Widespread noncoding circular RNAs in plants
Widespread noncoding circular RNAs in plants
复制标题
植物中广泛存在的非编码环状RNA
DOI：
10.1111/nph.13585
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发表时间：
2015-10-01
期刊：
影响因子：
9.4
通讯作者：
Fan, Longjiang
中科院分区：
文献类型：
--
作者：
Ye, Chu-Yu;Chen, Li;Fan, Longjiang
在动物中已经发现了大量具有调控功能的非编码环状RNA，但对植物环状RNA的研究还很少。我们利用公开的RNA-Seq数据对水稻和拟南芥的CircRNAs进行了全基因组鉴定，分析和比较了植物和动物的CircRNAs的特征。在水稻和拟南芥中分别鉴定出12037个和6012个CircRNA，其中56%(10/18)的水稻外显子CircRNA得到了实验验证。超过700个外显子CircRNAs的亲本基因是水稻和拟南芥之间的同源基因，这表明CircRNAs在植物中是保守的。植物CircRNAs两侧的内含子比线性基因的内含子长得多，重复元件和反向互补序列也比动物CircRNAs两侧的内含子少。植物CircRNAs表现出不同的表达模式，27个水稻外显子CircRNAs在缺磷和缺磷条件下差异表达。一些CircRNAs及其亲本基因的表达谱呈显著正相关。我们的研究结果表明，CircRNAs在植物中广泛存在，揭示了植物和动物之间CircRNAs的共同和不同的特征，并提示CircRNAs可能是植物中一类关键的非编码调控因子。
A large number of noncoding circular RNAs (circRNAs) with regulatory potency have been identified in animals, but little attention has been given to plant circRNAs. We performed genome-wide identification of circRNAs in Oryza sativa and Arabidopsis thaliana using publically available RNA-Seq data, analyzed and compared features of plant and animal circRNAs. circRNAs (12037 and 6012) were identified in Oryzasativa and Arabidopsisthaliana, respectively, with 56% (10/18) of the sampled rice exonic circRNAs validated experimentally. Parent genes of over 700 exonic circRNAs were orthologues between rice and Arabidopsis, suggesting conservation of circRNAs in plants. The introns flanking plant circRNAs were much longer than introns from linear genes, and possessed less repetitive elements and reverse complementary sequences than the flanking introns of animal circRNAs. Plant circRNAs showed diverse expression patterns, and 27 rice exonic circRNAs were found to be differentially expressed under phosphate-sufficient and -starvation conditions. A significantly positive correlation was observed for the expression profiles of some circRNAs and their parent genes. Our results demonstrated that circRNAs are widespread in plants, revealed the common and distinct features of circRNAs between plants and animals, and suggested that circRNAs could be a critical class of noncoding regulators in plants.