Ding Feng, Cui Peng, Wang Zhenyu, Zhang Shoudong, Ali Shahjahan, Xiong Liming
Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
BMC Genomics. 2014 Jun 4;15(1):431. doi: 10.1186/1471-2164-15-431.
Alternative splicing (AS) of precursor mRNA (pre-mRNA) is an important gene regulation process that potentially regulates many physiological processes in plants, including the response to abiotic stresses such as salt stress.
To analyze global changes in AS under salt stress, we obtained high-coverage (~200 times) RNA sequencing data from Arabidopsis thaliana seedlings that were treated with different concentrations of NaCl. We detected that ~49% of all intron-containing genes were alternatively spliced under salt stress, 10% of which experienced significant differential alternative splicing (DAS). Furthermore, AS increased significantly under salt stress compared with under unstressed conditions. We demonstrated that most DAS genes were not differentially regulated by salt stress, suggesting that AS may represent an independent layer of gene regulation in response to stress. Our analysis of functional categories suggested that DAS genes were associated with specific functional pathways, such as the pathways for the responses to stresses and RNA splicing. We revealed that serine/arginine-rich (SR) splicing factors were frequently and specifically regulated in AS under salt stresses, suggesting a complex loop in AS regulation for stress adaptation. We also showed that alternative splicing site selection (SS) occurred most frequently at 4 nucleotides upstream or downstream of the dominant sites and that exon skipping tended to link with alternative SS.
Our study provided a comprehensive view of AS under salt stress and revealed novel insights into the potential roles of AS in plant response to salt stress.
前体mRNA（pre-mRNA）的可变剪接（AS）是一种重要的基因调控过程，可能调控植物中的许多生理过程，包括对盐胁迫等非生物胁迫的响应。
为了分析盐胁迫下AS的全局变化，我们从用不同浓度NaCl处理的拟南芥幼苗中获得了高覆盖度（约200倍）的RNA测序数据。我们检测到，在盐胁迫下，所有含内含子的基因中约49%发生了可变剪接，其中10%经历了显著的差异可变剪接（DAS）。此外，与非胁迫条件相比，盐胁迫下AS显著增加。我们证明，大多数DAS基因不受盐胁迫的差异调控，这表明AS可能代表了响应胁迫的一个独立的基因调控层面。我们对功能类别的分析表明，DAS基因与特定的功能途径相关，如对胁迫和RNA剪接的响应途径。我们发现，富含丝氨酸/精氨酸（SR）的剪接因子在盐胁迫下的AS中频繁且特异性地受到调控，这表明在AS调控中存在一个复杂的循环以适应胁迫。我们还表明，可变剪接位点选择（SS）最常发生在主导位点上游或下游的4个核苷酸处，并且外显子跳跃倾向于与可变SS相关联。
我们的研究提供了盐胁迫下AS的全面视图，并揭示了AS在植物对盐胁迫响应中的潜在作用的新见解。
