{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T14:27:40Z","timestamp":1783434460279,"version":"3.54.6"},"reference-count":35,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T00:00:00Z","timestamp":1773619200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["32472943"],"award-info":[{"award-number":["32472943"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Changsha Science and Technology Plan Natural Science Foundation","award":["kq2402188"],"award-info":[{"award-number":["kq2402188"]}]},{"name":"Science and Technology Projects of Xizang Autonomous Region","award":["XZ202501ZY0143"],"award-info":[{"award-number":["XZ202501ZY0143"]}]},{"name":"Guizhou Agricultural Science and Technology","award":["2024-27"],"award-info":[{"award-number":["2024-27"]}]},{"name":"Central Universities","award":["SWU-KT22013"],"award-info":[{"award-number":["SWU-KT22013"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Veterinary Sciences"],"abstract":"<jats:p>(1) Background: Swine hepatitis E (SHE) is an emerging zoonotic disease caused by the swine hepatitis E virus (SHEV). The open reading frame 3 (ORF3) protein is a recognized virulence factor of SHEV. Jaundice, the typical clinical sign of SHE, primarily results from disruptions in bile production, secretion, and excretion. However, the mechanism by which SHEV ORF3 influences bile metabolism remains unclear. (2) Methods: Building on our previous work involving adenovirus-mediated overexpression of genotype IV SHEV ORF3 in HepG2 cells and subsequent high-throughput lncRNA\/transcriptome sequencing, this study performed KEGG enrichment analysis on differentially expressed lncRNAs. Candidate lncRNAs were validated via qRT-PCR. Cis-regulated target genes were predicted by integrating differentially expressed mRNA data. Furthermore, AlphaFold 3.0 was employed to analyze the molecular binding sites between lncRNA UBC (MSTRG.6881.4) and its target, UBC protein. (3) Results: We identified three lncRNAs associated with the bile secretion pathway (ko 04976) in HepG2 cells expressing genotype IV SHEV ORF3, which were further confirmed by qRT-PCR: lncRNA UBC (MSTRG.6881.4), lncRNA UBC (MSTRG.6881.9), and lncRNA UBC (MSTRG.6881.12). Bioinformatics prediction suggested six lncRNA-mRNA regulatory networks involved these lncRNAs and two downregulated UBC mRNA transcripts (ENST00000540700 and ENST00000536769). Molecular docking indicated that nucleotides 395U and 41C of lncRNA UBC (MSTRG.6881.4) could potentially bind to residues 82Lys, 88Thr, and 90Thr of the UBC protein, with predicted binding energies ranging from \u22124.73 to \u22120.75 kcal\/mol. (4) Conclusions: The successful identification of bile secretion-related lncRNAs, coupled with the prediction of their regulatory networks and molecular interaction sites, has advanced our understanding of SHEV ORF3 function and the pathogenesis of SHEV infection.<\/jats:p>","DOI":"10.3390\/vetsci13030276","type":"journal-article","created":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T15:21:16Z","timestamp":1773674476000},"page":"276","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Integrated Bioinformatics Analysis Reveals the Impact of SHEV ORF3-Related LncRNA Network on Bile Secretion Pathway (ko 04976) in HepG2 Cells"],"prefix":"10.3390","volume":"13","author":[{"given":"Hanwei","family":"Jiao","sequence":"first","affiliation":[{"name":"The College of Veterinary Medicine, Southwest University, Chongqing 402460, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiya","family":"Li","sequence":"additional","affiliation":[{"name":"The College of Veterinary Medicine, Southwest University, Chongqing 402460, China"},{"name":"College of Veterinary Medicine, Jilin Agricultural University, Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengping","family":"Wu","sequence":"additional","affiliation":[{"name":"The College of Veterinary Medicine, Southwest University, Chongqing 402460, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lingjie","family":"Wang","sequence":"additional","affiliation":[{"name":"The College of Veterinary Medicine, Southwest University, Chongqing 402460, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Zhao","sequence":"additional","affiliation":[{"name":"Institute of Animal Husbandry and Veterinary Medicine of Guizhou Academy of Agricultural Science, Ministry of Agriculture and Rural Affairs Key Laboratory of Crop Genitic Resources and Germplasm Innovation in Karst Region, Guiyang 550005, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yulong","family":"Yin","sequence":"additional","affiliation":[{"name":"Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Cao","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Jilin Agricultural University, Changchun 130118, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leli","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,3,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2276336","DOI":"10.1080\/22221751.2023.2276336","article-title":"Vital role of autophagy flux inhibition of placental trophoblast cells in pregnancy disorders induced by HEV infection","volume":"12","author":"Yang","year":"2023","journal-title":"Emerg. Microbes Infect."