{Reference Type}: Journal Article
{Title}: Effects of functional defects in the NMD pathway on rice phenotype and transcriptome.
{Author}: Wu YY;Zhou XY;Wu YF;Huang J;
{Journal}: Yi Chuan
{Volume}: 46
{Issue}: 7
{Year}: 2024 Jul
暂无{DOI}: 10.16288/j.yczz.24-063
{Abstract}: Nonsense-mediated mRNA decay (NMD) is an important RNA quality control pathway. It aids in degrading harmful erroneous mRNA, thereby preserving a stable and healthy internal environment. In this study, we employed CRISPR/Cas9 and amiRNA technology to generate knock out or knock down mutants of realted genes in the rice NMD pathway. Through transcriptome sequencing and observing phenotype changes, the study explored the impact of NMD pathway defects on rice gene expression and alternative splicing. The results suggest that even partial defects will induce phenotypic changes such as plant height and pollen vitality to different degrees, showing necessity of NMD factors. Gene expression analysis reveals that most differentially expressed genes are upregulated in the mutants, with ko-upf1-like and kd-upf1 defects having a more significant impact than kd-upf2 and kd-upf3. Specifically, NMD pathway defects result in increased expression levels of rice defense response-related genes and decreased expression levels of secondary metabolism-related genes, with a wider range of affected genes observed in 60-day-old senescence mutants. Transcript analysis indicates that different NMD related genes defects alter hundreds of alternative splicing events, mostly enriched in genes involving alternative splicing regulatory pathways. Approximately half of these events are shared among different mutants, and a substantial number of affected transcripts show NMD target features. NMD could affect both the transcript abundance and their splicing subtypes to regulate the defense response and early-senescence associated pathways, which plays a vital role in rice growth and reproduction.<BR>无义介导的mRNA降解途径(nonsense-mediated mRNA decay，NMD)是细胞内一种关键的RNA质量控制途径，能够有效的降解细胞内错误的mRNA，以保持细胞内部环境的稳定与健康。本研究通过CRISPR/Cas9及amiRNA技术获得水稻NMD途径相关基因UPF1、UPF1-like、UPF2、UPF3的敲除或敲低型突变体，结合转录组测序和表型观察，探究NMD途径缺陷对水稻基因表达及可变剪接(alternative splicing，AS)的影响。研究结果表明，NMD途径为水稻正常生长所必需，部分缺陷也会造成株高、花粉活力等表型不同程度的变化。对基因表达的分析显示，NMD途径缺陷影响的基因大多表达上调，且ko-upf1-like和kd-upf1对基因表达的影响大于kd-upf2和kd-upf3。具体而言，NMD途径缺陷在水稻中引发了防御反应相关基因表达量的上升及次生代谢相关基因表达量的下降，且在60天龄早衰突变体中影响的基因更为广泛。转录组分析显示，不同的NMD途径相关基因缺陷均改变了数百个可变剪接，这些存在差异可变剪接的基因多与可变剪接调控通路相关，约有一半在不同突变体中共享，且大量富集了NMD靶标的特征。NMD途径能够通过影响可变剪接形式，改变转录本丰度等多种形式，调控防御反应和衰老等通路基因的表达，在水稻维持正常生理功能的过程中有着重要作用。.