Emerging roles of circRNAs in regulating thermal and hypoxic stresses in Apostichopus japonicus (Echinodermata: Holothuroidea)

Some sea cucumbers are economically and ecologically important, but they are threatened by thermal and hypoxic stress in changing oceanographic conditions. We construct circRNAs profiles, reveal circRNAs characters, and illustrate the potential regulatory roles of circRNAs in one commercially import...

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Autores principales:	Da Huo, Lina Sun, Jingchun Sun, Chenggang Lin, Shilin Liu, Libin Zhang, Hongsheng Yang
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Circular RNA Echinoderm Heat Anoxia Environmental stress Environmental pollution TD172-193.5 Environmental sciences GE1-350
Acceso en línea:	https://doaj.org/article/3186266c748a418388a53dfb6e588df5
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spelling	oai:doaj.org-article:3186266c748a418388a53dfb6e588df52021-11-26T04:23:11ZEmerging roles of circRNAs in regulating thermal and hypoxic stresses in Apostichopus japonicus (Echinodermata: Holothuroidea)0147-651310.1016/j.ecoenv.2021.112994https://doaj.org/article/3186266c748a418388a53dfb6e588df52021-12-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S0147651321011064https://doaj.org/toc/0147-6513Some sea cucumbers are economically and ecologically important, but they are threatened by thermal and hypoxic stress in changing oceanographic conditions. We construct circRNAs profiles, reveal circRNAs characters, and illustrate the potential regulatory roles of circRNAs in one commercially important species of sea cucumber, Apostichopus japonicus. Reads are distributed in intergenic (44.14%), exonic (48.26%) and intronic (7.60%) regions of the genome. A total of 1684 circRNAs were identified, and the most common spliced length is 269 nt in the present study. In three treatments (HT [thermal stress], LO [hypoxic stress], and HL [combined thermal and hypoxic stress]), 24, 27 and 27 differentially expressed (DE) circRNAs were identified, respectively. Five novel DE-circRNAs commonly occur in these treatments (novel_circ_0003311, novel_circ_0000229, novel_circ_0003944, novel_circ_0001458 and novel_circ_0000707), and based on them, potential circRNA-miRNA binding pairs were predicted. Sanger sequencing, RNase R treatment experiment and qPCR validation identified the accuracy of the circRNAs. Key circRNAs identified in the present study were covalently closed and were more stable under RNase R treatment than linear RNAs. Based on function analysis, circRNAs could regulate metabolic process, signal transduction, and ion responses in A. japonicus when exposed to thermal and hypoxic stress, and ‘regulation of response to stimulus’ is a common gene ontology (GO) term that is significantly enriched in each treatment; GO terms for ‘DNA’ and ‘stress’ are commonly enriched in heat-related treatments (HT and HL); and GO terms for ‘protein’ are commonly enriched in hypoxia-related treatments (LO and HL). When environmentally stressed, ‘metabolism,’ ‘transport and catabolism,’ ‘membrane transport,’ and ‘signal transduction’ were significantly responded in sea cucumber based on KEGG analysis. We provide insights into circRNA functions in stress regulation and lay a foundation for invertebrate circRNA research.Da HuoLina SunJingchun SunChenggang LinShilin LiuLibin ZhangHongsheng YangElsevierarticleCircular RNAEchinodermHeatAnoxiaEnvironmental stressEnvironmental pollutionTD172-193.5Environmental sciencesGE1-350ENEcotoxicology and Environmental Safety, Vol 228, Iss , Pp 112994- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Circular RNA Echinoderm Heat Anoxia Environmental stress Environmental pollution TD172-193.5 Environmental sciences GE1-350
spellingShingle	Circular RNA Echinoderm Heat Anoxia Environmental stress Environmental pollution TD172-193.5 Environmental sciences GE1-350 Da Huo Lina Sun Jingchun Sun Chenggang Lin Shilin Liu Libin Zhang Hongsheng Yang Emerging roles of circRNAs in regulating thermal and hypoxic stresses in Apostichopus japonicus (Echinodermata: Holothuroidea)
description	Some sea cucumbers are economically and ecologically important, but they are threatened by thermal and hypoxic stress in changing oceanographic conditions. We construct circRNAs profiles, reveal circRNAs characters, and illustrate the potential regulatory roles of circRNAs in one commercially important species of sea cucumber, Apostichopus japonicus. Reads are distributed in intergenic (44.14%), exonic (48.26%) and intronic (7.60%) regions of the genome. A total of 1684 circRNAs were identified, and the most common spliced length is 269 nt in the present study. In three treatments (HT [thermal stress], LO [hypoxic stress], and HL [combined thermal and hypoxic stress]), 24, 27 and 27 differentially expressed (DE) circRNAs were identified, respectively. Five novel DE-circRNAs commonly occur in these treatments (novel_circ_0003311, novel_circ_0000229, novel_circ_0003944, novel_circ_0001458 and novel_circ_0000707), and based on them, potential circRNA-miRNA binding pairs were predicted. Sanger sequencing, RNase R treatment experiment and qPCR validation identified the accuracy of the circRNAs. Key circRNAs identified in the present study were covalently closed and were more stable under RNase R treatment than linear RNAs. Based on function analysis, circRNAs could regulate metabolic process, signal transduction, and ion responses in A. japonicus when exposed to thermal and hypoxic stress, and ‘regulation of response to stimulus’ is a common gene ontology (GO) term that is significantly enriched in each treatment; GO terms for ‘DNA’ and ‘stress’ are commonly enriched in heat-related treatments (HT and HL); and GO terms for ‘protein’ are commonly enriched in hypoxia-related treatments (LO and HL). When environmentally stressed, ‘metabolism,’ ‘transport and catabolism,’ ‘membrane transport,’ and ‘signal transduction’ were significantly responded in sea cucumber based on KEGG analysis. We provide insights into circRNA functions in stress regulation and lay a foundation for invertebrate circRNA research.
format	article
author	Da Huo Lina Sun Jingchun Sun Chenggang Lin Shilin Liu Libin Zhang Hongsheng Yang
author_facet	Da Huo Lina Sun Jingchun Sun Chenggang Lin Shilin Liu Libin Zhang Hongsheng Yang
author_sort	Da Huo
title	Emerging roles of circRNAs in regulating thermal and hypoxic stresses in Apostichopus japonicus (Echinodermata: Holothuroidea)
title_short	Emerging roles of circRNAs in regulating thermal and hypoxic stresses in Apostichopus japonicus (Echinodermata: Holothuroidea)
title_full	Emerging roles of circRNAs in regulating thermal and hypoxic stresses in Apostichopus japonicus (Echinodermata: Holothuroidea)
title_fullStr	Emerging roles of circRNAs in regulating thermal and hypoxic stresses in Apostichopus japonicus (Echinodermata: Holothuroidea)
title_full_unstemmed	Emerging roles of circRNAs in regulating thermal and hypoxic stresses in Apostichopus japonicus (Echinodermata: Holothuroidea)
title_sort	emerging roles of circrnas in regulating thermal and hypoxic stresses in apostichopus japonicus (echinodermata: holothuroidea)
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/3186266c748a418388a53dfb6e588df5
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Emerging roles of circRNAs in regulating thermal and hypoxic stresses in Apostichopus japonicus (Echinodermata: Holothuroidea)

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