Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage.
Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage.
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被子植物长链非编码RNA的比较分析及大白菜热应激响应的长链非编码RNA的表征
DOI：
10.1038/s41438-021-00484-4
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发表时间：
2021-03-01
影响因子：
8.7
通讯作者：
Li N
中科院分区：
文献类型：
--
作者：
Song X;Hu J;Wu T;Yang Q;Feng X;Lin H;Feng S;Cui C;Yu Y;Zhou R;Gong K;Yu T;Pei Q;Li N
Long noncoding RNAs (lncRNAs) are widely present in different species and play critical roles in response to abiotic stresses. However, the functions of lncRNAs in Chinese cabbage under heat stress remain unknown. Here, we first conducted a global comparative analysis of 247,242 lncRNAs among 37 species. The results indicated that lncRNAs were poorly conserved among different species, and only 960 lncRNAs were homologous to 524 miRNA precursors. We then carried out lncRNA sequencing for a genome-wide analysis of lncRNAs and their target genes in Chinese cabbage at different stages of heat treatment. In total, 18,253 lncRNAs were identified, of which 1229 differentially expressed (DE) lncRNAs were characterized as being heat-responsive. The ceRNA network revealed that 38 lncRNAs, 16 miRNAs, and 167 mRNAs were involved in the heat response in Chinese cabbage. Combined analysis of the cis-and trans-regulated genes indicated that the targets of DE lncRNAs were significantly enriched in the “protein processing in endoplasmic reticulum” and “plant hormone signal transduction” pathways. Furthermore, the majority of HSP and PYL genes involved in these two pathways exhibited similar expression patterns and responded to heat stress rapidly. Based on the networks of DE lncRNA-mRNAs, 29 and 22 lncRNAs were found to interact with HSP and PYL genes, respectively. Finally, the expression of several critical lncRNAs and their targets was verified by qRT-PCR. Overall, we conducted a comparative analysis of lncRNAs among 37 species and performed a comprehensive analysis of lncRNAs in Chinese cabbage. Our findings expand the knowledge of lncRNAs involved in the heat stress response in Chinese cabbage, and the identified lncRNAs provide an abundance of resources for future comparative and functional studies.
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影响因子：
9.8
作者：
Cobb M
通讯作者：
Cobb M
影响因子：
14.9
作者：
Federhen S
通讯作者：
Federhen S
芜菁花粉发育和受精过程中长非编码RNA的系统鉴定
影响因子：
7.2
作者：
Huang, Li;Dong, Heng;Cao, Jiashu
通讯作者：
Cao, Jiashu
DOI：
10.1073/pnas.1419030111
发表时间：
2014-11-11
影响因子：
11.1
作者：
Csorba, Tibor;Questa, Julia I.;Dean, Caroline
通讯作者：
Dean, Caroline
影响因子：
4.6
作者：
Ahmed, Waqas;Xia, Yanshi;Guo, Peiguo
通讯作者：
Guo, Peiguo