High throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D68

Abstract Background With the advancement of sequencing technologies, a plethora of noncoding RNA (ncRNA) species have been widely discovered, including microRNAs (miRNAs), circular RNAs (circRNAs), and long ncRNAs (lncRNAs). However, the mechanism of these non-coding RNAs in diseases caused by enter...

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Autores principales:	Junzhuo Si, Xia Tang, Lei Xu, Huichao Fu, Huayi Li, Yonglin He, Jiajia Bao, Jialing Tang, Anlong Li, Nan Lu, Chun Yang
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Enterovirus D68 Whole transcriptome sequencing Infection Hub mRNAs ceRNA regulatory network Infectious and parasitic diseases RC109-216
Acceso en línea:	https://doaj.org/article/ed2a56b59a1b474e9cafb8be6a4c2b2b
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spelling	oai:doaj.org-article:ed2a56b59a1b474e9cafb8be6a4c2b2b2021-11-14T12:05:23ZHigh throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D6810.1186/s12985-021-01686-x1743-422Xhttps://doaj.org/article/ed2a56b59a1b474e9cafb8be6a4c2b2b2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12985-021-01686-xhttps://doaj.org/toc/1743-422XAbstract Background With the advancement of sequencing technologies, a plethora of noncoding RNA (ncRNA) species have been widely discovered, including microRNAs (miRNAs), circular RNAs (circRNAs), and long ncRNAs (lncRNAs). However, the mechanism of these non-coding RNAs in diseases caused by enterovirus d68 (EV-D68) remains unclear. The goal of this research was to identify significantly altered circRNAs, lncRNAs, miRNAs, and mRNAs pathways in RD cells infected with EV-D68, analyze their target relationships, demonstrate the competing endogenous RNA (ceRNA) regulatory network, and evaluate their biological functions. Methods The total RNAs were sequenced by high-throughput sequencing technology, and differentially expressed genes between control and infection groups were screened using bioinformatics method. We discovered the targeting relationship between three ncRNAs and mRNA using bioinformatics methods, and then built a ceRNA regulatory network centered on miRNA. The biological functions of differentially expressed mRNAs (DEmRNAs) were discovered through GO and KEGG enrichment analysis. Create a protein interaction network (PPI) to seek for hub mRNAs and learn more about protein–protein interactions. The relative expression was verified using RT-qPCR. The effects of Fos and ARRDC3 on virus replication were confirmed using RT-qPCR, virus titer (TCID50/ml), Western blotting. Results 375 lncRNAs (154 upregulated and 221 downregulated), 33 circRNAs (32 upregulated and 1 downregulated), 96 miRNAs (49 upregulated and 47 downregulated), and 239 mRNAs (135 upregulated and 104 downregulated) were identified as differently in infected group compare to no-infected group. A single lncRNA or circRNA can be connected with numerous miRNAs, which subsequently coregulate additional mRNAs, according to the ceRNA regulatory network. The majority of DEmRNAs were shown to be connected to DNA binding, transcription regulation by RNA polymerase II, transcription factor, MAPK signaling pathways, Hippo signal pathway, and apoptosis pathway, according to GO and KEGG pathway enrichment analysis. The hub mRNAs with EGR1, Fos and Jun as the core were screened through PPI interaction network. We preliminarily demonstrated that the Fos and ARRDC3 genes can suppress EV-D68 viral replication in order to further verify the results of full transcriptome sequencing. Conclusion The results of whole transcriptome analysis after EV-D68 infection of RD cells were first reported in this study, and for the first time, a ceRNA regulation network containing miRNA at its center was established for the first time. The Fos and ARRDC3 genes were found to hinder viral in RD cells. This study establishes a novel insight host response during EV-D68 infection and further investigated potential drug targets.Junzhuo SiXia TangLei XuHuichao FuHuayi LiYonglin HeJiajia BaoJialing TangAnlong LiNan LuChun YangBMCarticleEnterovirus D68Whole transcriptome sequencingInfectionHub mRNAsceRNA regulatory networkInfectious and parasitic diseasesRC109-216ENVirology Journal, Vol 18, Iss 1, Pp 1-18 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Enterovirus D68 Whole transcriptome sequencing Infection Hub mRNAs ceRNA regulatory network Infectious and parasitic diseases RC109-216
