Hundreds of LncRNAs Display Circadian Rhythmicity in Zebrafish Larvae.
Hundreds of LncRNAs Display Circadian Rhythmicity in Zebrafish Larvae.
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斑马鱼幼虫中数百个 LncRNA 显示昼夜节律
作者：
Mishra SK;Zhong Z;Wang H
长非编码RNA(LncRNAs)在包括昼夜节律在内的各种生命过程中起着至关重要的作用。尽管下一代测序技术促进了对lncRNA的更快剖析，但由此产生的数据集需要复杂的计算分析。特别是，lncRNAs在生物钟中的调节作用还远未完全了解。在本研究中，我们对斑马鱼幼体在恒暗(DD)和恒光(LL)条件下的转录组进行了昼夜节律分析，利用最先进的计算方法从斑马鱼幼体中识别了大约3220个lncRNA，然后分别发现了269和309个在DD和LL条件下具有昼夜节律性的lncRNAs，其中30个在DD和LL条件下同时表达。随后，对所有这些循环表达的lncRNA进行了GO、COG和KEGG途径的富集化分析，表明它们可能参与了许多生物学过程。将这些循环表达的斑马鱼幼体lncRNAs与斑马鱼松果体和睾丸中节律性表达的lncRNAs进行比较，发现在斑马鱼松果体和睾丸中分别有9个(DD)和12个(LL)幼体共表达。有趣的是，在这些共表达的循环表达的lncRNAs编码的多肽中，三个多肽(DD)和一个多肽(LL)被发现具有蛋白质数据库中的已知结构域。此外，对这些循环表达的斑马鱼幼体与人和小鼠基因组的保守性分析发现，在DD和LL条件下，这三个物种分别分享了一个和四个LncRNA。我们还研究了保守的lncRNA编码的多肽，发现其中一个在DD条件下在这三个物种中保守，并对其三维结构和功能进行了计算预测。我们的研究表明，斑马鱼幼虫的数百个lncRNA具有昼夜节律性，应该有助于为进一步的功能研究奠定基础。
Long noncoding RNAs (lncRNAs) have been shown to play crucial roles in various life processes, including circadian rhythms. Although next generation sequencing technologies have facilitated faster profiling of lncRNAs, the resulting datasets require sophisticated computational analyses. In particular, the regulatory roles of lncRNAs in circadian clocks are far from being completely understood. In this study, we conducted RNA-seq-based transcriptome analysis of zebrafish larvae under both constant darkness (DD) and constant light (LL) conditions in a circadian manner, employing state-of-the-art computational approaches to identify approximately 3220 lncRNAs from zebrafish larvae, and then uncovered 269 and 309 lncRNAs displaying circadian rhythmicity under DD and LL conditions, respectively, with 30 of them are coexpressed under both DD and LL conditions. Subsequently, GO, COG, and KEGG pathway enrichment analyses of all these circadianly expressed lncRNAs suggested their potential involvement in numerous biological processes. Comparison of these circadianly expressed zebrafish larval lncRNAs, with rhythmically expressed lncRNAs in the zebrafish pineal gland and zebrafish testis, revealed that nine (DD) and twelve (LL) larval lncRNAs are coexpressed in the zebrafish pineal gland and testis, respectively. Intriguingly, among peptides encoded by these coexpressing circadianly expressed lncRNAs, three peptides (DD) and one peptide (LL) were found to have the known domains from the Protein Data Bank. Further, the conservation analysis of these circadianly expressed zebrafish larval lncRNAs with human and mouse genomes uncovered one lncRNA and four lncRNAs shared by all three species under DD and LL conditions, respectively. We also investigated the conserved lncRNA-encoded peptides and found one peptide under DD condition conserved in these three species and computationally predicted its 3D structure and functions. Our study reveals that hundreds of lncRNAs from zebrafish larvae exhibit circadian rhythmicity and should help set the stage for their further functional studies.
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DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
影响因子：
56.9
作者：
Carninci, P;Kasukawa, T;Hayashizaki, Y
通讯作者：
Hayashizaki, Y
影响因子：
3.3
作者：
Gonzalez-Barrios, Maria;Fierro-Gonzalez, Juan Carlos;Miranda-Vizuete, Antonio
通讯作者：
Miranda-Vizuete, Antonio
影响因子：
3
作者：
Beer K;Helfrich-Förster C
通讯作者：
Helfrich-Förster C
长非编码RNA扰乱肝癌细胞的昼夜节律，促进肝癌发生
影响因子：
4.8
作者：
Cui, Ming;Zheng, Minying;Sun, Baodi;Wang, Yue;Ye, Lihong;Zhang, Xiaodong
通讯作者：
Zhang, Xiaodong