Identification of Rhythmically Expressed LncRNAs in the Zebrafish Pineal Gland and Testis.
Identification of Rhythmically Expressed LncRNAs in the Zebrafish Pineal Gland and Testis.
复制标题
斑马鱼松果体和睾丸中节律性表达的 LncRNA 的鉴定
DOI：
10.3390/ijms22157810
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发表时间：
2021-07-22
影响因子：
5.6
通讯作者：
Wang H
中科院分区：
文献类型：
--
作者：
Mishra SK;Liu T;Wang H
已知非编码RNA有助于各种基本生命过程，如发育、代谢和昼夜节律。然而，在庞大的非编码RNA数据集中，仍有许多未被揭示的信息，这需要进一步的生物信息学分析和实验研究，特别是lncRNA的编码潜力和lncRNA编码肽的功能尚未得到全面研究。通过将时间过程实验与最先进的计算技术相结合，我们从自己的实验和已发表的研究中研究了数万条斑马鱼lncRNA，包括睾丸和松果体的时间序列转录组分析。这些数据的节律性分析揭示了大约700种来自松果体和睾丸的节律性表达的lncRNA，并分析了它们的GO、COG和KEGG通路功能。比较和保守分析确定了14个松果体和睾丸之间共享的节律性表达的lncRNA，以及15个松果体lncRNA和3个睾丸lncRNA在斑马鱼，小鼠和人类之间保守。此外，我们计算分析了保守的lncRNA编码的肽，并揭示了三个松果体和睾丸lncRNA编码的肽保守的这三个物种，这是进一步研究其三维（3D）结构和潜在的功能。我们的计算结果提供了新的注释和调节机制的数百个有节奏地表达的松果体和睾丸lncRNA在斑马鱼，并设置了阶段，在不久的将来，他们的实验研究。
Noncoding RNAs have been known to contribute to a variety of fundamental life processes, such as development, metabolism, and circadian rhythms. However, much remains unrevealed in the huge noncoding RNA datasets, which require further bioinformatic analysis and experimental investigation—and in particular, the coding potential of lncRNAs and the functions of lncRNA-encoded peptides have not been comprehensively studied to date. Through integrating the time-course experimentation with state-of-the-art computational techniques, we studied tens of thousands of zebrafish lncRNAs from our own experiments and from a published study including time-series transcriptome analyses of the testis and the pineal gland. Rhythmicity analysis of these data revealed approximately 700 rhythmically expressed lncRNAs from the pineal gland and the testis, and their GO, COG, and KEGG pathway functions were analyzed. Comparative and conservative analyses determined 14 rhythmically expressed lncRNAs shared between both the pineal gland and the testis, and 15 pineal gland lncRNAs as well as 3 testis lncRNAs conserved among zebrafish, mice, and humans. Further, we computationally analyzed the conserved lncRNA-encoded peptides, and revealed three pineal gland and one testis lncRNA-encoded peptides conserved among these three species, which were further investigated for their three-dimensional (3D) structures and potential functions. Our computational findings provided novel annotations and regulatory mechanisms for hundreds of rhythmically expressed pineal gland and testis lncRNAs in zebrafish, and set the stage for their experimental studies in the near future.
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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：
10.5
作者：
Cabili, Moran N.;Trapnell, Cole;Rinn, John L.
通讯作者：
Rinn, John L.
影响因子：
9.5
作者：
Galperin, Michael Y.;Kristensen, David M.;Koonin, Eugene V.
通讯作者：
Koonin, Eugene V.
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