Dynamic changes in the transcriptome landscape of Arabidopsis thaliana in response to cold stress.
Dynamic changes in the transcriptome landscape of Arabidopsis thaliana in response to cold stress.
复制标题
拟南芥转录组景观响应冷胁迫的动态变化
DOI：
10.3389/fpls.2022.983460
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发表时间：
2022
影响因子：
5.6
通讯作者：
中科院分区：
文献类型：
--
作者：
植物必须重新编程基因表达，以适应不断变化的环境温度。随着极端低温发生的增多，冷胁迫对植物的负面影响，尤其是对植物生长发育的负面影响越来越严重。本研究利用链特异RNA测序技术(ssRNA-seq)研究了低温(4℃)胁迫不同时间拟南芥转录组图谱的动态变化。总共有7623个差异表达基因(Deg)在低温处理过程中表现出动态的时间变化。基因本体论(GO)和京都基因和基因组百科全书(KEGG)途径富集化分析表明，这些基因富含冷反应、次生代谢过程、光合作用、硫代葡萄糖苷生物合成和植物激素信号转导途径。同时，对转录本组装后的长非编码RNA(LncRNAs)进行了鉴定，从中预测了247个差异表达的LncRNAs(DElncRNAs)及其潜在的靶基因。已鉴定出3,621个与RNA剪接和剪接体相关的差异选择性剪接(DAS)基因，表明寒冷中的选择性剪接(AS)增加了转录体的复杂性。此外，还鉴定了52个基因家族的739个冷调节转录因子。本研究分析了冷胁迫下转录组图谱的动态变化，揭示了短期和长期冷处理过程中更完整的转录模式，为植物如何受冷胁迫影响的功能研究提供了新的见解。
Plants must reprogram gene expression to adapt constantly changing environmental temperatures. With the increased occurrence of extremely low temperatures, the negative effects on plants, especially on growth and development, from cold stress are becoming more and more serious. In this research, strand-specific RNA sequencing (ssRNA-seq) was used to explore the dynamic changes in the transcriptome landscape of Arabidopsis thaliana exposed to cold temperatures (4°C) at different times. In total, 7,623 differentially expressed genes (DEGs) exhibited dynamic temporal changes during the cold treatments. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the DEGs were enriched in cold response, secondary metabolic processes, photosynthesis, glucosinolate biosynthesis, and plant hormone signal transduction pathways. Meanwhile, long non-coding RNAs (lncRNAs) were identified after the assembly of the transcripts, from which 247 differentially expressed lncRNAs (DElncRNAs) and their potential target genes were predicted. 3,621 differentially alternatively spliced (DAS) genes related to RNA splicing and spliceosome were identified, indicating enhanced transcriptome complexity due to the alternative splicing (AS) in the cold. In addition, 739 cold-regulated transcription factors (TFs) belonging to 52 gene families were identified as well. This research analyzed the dynamic changes of the transcriptome landscape in response to cold stress, which reveals more complete transcriptional patterns during short- and long-term cold treatment and provides new insights into functional studies of that how plants are affected by cold stress.
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影响因子：
5.6
作者：
Cao F;Cheng H;Cheng S;Li L;Xu F;Yu W;Yuan H
通讯作者：
Yuan H
影响因子：
5.3
作者：
Dong, Chun-Hai;Hu, Xiangyang;Zhu, Jian-Kang
通讯作者：
Zhu, Jian-Kang
影响因子：
7.4
作者：
Chen, Yang-Er;Yuan, Shu;Schrodera, Wolfgang P.
通讯作者：
Schrodera, Wolfgang P.
影响因子：
64.8
作者：
Engreitz JM;Haines JE;Perez EM;Munson G;Chen J;Kane M;McDonel PE;Guttman M;Lander ES
通讯作者：
Lander ES
影响因子：
7
作者：
Filichkin, Sergei A.;Priest, Henry D.;Mockler, Todd C.
通讯作者：
Mockler, Todd C.