Profiles analysis reveals circular RNAs involving zebrafish physiological development

• Published in: Journal of cellular physiology Vol. 234; no. 9; pp. 15922 - 15933
• Main Authors: Liu, Heng, Hu, Yin, Yin, Jing, Yan, Xiang‐Yun, Chen, Wen‐Juan, Jiang, Cheng‐Yao, Hu, Xiao‐Shan, Wang, Xing‐Yun, Zhu, Jin‐Gai, Yu, Zhang‐Bin, Han, Shu‐Ping
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 01.09.2019
• Subjects: Algorithms; Axon guidance; Axonogenesis; Bioinformatics; Blastula; Cardiovascular system; circular RNA; Danio rerio; Embryogenesis; embryonic development; Embryonic growth stage; Embryos; Genes; miRNA; miRNA sponges; Polypeptides; Retina; RNA polymerase II; Segmentation; Splicing; Transcription; Zebrafish; miRNA sponges; danio rerio; circular RNA; embryonic development; RNA polymerase II
• ISSN: 0021-9541; 1097-4652
• DOI: 10.1002/jcp.28250

Recent studies have found that known functions of circular RNAs (circRNAs) include sequestration of microRNAs (miRNAs) or proteins, modulation of transcription and interference with splicing, and even translation to produce polypeptides. The zebrafish model is also demonstrably similar to humans in many studies. To explore the changes in circRNAs during embryonic development and to further research the mechanism of action of circRNAs in development‐related diseases, Zebrafish embryos at the blastula period, gastrula period, segmentation period, throat stage, and incubation period were collected. Illumina deep‐sequencing technology and CircRNA Identifier (CIRI) algorithm were used to detect circRNAs. In total, we identified 1,028 circRNAs (junction reads ≥5 and p < 0.05). Considering that the function of circRNAs is related to host genes, a bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways, cardiovascular system development, retinal ganglion cell axon guidance, and so on. Moreover, circRNAs can participate in biological regulation through the function of miRNA sponges. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR‐19b, miR‐124, and so on. Some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points, suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in a zebrafish model. Recent studies have found that known functions of circRNAs include sequestration of miRNAs or proteins, modulation of transcription and interference with splicing, and even translation to produce polypeptides. The zebrafish model is also demonstrably similar to humans in many studies. To explore the changes in circRNAs during embryonic development, further to research the mechanism of action of circRNAs in development‐related diseases, Zebrafish embryos at the blastula period, gastrula period, segmentation period, throat stage, and incubation period were collected. Illumina deep‐sequencing technology and CIRI algorithm were used to detect circRNAs. In total, we identified 1,028 RNAs (junction reads ≥ 5 and p < 0.05). Considering that the function of circRNA is related to host genes, bioinformatics analysis revealed thaht these differentially expressed host genes are involved in NOTCH signaling pathways, cardiovascular system development, retinal ganglion cell axon guidance, and so on. Moreover, circRNAs can participate in biological regulation through miRNA sponge function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR‐19b, miR‐124, and so on. Some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points, suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in a zebrafish model.