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"218","DOI":"10.36233\/0507-4088-2020-65-4-218-227","article-title":"Seroprevalence of hepatitis E virus (Hepeviridae: Orthohepevirus: Orthohepevirus A) among pregnant women in the highly endemic region of Kyrgyzstan","volume":"65","author":"Alatortseva","year":"2020","journal-title":"Probl. Virol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"e2419946122","DOI":"10.1073\/pnas.2419946122","article-title":"Proteasomal processing of the viral replicase ORF1 facilitates HEV-induced liver fibrosis","volume":"122","author":"Zhang","year":"2025","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1128\/JVI.02208-14","article-title":"Quantitative proteomics identifies host factors modulated during acute hepatitis E virus infection in the swine model","volume":"89","author":"Chafey","year":"2015","journal-title":"J. Virol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1648030","DOI":"10.1155\/2016\/1648030","article-title":"Transcriptome Analysis of HepG2 Cells Expressing ORF3 from Swine Hepatitis E Virus to Determine the Effects of ORF3 on Host Cells","volume":"2016","author":"Xu","year":"2016","journal-title":"BioMed Res. Int."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1810","DOI":"10.14202\/vetworld.2024.1810-1820","article-title":"Seroprevalence of swine hepatitis E virus and the farmers\u2019 potential risk of infection in the Province of Bali, Indonesia","volume":"17","author":"Kardena","year":"2024","journal-title":"Vet. World"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Pezzoni, G., Stercoli, L., Pegoiani, E., and Brocchi, E. (2021). Antigenic Characterization of ORF2 and ORF3 Proteins of Hepatitis E Virus (HEV). Viruses, 13.","DOI":"10.3390\/v13071385"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"3563","DOI":"10.1002\/jmv.26226","article-title":"Dissecting the potential role of hepatitis E virus ORF1 nonstructural gene in cross-species infection by using intergenotypic chimeric viruses","volume":"92","author":"Tian","year":"2020","journal-title":"J. Med. Virol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"5637","DOI":"10.1128\/JVI.06711-11","article-title":"The PSAP motif within the ORF3 protein of an avian strain of the hepatitis E virus is not critical for viral infectivity in vivo but plays a role in virus release","volume":"86","author":"Kenney","year":"2012","journal-title":"J. Virol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1111\/zph.12372","article-title":"Serological evidence of hepatitis E virus infection in pigs and jaundice among pig handlers in Bangladesh","volume":"64","author":"Haider","year":"2017","journal-title":"Zoonoses Public Health"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1677","DOI":"10.1038\/s41467-020-15337-2","article-title":"Stem cell-derived polarized hepatocytes","volume":"11","author":"Wu","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1038\/nature20149","article-title":"Local regulation of gene expression by lncRNA promoters, transcription and splicing","volume":"539","author":"Engreitz","year":"2016","journal-title":"Nature"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1038\/s41580-022-00566-8","article-title":"Long non-coding RNAs: Definitions, functions, challenges and recommendations","volume":"24","author":"Mattick","year":"2023","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1435","DOI":"10.1126\/science.1231776","article-title":"Epigenetic regulation by long noncoding RNAs","volume":"338","author":"Lee","year":"2012","journal-title":"Science"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Jiao, H., Shuai, X., Luo, Y., Zhou, Z., Zhao, Y., Li, B., Gu, G., Li, W., Li, M., and Zeng, H. (2021). Deep Insight Into Long Non-coding RNA and mRNA Transcriptome Profiling in HepG2 Cells Expressing Genotype IV Swine Hepatitis E Virus ORF3. Front. Vet. Sci., 8.","DOI":"10.3389\/fvets.2021.625609"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Jiao, H., Meng, C., Jiao, F., Zhou, G., Wang, L., Wu, S., Fan, C., Li, J., Cao, L., and Zhao, Y. (2025). Descriptive Comparative Transcriptomic Analysis of Genotype IV SHEV ORF3-Expressing HepG2 Cells. Microorganisms, 13.","DOI":"10.3390\/microorganisms13020412"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Luo, W., Li, J., Wu, S., Wang, L., Yin, Y., Cao, X., Wang, L., and Jiao, H. (2026). Integrated Transcriptomics Reveals a SHEV ORF3-Mediated circRNA Network That Disrupts Riboflavin Metabolism and Activates the ko05212 Pathway. Vet. Sci., 13.","DOI":"10.3390\/vetsci13030253"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/s41392-020-00450-x","article-title":"The role of m6A modification in the biological functions and diseases","volume":"6","author":"Jiang","year":"2021","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"164","DOI":"10.3892\/ijmm.2025.5605","article-title":"m6A modification of non-coding RNA: Mechanisms, functions and potential values in human diseases (Review)","volume":"56","author":"Yi","year":"2025","journal-title":"Int. J. Mol. Med."