Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress.
Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress.
复制标题
对影响水稻镉胁迫早期根部发育的长非编码 RNA 进行全基因组分析
DOI：
10.1186/s12864-018-4807-6
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发表时间：
2018-06-15
期刊：
影响因子：
4.4
通讯作者：
Bian J
中科院分区：
文献类型：
--
作者：
Chen L;Shi S;Jiang N;Khanzada H;Wassan GM;Zhu C;Peng X;Xu J;Chen Y;Yu Q;He X;Fu J;Chen X;Hu L;Ouyang L;Sun X;He H;Bian J
研究背景长链非编码RNA（lncRNA）在植物逆境应答的多种生物学过程中的基因调控网络中起着重要作用。然而，对水稻镉（Cd）胁迫下表达的lncRNA的系统分析却很少研究。因此，我们提出的表征和表达的lncRNA在水稻根发育的早期阶段，在响应镉stress.ResultsThe lncRNA深度测序显示差异表达的lncRNA镉胁迫和正常条件。镉应激组中，69个lncRNA上调，75个lncRNA下调。此外，在120个差异表达的lncRNA和362个顺式差异表达基因中检测到386个匹配的lncRNA-mRNA对，并且靶基因相关通路分析显示半胱氨酸和甲硫氨酸代谢通路相关基因的显著变化。对于反式基因，总共检测到144个lncRNA和差异表达蛋白编码基因的28，276个相互作用关系。途径分析发现，次生代谢产物，如苯丙烷类和苯丙氨酸，光合作用途径相关基因的镉胁迫显着改变。这些结果表明，lncRNA可能通过顺式调控富含半胱氨酸的多肽代谢基因，反式调控次生代谢和光合作用基因，从而激活水稻对镉胁迫的各种生理生化反应。它还扩展了我们对lncRNA生物学功能的认识，并有助于水稻基因组的注释。
BackgroundLong non-coding RNAs (lncRNAs) have been found to play a vital role in several gene regulatory networks involved in the various biological processes in plants related to stress response. However, systematic analyses of lncRNAs expressed in rice Cadmium (Cd) stress are seldom studied. Thus, we presented the characterization and expression of lncRNAs in rice root development at an early stage in response to Cd stress.ResultsThe lncRNA deep sequencing revealed differentially expressed lncRNAs among Cd stress and normal condition. In the Cd stress group, 69 lncRNAs were up-regulated and 75 lncRNAs were down-regulated. Furthermore, 386 matched lncRNA-mRNA pairs were detected for 120 differentially expressed lncRNAs and 362 differentially expressed genes in cis, and target gene-related pathway analyses exhibited significant variations in cysteine and methionine metabolism pathway-related genes. For the genes in trans, overall, 28,276 interaction relationships for 144 lncRNAs and differentially expressed protein-coding genes were detected. The pathway analyses found that secondary metabolites, such as phenylpropanoids and phenylalanine, and photosynthesis pathway-related genes were significantly altered by Cd stress. All of these results indicate that lncRNAs may regulate genes of cysteine-rich peptide metabolism in cis, as well as secondary metabolites and photosynthesis in trans, to activate various physiological and biochemical reactions to respond to excessive Cd.ConclusionThe present study could provide a valuable resource for lncRNA studies in response to Cd treatment in rice. It also expands our knowledge about lncRNA biological function and contributes to the annotation of the rice genome.
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影响因子：
12.3
作者：
Li L;Eichten SR;Shimizu R;Petsch K;Yeh CT;Wu W;Chettoor AM;Givan SA;Cole RA;Fowler JE;Evans MM;Scanlon MJ;Yu J;Schnable PS;Timmermans MC;Springer NM;Muehlbauer GJ
通讯作者：
Muehlbauer GJ
影响因子：
4.3
作者：
Bhatia G;Goyal N;Sharma S;Upadhyay SK;Singh K
通讯作者：
Singh K
DOI：
10.1016/j.gpb.2015.02.003
发表时间：
2015-06
期刊：
Genomics, proteomics & bioinformatics
影响因子：
--
作者：
Liu X;Hao L;Li D;Zhu L;Hu S
通讯作者：
Hu S
影响因子：
10.5
作者：
Cabili, Moran N.;Trapnell, Cole;Rinn, John L.
通讯作者：
Rinn, John L.
影响因子：
7
作者：
Ben Amor, Besma;Wirth, Sonia;Crespi, Martin
通讯作者：
Crespi, Martin