Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China.
Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588.
Plant Cell. 2020 Aug;32(8):2457-2473. doi: 10.1105/tpc.19.00716. Epub 2020 May 29.
Deep sequencing of DNase-I treated chromatin (DNase-seq) can be used to identify DNase I-hypersensitive sites (DHSs) and facilitates genome-scale mining of de novo -regulatory DNA elements. Here, we adapted DNase-seq to generate genome-wide maps of DHSs using control and cold-treated leaf, stem, and root tissues of three widely studied grass species: , foxtail millet (), and sorghum (). Functional validation demonstrated that 12 of 15 DHSs drove reporter gene expression in transiently transgenic protoplasts. DHSs under both normal and cold treatment substantially differed among tissues and species. Intriguingly, the putative DHS-derived transcription factors (TFs) are largely colocated among tissues and species and include 17 ubiquitous motifs covering all grass taxa and all tissues examined in this study. This feature allowed us to reconstruct a regulatory network that responds to cold stress. Ethylene-responsive TFs SHINE3, ERF2, and ERF9 occurred frequently in cold feedback loops in the tissues examined, pointing to their possible roles in the regulatory network. Overall, we provide experimental annotation of 322,713 DHSs and 93 derived cold-response TF binding motifs in multiple grasses, which could serve as a valuable resource for elucidating the transcriptional networks that function in the cold-stress response and other physiological processes.
利用 DNA 酶 I 处理染色质的深度测序（DNase-seq）可用于鉴定 DNA 酶 I 超敏位点（DHSs），并促进新的调控 DNA 元件的全基因组挖掘。在这里，我们采用 DNase-seq 技术，利用三种广泛研究的禾本科植物（、黍（）和高粱（））的对照和冷处理叶片、茎和根组织，生成 DHSs 的全基因组图谱。功能验证表明，在瞬时转化的原生质体中，15 个 DHSs 中有 12 个驱动报告基因表达。正常和冷处理条件下的 DHSs 在组织和物种之间存在显著差异。有趣的是，假定的 DHS 衍生转录因子（TFs）在组织和物种之间基本一致，包括 17 个普遍存在的基序，涵盖了所有的禾本科植物类群和本研究中检查的所有组织。这一特征使我们能够重建一个响应冷胁迫的调控网络。在研究的组织中，乙烯响应 TF SHINE3、ERF2 和 ERF9 经常出现在冷反馈环中，这表明它们在调控网络中可能发挥作用。总体而言，我们在多种禾本科植物中提供了 322,713 个 DHSs 和 93 个衍生的冷响应 TF 结合基序的实验注释，这可能成为阐明在冷应激反应和其他生理过程中发挥作用的转录网络的有价值资源。
