Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice.
Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice.
复制标题
全基因组筛选和功能分析鉴定了大量参与水稻有性繁殖的长链非编码RNA。
DOI：
10.1186/s13059-014-0512-1
复制
发表时间：
2014-12-03
期刊：
影响因子：
12.3
通讯作者：
Chen YQ
中科院分区：
文献类型：
--
作者：
Zhang YC;Liao JY;Li ZY;Yu Y;Zhang JP;Li QF;Qu LH;Shu WS;Chen YQ
背景长非编码RNA(Long Non Coding RNAs，LncRNAs)在哺乳动物和植物的多种生物学过程中发挥着重要作用。然而，对植物中lncRNAs的系统研究落后于哺乳动物。最近，在拟南芥和小麦中已经发现了lncRNAs，但关于水稻基因组中潜在的lncRNAs的系统筛选还没有报道。结果在本研究中，我们对授粉后5天的水稻花药、雌蕊和种子以及发芽后14天的新梢样品进行了全转录体链特异RNA测序(ssRNA-seq)。利用这些数据，再加上40个可用的水稻RNA-seq数据集，我们系统地分析了水稻的lncRNAs，并最终确定了参与生殖过程的lncRNAs。结果表明，水稻LncRNAs与拟南芥和哺乳动物相比具有一些不同的特征，并且以高度组织特异性或阶段特异性的方式表达。我们进一步验证了一组在生殖阶段优先表达的lncRNAs的功能，并鉴定了几个lncRNAs为竞争内源RNAs(CeRNAs)，它们在一种靶标模仿中隔离miR160或miR164。更重要的是，发现了一个lncRNA，XLOC_057324，在穗发育和育性中起作用。结论通过全基因组筛选和功能分析，获得了一组与水稻有性繁殖相关的插入突变体。这些结果还提供了水稻中LncRNAs和相关插入突变体的来源。
BackgroundLong noncoding RNAs (lncRNAs) play important roles in a wide range of biological processes in mammals and plants. However, the systematic examination of lncRNAs in plants lags behind that in mammals. Recently, lncRNAs have been identified inArabidopsisand wheat; however, no systematic screening of potential lncRNAs has been reported for the rice genome.ResultsIn this study, we perform whole transcriptome strand-specific RNA sequencing (ssRNA-seq) of samples from rice anthers, pistils, and seeds 5 days after pollination and from shoots 14 days after germination. Using these data, together with 40 available rice RNA-seq datasets, we systematically analyze rice lncRNAs and definitively identify lncRNAs that are involved in the reproductive process. The results show that rice lncRNAs have some different characteristics compared to those ofArabidopsisand mammals and are expressed in a highly tissue-specific or stage-specific manner. We further verify the functions of a set of lncRNAs that are preferentially expressed in reproductive stages and identify several lncRNAs as competing endogenous RNAs (ceRNAs), which sequester miR160 or miR164 in a type of target mimicry. More importantly, one lncRNA, XLOC_057324, is demonstrated to play a role in panicle development and fertility. We also develop a source of rice lncRNA-associated insertional mutants.ConclusionsGenome-wide screening and functional analysis enabled the identification of a set of lncRNAs that are involved in the sexual reproduction of rice. The results also provide a source of lncRNAs and associated insertional mutants in rice.
登录
查看更多内容
在致癌 BRAF 诱导的黑色素瘤小鼠模型中体内鉴定肿瘤抑制性 PTEN ceRNA。
影响因子：
64.5
作者：
Karreth FA;Tay Y;Perna D;Ala U;Tan SM;Rust AG;DeNicola G;Webster KA;Weiss D;Perez-Mancera PA;Krauthammer M;Halaban R;Provero P;Adams DJ;Tuveson DA;Pandolfi PP
通讯作者：
Pandolfi PP
影响因子：
50.3
作者：
Hu X;Feng Y;Zhang D;Zhao SD;Hu Z;Greshock J;Zhang Y;Yang L;Zhong X;Wang LP;Jean S;Li C;Huang Q;Katsaros D;Montone KT;Tanyi JL;Lu Y;Boyd J;Nathanson KL;Li H;Mills GB;Zhang L
通讯作者：
Zhang L
影响因子：
4.9
作者：
Chen, Songbiao;Tao, Lizen;Wang, Guo-Liang
通讯作者：
Wang, Guo-Liang
影响因子：
1.9
作者：
Cho, JK;Koo, DH;Hur, Y
通讯作者：
Hur, Y
影响因子：
10.5
作者：
Cabili, Moran N.;Trapnell, Cole;Rinn, John L.
通讯作者：
Rinn, John L.