stress and discovered TE-mediated regulons targeted by TFs such as BRB/BPC, HD, HSF, GATA, NAC, DREB/CBF and MYB factors in Arabidopsis and AP2/ERF/B3, NAC, NF-Y, MYB, CXC and HD factors in tomato.
Overall, we map TE-mediated plant stress regulatory networks using numerous stress expression profile studies for two contrasting plant species to study the regulatory role TEs play in the response to stress. As TE-mediated gene regulation allows plants to adapt more rapidly to new environmental conditions, this study contributes to the future development of climate-resilient plants.
转座元件（TE）构成了许多植物基因组的很大一部分，并在基因组进化中发挥着创新作用。一些 TE 可以通过作为应激反应调节基序影响附近基因的表达来参与基因调控。为了描绘 TE 介导的植物应激调节网络，我们采用了两步计算方法，包括识别应激反应基因附近的 TE，然后在这些 TE 序列中搜索顺式调节基序，并将其与已知的调节因子联系起来。通过对 RNA-seq 表达谱和基因组注释的系统荟萃分析，我们研究了 TE 贫乏的拟南芥和 TE 丰富的番茄中，附近基因上游、下游或内含子中 TE 超家族的存在与这些基因在各种应激条件下的差异表达之间的关系。
我们发现，应激条件下经常表达的基因在其基因组附近有各种 TE 超家族的成员，例如拟南芥中蛋白质毒性应激下的 SINE、热应激下的 Copia 和 Gypsy，以及感染时的 EPRV 和 hAT，以及光应激下的 Harbinger、LINE 和 Retrotransposon。这些应激特异性基因附近的 TE 大多位于内含子中，并且在上调基因附近比下调基因更易检测到。类似的应激条件通常与相同的 TE 超家族有关。此外，我们在这些 TE 的序列中检测到了新的和已知的基序，这些基序表明这些 TE 在应激时被调控。接下来，我们构建了在应激时通过结合这些 TE 到其靶基因来发挥作用的 TF 调节网络，并发现了 TE 介导的受 BRB/BPC、HD、HSF、GATA、NAC、DREB/CBF 和 MYB 因子等 TF 靶向的调节子在拟南芥和 AP2/ERF/B3、NAC、NF-Y、MYB、CXC 和 HD 因子等番茄中。
总体而言，我们使用两种对比鲜明的植物物种的大量应激表达谱研究来绘制 TE 介导的植物应激调节网络，以研究 TE 在应激反应中发挥的调节作用。由于 TE 介导的基因调控使植物能够更快地适应新的环境条件，因此这项研究有助于未来开发具有抗逆性的植物。
