ZIKV infection effects changes in gene splicing, isoform composition and lncRNA expression in human neural progenitor cells
Abstract Background The Zika virus (ZIKV) is a mosquito-borne flavivirus that causes microcephaly and Guillain-Barré syndrome in infected individuals. To obtain insights into the mechanism of ZIKV infection and pathogenesis, we analyzed the transcriptome of ZIKV infected human neural progenitor cell...
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| Format: | Article |
| Language: | English |
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BMC
2017-11-01
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| Series: | Virology Journal |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12985-017-0882-6 |
| _version_ | 1818543666964201472 |
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| author | Benxia Hu Yongxia Huo Liping Yang Guijun Chen Minhua Luo Jinlong Yang Jumin Zhou |
| author_facet | Benxia Hu Yongxia Huo Liping Yang Guijun Chen Minhua Luo Jinlong Yang Jumin Zhou |
| author_sort | Benxia Hu |
| collection | DOAJ |
| description | Abstract Background The Zika virus (ZIKV) is a mosquito-borne flavivirus that causes microcephaly and Guillain-Barré syndrome in infected individuals. To obtain insights into the mechanism of ZIKV infection and pathogenesis, we analyzed the transcriptome of ZIKV infected human neural progenitor cells (hNPCs) for changes in alternative splicing (AS), gene isoform (ISO) composition and long noncoding RNAs (lncRNAs) expression. Methods We analyzed differentially expressed lncRNAs, AS, ISO from RNA-seq data in ZIKV infected hNPCs. Results We obtained 149 differentially expressed lncRNAs, including potential viral targets to modulate cellular processes such as cell cycle, apoptosis and immune response. The infection induced 262 cases of AS occurring in 229 genes, which were enriched in cell death, RNA processing, transport, and neuron development. Among 691 differentially expressed ISOs, upregulated ISOs were enriched in signaling, regulation of transcription, and amino acid biosynthesis, while downregulated ISOs were mostly enriched in cell cycle. Importantly, these analyses revealed specific links between ZIKV induced changes in cellular pathways and the type of changes in the host transcriptome, suggesting important regulatory mechanisms. Conclusions Our analyses revealed candidate lncRNAs, AS events and ISOs which may function in ZIKV infection induced cell cycle disruption, apoptosis and attenuation of neurogenesis, and shed light on the roles of lncRNAs, AS and ISOs in virus-host interactions, and would facilitate future studies of ZIKV infection and pathogenesis. |
| first_indexed | 2024-12-11T22:38:24Z |
| format | Article |
| id | doaj.art-2167d12262e241bb9a28fb0006eab5de |
| institution | Directory Open Access Journal |
| issn | 1743-422X |
| language | English |
| last_indexed | 2024-12-11T22:38:24Z |
| publishDate | 2017-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Virology Journal |
| spelling | doaj.art-2167d12262e241bb9a28fb0006eab5de2022-12-22T00:47:52ZengBMCVirology Journal1743-422X2017-11-0114111110.1186/s12985-017-0882-6ZIKV infection effects changes in gene splicing, isoform composition and lncRNA expression in human neural progenitor cellsBenxia Hu0Yongxia Huo1Liping Yang2Guijun Chen3Minhua Luo4Jinlong Yang5Jumin Zhou6Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of ZoologyKey Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of ZoologyKey Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of ZoologyKey Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of ZoologyState Key Laboratory of Virology, CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Wuhan Institute of VirologyBGI-Yunnan, BGI-ShenzhenKey Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of ZoologyAbstract Background The Zika virus (ZIKV) is a mosquito-borne flavivirus that causes microcephaly and Guillain-Barré syndrome in infected individuals. To obtain insights into the mechanism of ZIKV infection and pathogenesis, we analyzed the transcriptome of ZIKV infected human neural progenitor cells (hNPCs) for changes in alternative splicing (AS), gene isoform (ISO) composition and long noncoding RNAs (lncRNAs) expression. Methods We analyzed differentially expressed lncRNAs, AS, ISO from RNA-seq data in ZIKV infected hNPCs. Results We obtained 149 differentially expressed lncRNAs, including potential viral targets to modulate cellular processes such as cell cycle, apoptosis and immune response. The infection induced 262 cases of AS occurring in 229 genes, which were enriched in cell death, RNA processing, transport, and neuron development. Among 691 differentially expressed ISOs, upregulated ISOs were enriched in signaling, regulation of transcription, and amino acid biosynthesis, while downregulated ISOs were mostly enriched in cell cycle. Importantly, these analyses revealed specific links between ZIKV induced changes in cellular pathways and the type of changes in the host transcriptome, suggesting important regulatory mechanisms. Conclusions Our analyses revealed candidate lncRNAs, AS events and ISOs which may function in ZIKV infection induced cell cycle disruption, apoptosis and attenuation of neurogenesis, and shed light on the roles of lncRNAs, AS and ISOs in virus-host interactions, and would facilitate future studies of ZIKV infection and pathogenesis.http://link.springer.com/article/10.1186/s12985-017-0882-6lncRNAGene isoformAlternative splicinghNPCZIKV |
| spellingShingle | Benxia Hu Yongxia Huo Liping Yang Guijun Chen Minhua Luo Jinlong Yang Jumin Zhou ZIKV infection effects changes in gene splicing, isoform composition and lncRNA expression in human neural progenitor cells Virology Journal lncRNA Gene isoform Alternative splicing hNPC ZIKV |
| title | ZIKV infection effects changes in gene splicing, isoform composition and lncRNA expression in human neural progenitor cells |
| title_full | ZIKV infection effects changes in gene splicing, isoform composition and lncRNA expression in human neural progenitor cells |
| title_fullStr | ZIKV infection effects changes in gene splicing, isoform composition and lncRNA expression in human neural progenitor cells |
| title_full_unstemmed | ZIKV infection effects changes in gene splicing, isoform composition and lncRNA expression in human neural progenitor cells |
| title_short | ZIKV infection effects changes in gene splicing, isoform composition and lncRNA expression in human neural progenitor cells |
| title_sort | zikv infection effects changes in gene splicing isoform composition and lncrna expression in human neural progenitor cells |
| topic | lncRNA Gene isoform Alternative splicing hNPC ZIKV |
| url | http://link.springer.com/article/10.1186/s12985-017-0882-6 |
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