Identification and characterization of ncRNA-associated ceRNA networks in Arabidopsis leaf development.
Identification and characterization of ncRNA-associated ceRNA networks in Arabidopsis leaf development.
复制标题
拟南芥叶片发育中 ncRNA 相关 ceRNA 网络的鉴定和表征
DOI：
10.1186/s12864-018-4993-2
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发表时间：
2018-08-13
期刊：
影响因子：
4.4
通讯作者：
Chen M
中科院分区：
文献类型：
--
作者：
Meng X;Zhang P;Chen Q;Wang J;Chen M
叶片发育是一个复杂的生物学过程，伴随着广泛的转录变化。许多蛋白质编码基因在植物叶中都被表征了，但是对非编码RNA（NCRNA）的关注很少。此外，越来越多的证据表明，在真核转录组中存在RNA物种之间的复杂相互作用，包括蛋白质编码的RNA和NCRNA，但是在植物叶中仍然难以捉摸。
我们检测到了新的NCRNA，例如圆形RNA（CIRCRNA）和长的非编码RNA（LNCRNA），并进一步构建并分析了拟南芥叶片中其相关的竞争性内源性RNA（CERNA）网络。转录组分析在叶片发育过程中显示出广泛的变化。此外，对其他植物叶片中circrnas的全面检测表明，circrnas在植物叶中广泛存在。为了研究拟南芥叶片中复杂的转录后相互作用，我们构建了一个全球circrna/lncRNA相关的Cerna网络。功能分析表明，CERNA与叶片发育高度相关。这些CERNA可以分为六个簇，这些簇富含不同的功能类别。进一步构建了阶段特异性的CERNA网络，比较分析揭示了阶段常见和特定集线器CERNA的不同作用。
我们的结果表明，了解CERNA相互作用将导致对叶片发育涉及的基因法规的见解。
本文的在线版本（10.1186/S12864-018-4993-2）包含补充材料，可供授权用户使用。
BackgroundLeaf development is a complex biological process that is accompanied by wide transcriptional changes. Many protein-coding genes have been characterized in plant leaves, but little attention has been given to noncoding RNAs (ncRNAs). Moreover, increasing evidence indicates that an intricate interplay among RNA species, including protein-coding RNAs and ncRNAs, exists in eukaryotic transcriptomes, however, it remains elusive in plant leaves.ResultsWe detected novel ncRNAs, such as circular RNAs (circRNAs) and long noncoding RNAs (lncRNAs), and further constructed and analyzed their associated competitive endogenous RNA (ceRNA) networks in Arabidopsis leaves. Transcriptome profiling showed extensive changes during leaf development. In addition, comprehensive detection of circRNAs in other plant leaves suggested that circRNAs are widespread in plant leaves. To investigate the complex post-transcriptional interactions in Arabidopsis leaves, we constructed a global circRNA/lncRNA-associated ceRNA network. Functional analysis revealed that ceRNAs were highly correlated with leaf development. These ceRNAs could be divided into six clusters, which were enriched for different functional classes. Stage-specific ceRNA networks were further constructed and comparative analysis revealed different roles of stage common and specific hub ceRNAs.ConclusionsOur results demonstrate that understanding the ceRNA interactions will lead insights into gene regulations implicated in leaf development.
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