Identification of Differentially Expressed Non-coding RNA in Porcine Alveolar Macrophages from Tongcheng and Large White Pigs Responded to PRRSV

Abstract Porcine reproductive and respiratory syndrome (PRRS) is one of the most ruinous diseases in pig production. Our previous work showed that Tongcheng pigs (TC) were less susceptible to PRRS virus (PRRSV) than Large White (LW) pigs. To elucidate the difference in PRRSV resistance between the t...

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Autores principales:	Yueran Zhen, Fengqing Wang, Wan Liang, Jianjian Liu, Guoli Gao, Yan Wang, Xuewen Xu, Qiuju Su, Qingde Zhang, Bang Liu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	PRRS Virus (PRRSV) Porcine Alveolar Macrophages (PAMs) Tongcheng (TC) Differentially Expressed miRNAs (DEmiRNAs) Porcine Reproductive And Respiratory Syndrome (PRRS) Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5fe63d563fe3495681490063583ee1d2
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spelling	oai:doaj.org-article:5fe63d563fe3495681490063583ee1d22021-12-02T11:40:24ZIdentification of Differentially Expressed Non-coding RNA in Porcine Alveolar Macrophages from Tongcheng and Large White Pigs Responded to PRRSV10.1038/s41598-018-33891-02045-2322https://doaj.org/article/5fe63d563fe3495681490063583ee1d22018-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-33891-0https://doaj.org/toc/2045-2322Abstract Porcine reproductive and respiratory syndrome (PRRS) is one of the most ruinous diseases in pig production. Our previous work showed that Tongcheng pigs (TC) were less susceptible to PRRS virus (PRRSV) than Large White (LW) pigs. To elucidate the difference in PRRSV resistance between the two breeds, small RNA-seq and ribo-zero RNA-seq were used to identify differentially expressed non-coding RNAs (including miRNAs and lincRNAs) responded to PRRSV in porcine alveolar macrophages (PAMs) from TC and LW pigs. Totally, 250 known mature miRNAs were detected. For LW pigs, there were 44 down-regulated and 67 up-regulated miRNAs in infection group; while for TC pigs, 12 down-regulated and 23 up-regulated miRNAs in TC infection group were identified. The target genes of the common differentially expressed miRNAs (DEmiRNAs) in these two breeds were enriched in immune-related processes, including apoptosis process, inflammatory response, T cell receptor signaling pathway and so on. In addition, 5 shared DEmiRNAs (miR-181, miR-1343, miR-296-3p, miR-199a-3p and miR-34c) were predicted to target PRRSV receptors, of which miR-199a-3p was validated to inhibit the expression of CD151. Interestingly, miR-378 and miR-10a-5p, which could inhibit PRRSV replication, displayed higher expression level in TC control group than that in LW control group. Contrarily, miR-145-5p and miR-328, which were specifically down-regulated in LW pigs, could target inhibitory immunoreceptors and may involve in immunosuppression caused by PRRSV. This indicates that DEmiRNAs are involved in the regulation of the immunosuppression and immune escape of the two breeds. Furthermore, we identified 616 lincRNA transcripts, of which 48 and 30 lincRNAs were differentially expressed in LW and TC pigs, respectively. LincRNA TCONS_00125566 may play an important role in the entire regulatory network, and was predicted to regulate the expression of immune-related genes through binding with miR-1343 competitively. In conclusion, this study provides an important resource for further revealing the interaction between host and virus, which will specify a new direction for anti-PRRSV research.Yueran ZhenFengqing WangWan LiangJianjian LiuGuoli GaoYan WangXuewen XuQiuju SuQingde ZhangBang LiuNature PortfolioarticlePRRS Virus (PRRSV)Porcine Alveolar Macrophages (PAMs)Tongcheng (TC)Differentially Expressed miRNAs (DEmiRNAs)Porcine Reproductive And Respiratory Syndrome (PRRS)MedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-11 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	PRRS Virus (PRRSV) Porcine Alveolar Macrophages (PAMs) Tongcheng (TC) Differentially Expressed miRNAs (DEmiRNAs) Porcine Reproductive And Respiratory Syndrome (PRRS) Medicine R Science Q
