title: The Novel Landscape of Long Non-Coding RNAs in Response to Human Foamy Virus Infection Characterized by RNA-Seq.
abstract: Human foamy virus (HFV) is a complex and unique retrovirus with the longest genomes among retroviruses that are used as vectors for gene therapy. Long non-coding RNAs (lncRNAs) are regarded as key regulators that are involved in diverse biological processes during viral infection. However, the role of lncRNAs in HFV infection remains unknown. In this study, we utilized next-generation sequencing to first characterize lncRNAs in 293T cells after HFV infection, evaluating length distribution, exon number distribution, volcano picture, and lncRNA class distribution. We identified 11,336 lncRNAs (4,729 upregulated lncRNAs and 6,588 downregulated lncRNAs) and 61,367 mRNAs (30,133 upregulated mRNAs and 31,220 downregulated mRNAs), which were differentially expressed in the HFV-infected 293T cells. Subsequently, six differentially expressed lncRNAs characterized using RNA-seq were confirmed by quantitative real-time polymerase chain reaction assays. Interestingly, Gene Ontology (GO)/Gene Ontology Tree Machine (GOTM) and Kyoto Encyclopedia of Gene and Genomes (KEGG) pathway analyses indicated that positive regulation of interleukin 8 (IL8) production and cytokine-cytokine receptor interaction might be involved in the functional enrichment of lncRNAs. Moreover, cis-acting and trans-acting regulatory networks show that NR_028036 may target the fas gene in a cis-acting manner and that ENST00000354838 may target the IL18 gene in a trans-acting manner. Overall, these results not only provide novel insights into the relationship between HFV and lncRNAs in the host response to infection but also have implications for the future wider application of HFV as a vector.
authors.affiliation: 1 Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University , Wuhan, China .
authors.forename: Shanshan
authors.initials: S
authors.lastname: Xu
authors.affiliation: 1 Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University , Wuhan, China .|2 Wuhan General Hospital , Guangzhou Military Command, Wuhan, China .
authors.forename: Lanlan
authors.initials: L
authors.lastname: Dong
authors.affiliation: 1 Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University , Wuhan, China .
authors.forename: Yingying
authors.initials: Y
authors.lastname: Shi
authors.affiliation: 1 Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University , Wuhan, China .
authors.forename: Liujun
authors.initials: L
authors.lastname: Chen
authors.affiliation: 1 Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University , Wuhan, China .
authors.forename: Peipei
authors.initials: P
authors.lastname: Yuan
authors.affiliation: 1 Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University , Wuhan, China .
authors.forename: Shuang
authors.initials: S
authors.lastname: Wang
authors.affiliation: 3 College of Life Sciences, Shanxi Normal University , Xi'an, Shanxi, China .
authors.forename: Zhi
authors.initials: Z
authors.lastname: Li
authors.affiliation: 3 College of Life Sciences, Shanxi Normal University , Xi'an, Shanxi, China .
authors.forename: Yan
authors.initials: Y
authors.lastname: Sun
authors.affiliation: 1 Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University , Wuhan, China .|4 Hubei Provincial Key Laboratory of Developmentally Originated Disease , Wuhan, China .
authors.forename: Song
authors.initials: S
authors.lastname: Han
authors.affiliation: 1 Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University , Wuhan, China .|4 Hubei Provincial Key Laboratory of Developmentally Originated Disease , Wuhan, China .
authors.forename: Jun
authors.initials: J
authors.lastname: Yin
authors.affiliation: 1 Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University , Wuhan, China .|4 Hubei Provincial Key Laboratory of Developmentally Originated Disease , Wuhan, China .
authors.forename: Biwen
authors.initials: B
authors.lastname: Peng
authors.affiliation: 1 Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University , Wuhan, China .|4 Hubei Provincial Key Laboratory of Developmentally Originated Disease , Wuhan, China .
authors.forename: Xiaohua
authors.initials: X
authors.lastname: He
authors.affiliation: 1 Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University , Wuhan, China .|4 Hubei Provincial Key Laboratory of Developmentally Originated Disease , Wuhan, China .
authors.forename: Wanhong
authors.initials: W
authors.lastname: Liu
mesh_terms: D057809:HEK293 Cells; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions; D006801:Humans; D062085:RNA, Long Noncoding / Q000032:analysis* / Q000235:genetics; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D053150:Simian foamy virus / Q000254:growth & development*
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger
keywords: HFV; differential expression; function; lncRNAs