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"9860","DOI":"10.1073\/pnas.94.18.9860","article-title":"A novel virus in swine is closely related to the human hepatitis E virus","volume":"94","author":"Meng","year":"1997","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Nan, Y., Wu, C., Zhao, Q., and Zhou, E.M. (2017). Zoonotic Hepatitis E Virus: An Ignored Risk for Public Health. Front. Microbiol., 8.","DOI":"10.3389\/fmicb.2017.02396"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1038\/s41426-018-0198-7","article-title":"Life cycle and morphogenesis of the hepatitis E virus","volume":"7","author":"Himmelsbach","year":"2018","journal-title":"Emerg. Microbes Infect."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Nan, Y., Wu, C., Zhao, Q., Sun, Y., Zhang, Y.J., and Zhou, E.M. (2018). Vaccine Development against Zoonotic Hepatitis E Virus: Open Questions and Remaining Challenges. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.00266"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.meegid.2018.12.017","article-title":"Potential effects of hepatitis E virus infection in swine on public health in China","volume":"68","author":"Zhou","year":"2019","journal-title":"Infect. Genet. Evol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1073\/pnas.1614955114","article-title":"Hepatitis E virus ORF3 is a functional ion channel required for release of infectious particles","volume":"114","author":"Ding","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1002\/hep.31002","article-title":"A Molecular Mechanism Underlying Genotype-Specific Intrahepatic Cholestasis Resulting From MYO5B Mutations","volume":"72","author":"Overeem","year":"2020","journal-title":"Hepatology"},{"key":"ref_27","first-page":"4367","article-title":"Delay in hepatocyte proliferation and prostaglandin D2 synthase expression for cholestasis due to endotoxin during partial hepatectomy in rats","volume":"20","author":"Wakasa","year":"2019","journal-title":"Mol. Med. Rep."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1007\/s10735-020-09861-0","article-title":"The involvement of genes related to bile secretion pathway in rat tooth germ development","volume":"51","author":"Yang","year":"2020","journal-title":"J. Mol. Histol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.meegid.2014.01.002","article-title":"Hepatitis E: An emerging disease","volume":"22","author":"Suay","year":"2014","journal-title":"Infect. Genet. Evol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.hbpd.2023.10.001","article-title":"Animal models of hepatitis E infection: Advances and challenges","volume":"23","author":"Xiang","year":"2024","journal-title":"Hepatobiliary Pancreat. Dis. Int."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1016\/j.ncrna.2025.01.004","article-title":"Long non-coding RNAs in humans: Classification, genomic organization and function","volume":"11","author":"Chodurska","year":"2025","journal-title":"Noncoding RNA Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1301","DOI":"10.1007\/s10072-024-07790-4","article-title":"The relevance of combined testing of cerebrospinal fluid glial fibrillary acidic protein and ubiquitin C-terminal hydrolase L1 in multiple sclerosis and peripheral neuropathy","volume":"46","author":"Csecsei","year":"2025","journal-title":"Neurol. Sci."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Kim, Y.J., Jeong, I.H., Ha, J.H., Kim, Y.S., Sung, S., Jang, J.H., and Choung, Y.-H. (2024). The Suppression of Ubiquitin C-Terminal Hydrolase L1 Promotes the Transdifferentiation of Auditory Supporting Cells into Hair Cells by Regulating the mTOR Pathway. Cells, 13.","DOI":"10.3390\/cells13090737"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Zhang, C., Zhang, S., Kong, F., Xiao, Y., She, K., Jin, Y., Li, J., Qadeer, A., Zheng, X., and Ji, S. (2023). Ubiquitin C-Terminal Hydrolase L5 Plays an Essential Role in the Fly Innate Immune Defense against Bacterial Infection. Front. Biosci. (Landmark Ed)., 28.","DOI":"10.31083\/j.fbl2811294"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/s41374-022-00731-9","article-title":"LncRNA MAPKAPK5_AS1 facilitates cell proliferation in hepatitis B virus -related hepatocellular carcinoma","volume":"102","author":"Tao","year":"2022","journal-title":"Lab. Invest."}],"container-title":["Veterinary Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-7381\/13\/3\/276\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T05:35:42Z","timestamp":1773812142000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-7381\/13\/3\/276"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,16]]},"references-count":35,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2026,3]]}},"alternative-id":["vetsci13030276"],"URL":"https:\/\/doi.org\/10.3390\/vetsci13030276","relation":{},"ISSN":["2306-7381"],"issn-type":[{"value":"2306-7381","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,16]]}}}