spellingShingle	PRRS Virus (PRRSV) Porcine Alveolar Macrophages (PAMs) Tongcheng (TC) Differentially Expressed miRNAs (DEmiRNAs) Porcine Reproductive And Respiratory Syndrome (PRRS) Medicine R Science Q Yueran Zhen Fengqing Wang Wan Liang Jianjian Liu Guoli Gao Yan Wang Xuewen Xu Qiuju Su Qingde Zhang Bang Liu Identification of Differentially Expressed Non-coding RNA in Porcine Alveolar Macrophages from Tongcheng and Large White Pigs Responded to PRRSV
description	Abstract Porcine reproductive and respiratory syndrome (PRRS) is one of the most ruinous diseases in pig production. Our previous work showed that Tongcheng pigs (TC) were less susceptible to PRRS virus (PRRSV) than Large White (LW) pigs. To elucidate the difference in PRRSV resistance between the two breeds, small RNA-seq and ribo-zero RNA-seq were used to identify differentially expressed non-coding RNAs (including miRNAs and lincRNAs) responded to PRRSV in porcine alveolar macrophages (PAMs) from TC and LW pigs. Totally, 250 known mature miRNAs were detected. For LW pigs, there were 44 down-regulated and 67 up-regulated miRNAs in infection group; while for TC pigs, 12 down-regulated and 23 up-regulated miRNAs in TC infection group were identified. The target genes of the common differentially expressed miRNAs (DEmiRNAs) in these two breeds were enriched in immune-related processes, including apoptosis process, inflammatory response, T cell receptor signaling pathway and so on. In addition, 5 shared DEmiRNAs (miR-181, miR-1343, miR-296-3p, miR-199a-3p and miR-34c) were predicted to target PRRSV receptors, of which miR-199a-3p was validated to inhibit the expression of CD151. Interestingly, miR-378 and miR-10a-5p, which could inhibit PRRSV replication, displayed higher expression level in TC control group than that in LW control group. Contrarily, miR-145-5p and miR-328, which were specifically down-regulated in LW pigs, could target inhibitory immunoreceptors and may involve in immunosuppression caused by PRRSV. This indicates that DEmiRNAs are involved in the regulation of the immunosuppression and immune escape of the two breeds. Furthermore, we identified 616 lincRNA transcripts, of which 48 and 30 lincRNAs were differentially expressed in LW and TC pigs, respectively. LincRNA TCONS_00125566 may play an important role in the entire regulatory network, and was predicted to regulate the expression of immune-related genes through binding with miR-1343 competitively. In conclusion, this study provides an important resource for further revealing the interaction between host and virus, which will specify a new direction for anti-PRRSV research.
format	article
author	Yueran Zhen Fengqing Wang Wan Liang Jianjian Liu Guoli Gao Yan Wang Xuewen Xu Qiuju Su Qingde Zhang Bang Liu
author_facet	Yueran Zhen Fengqing Wang Wan Liang Jianjian Liu Guoli Gao Yan Wang Xuewen Xu Qiuju Su Qingde Zhang Bang Liu
author_sort	Yueran Zhen
title	Identification of Differentially Expressed Non-coding RNA in Porcine Alveolar Macrophages from Tongcheng and Large White Pigs Responded to PRRSV
title_short	Identification of Differentially Expressed Non-coding RNA in Porcine Alveolar Macrophages from Tongcheng and Large White Pigs Responded to PRRSV
title_full	Identification of Differentially Expressed Non-coding RNA in Porcine Alveolar Macrophages from Tongcheng and Large White Pigs Responded to PRRSV
title_fullStr	Identification of Differentially Expressed Non-coding RNA in Porcine Alveolar Macrophages from Tongcheng and Large White Pigs Responded to PRRSV
title_full_unstemmed	Identification of Differentially Expressed Non-coding RNA in Porcine Alveolar Macrophages from Tongcheng and Large White Pigs Responded to PRRSV
title_sort	identification of differentially expressed non-coding rna in porcine alveolar macrophages from tongcheng and large white pigs responded to prrsv
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/5fe63d563fe3495681490063583ee1d2
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Identification of Differentially Expressed Non-coding RNA in Porcine Alveolar Macrophages from Tongcheng and Large White Pigs Responded to PRRSV

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