Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China.
Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China; Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA.
Ecotoxicol Environ Saf. 2019 Nov 15;183:109485. doi: 10.1016/j.ecoenv.2019.109485. Epub 2019 Jul 31.
Alternative polyadenylation (APA) is an important way to regulate gene expression at the post-transcriptional level, and is extensively involved in plant stress responses. However, the systematic roles of APA regulation in response to abiotic and biotic stresses in rice at the genome scale remain unknown. To take advantage of available RNA-seq datasets, using a novel tool APAtrap, we identified thousands of genes with significantly differential usage of polyadenylation [poly(A)] sites in response to the abiotic stress (drought, heat shock, and cadmium) and biotic stress [bacterial blight (BB), rice blast, and rice stripe virus (RSV)]. Genes with stress-responsive APA dynamics commonly exhibited higher expression levels when their isoforms with short 3' untranslated region (3' UTR) were more abundant. The stress-responsive APA events were widely involved in crucial stress-responsive genes and pathways: e.g. APA acted as a negative regulator in heat stress tolerance; APA events were involved in DNA repair and cell wall formation under Cd stress; APA regulated chlorophyll metabolism, being associated with the pathogenesis of leaf diseases under RSV and BB challenges. Furthermore, APA events were found to be involved in glutathione metabolism and MAPK signaling pathways, mediating a crosstalk among the abiotic and biotic stress-responsive regulatory networks in rice. Analysis of large-scale datasets revealed that APA may regulate abiotic and biotic stress-responsive processes in rice. Such post-transcriptome diversities contribute to rice adaption to various environmental challenges. Our study would supply useful resource for further molecular assisted breeding of multiple stress-tolerant cultivars for rice.
可变多聚腺苷酸化 (APA) 是调控转录后基因表达的一种重要方式，广泛参与植物的应激反应。然而，在全基因组范围内，APA 调控在水稻应对非生物和生物胁迫中的系统作用仍不清楚。为了充分利用现有的 RNA-seq 数据集，我们使用一种新的工具 APAtrap，鉴定了数千个在应对非生物胁迫（干旱、热休克和镉）和生物胁迫（细菌性条斑病、稻瘟病和水稻条纹病毒）时，聚腺苷酸化 [poly(A)] 位点使用差异显著的基因。当具有较短 3' 非翻译区 (3'UTR) 的异构体丰度更高时，具有应激响应 APA 动态的基因通常表现出更高的表达水平。应激响应的 APA 事件广泛涉及关键的应激响应基因和途径：例如，APA 在耐热性中作为负调节剂发挥作用；在 Cd 胁迫下，APA 事件参与 DNA 修复和细胞壁形成；APA 调节叶绿素代谢，与 RSV 和 BB 挑战下叶病的发病机制相关。此外，发现 APA 事件参与谷胱甘肽代谢和 MAPK 信号通路，介导水稻中非生物和生物应激响应调控网络之间的串扰。对大规模数据集的分析表明，APA 可能调节水稻中对非生物和生物胁迫的响应过程。这种转录后组的多样性有助于水稻适应各种环境挑战。我们的研究将为水稻的多种抗逆性品种的分子辅助育种提供有用的资源。