spellingShingle	Enterovirus D68 Whole transcriptome sequencing Infection Hub mRNAs ceRNA regulatory network Infectious and parasitic diseases RC109-216 Junzhuo Si Xia Tang Lei Xu Huichao Fu Huayi Li Yonglin He Jiajia Bao Jialing Tang Anlong Li Nan Lu Chun Yang High throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D68
description	Abstract Background With the advancement of sequencing technologies, a plethora of noncoding RNA (ncRNA) species have been widely discovered, including microRNAs (miRNAs), circular RNAs (circRNAs), and long ncRNAs (lncRNAs). However, the mechanism of these non-coding RNAs in diseases caused by enterovirus d68 (EV-D68) remains unclear. The goal of this research was to identify significantly altered circRNAs, lncRNAs, miRNAs, and mRNAs pathways in RD cells infected with EV-D68, analyze their target relationships, demonstrate the competing endogenous RNA (ceRNA) regulatory network, and evaluate their biological functions. Methods The total RNAs were sequenced by high-throughput sequencing technology, and differentially expressed genes between control and infection groups were screened using bioinformatics method. We discovered the targeting relationship between three ncRNAs and mRNA using bioinformatics methods, and then built a ceRNA regulatory network centered on miRNA. The biological functions of differentially expressed mRNAs (DEmRNAs) were discovered through GO and KEGG enrichment analysis. Create a protein interaction network (PPI) to seek for hub mRNAs and learn more about protein–protein interactions. The relative expression was verified using RT-qPCR. The effects of Fos and ARRDC3 on virus replication were confirmed using RT-qPCR, virus titer (TCID50/ml), Western blotting. Results 375 lncRNAs (154 upregulated and 221 downregulated), 33 circRNAs (32 upregulated and 1 downregulated), 96 miRNAs (49 upregulated and 47 downregulated), and 239 mRNAs (135 upregulated and 104 downregulated) were identified as differently in infected group compare to no-infected group. A single lncRNA or circRNA can be connected with numerous miRNAs, which subsequently coregulate additional mRNAs, according to the ceRNA regulatory network. The majority of DEmRNAs were shown to be connected to DNA binding, transcription regulation by RNA polymerase II, transcription factor, MAPK signaling pathways, Hippo signal pathway, and apoptosis pathway, according to GO and KEGG pathway enrichment analysis. The hub mRNAs with EGR1, Fos and Jun as the core were screened through PPI interaction network. We preliminarily demonstrated that the Fos and ARRDC3 genes can suppress EV-D68 viral replication in order to further verify the results of full transcriptome sequencing. Conclusion The results of whole transcriptome analysis after EV-D68 infection of RD cells were first reported in this study, and for the first time, a ceRNA regulation network containing miRNA at its center was established for the first time. The Fos and ARRDC3 genes were found to hinder viral in RD cells. This study establishes a novel insight host response during EV-D68 infection and further investigated potential drug targets.
format	article
author	Junzhuo Si Xia Tang Lei Xu Huichao Fu Huayi Li Yonglin He Jiajia Bao Jialing Tang Anlong Li Nan Lu Chun Yang
author_facet	Junzhuo Si Xia Tang Lei Xu Huichao Fu Huayi Li Yonglin He Jiajia Bao Jialing Tang Anlong Li Nan Lu Chun Yang
author_sort	Junzhuo Si
title	High throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D68
title_short	High throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D68
title_full	High throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D68
title_fullStr	High throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D68
title_full_unstemmed	High throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D68
title_sort	high throughput sequencing of whole transcriptome and construct of cerna regulatory network in rd cells infected with enterovirus d68
publisher	BMC
publishDate	2021
url	https://doaj.org/article/ed2a56b59a1b474e9cafb8be6a4c2b2b
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High throughput sequencing of whole transcriptome and construct of ceRNA regulatory network in RD cells infected with enterovirus D68

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