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Article

Identification of Rhythmically Expressed LncRNAs in the Zebrafish Pineal Gland and Testis

by 1,2, 1,2 and 1,2,*
1
Center for Circadian Clocks, Soochow University, Suzhou 215123, China
2
School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, China
*
Author to whom correspondence should be addressed.
Academic Editor: Michał Dąbrowski
Int. J. Mol. Sci. 2021, 22(15), 7810; https://doi.org/10.3390/ijms22157810
Received: 18 June 2021 / Revised: 19 July 2021 / Accepted: 20 July 2021 / Published: 22 July 2021
(This article belongs to the Special Issue Functions of Non-coding DNA Regions)
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. View Full-Text
Keywords: noncoding RNAs; lncRNAs; lncRNA-encoded peptides; circadian rhythmicity; zebrafish; bioinformatics noncoding RNAs; lncRNAs; lncRNA-encoded peptides; circadian rhythmicity; zebrafish; bioinformatics
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MDPI and ACS Style

Mishra, S.K.; Liu, T.; Wang, H. Identification of Rhythmically Expressed LncRNAs in the Zebrafish Pineal Gland and Testis. Int. J. Mol. Sci. 2021, 22, 7810. https://doi.org/10.3390/ijms22157810

AMA Style

Mishra SK, Liu T, Wang H. Identification of Rhythmically Expressed LncRNAs in the Zebrafish Pineal Gland and Testis. International Journal of Molecular Sciences. 2021; 22(15):7810. https://doi.org/10.3390/ijms22157810

Chicago/Turabian Style

Mishra, Shital K., Taole Liu, and Han Wang. 2021. "Identification of Rhythmically Expressed LncRNAs in the Zebrafish Pineal Gland and Testis" International Journal of Molecular Sciences 22, no. 15: 7810. https://doi.org/10.3390/ijms22157810

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