Xiao Liu1,2,3, Xiaoqiong Duan4,2, Jacinta A Holmes2, Wenting Li2,5, Sae Hwan Lee2,6, Zeng Tu2,7, Chuanlong Zhu2,8, Shadi Salloum2, Anna Lidofsky2, Esperance A Schaefer2, Dachuan Cai2,9, Shilin Li4, Haoju Wang1, Yongfu Huang1, Yongju Zhao1, Ming-Lung Yu2,10, Zhiwen Xu3, Limin Chen4, Jian Hong2, Wenyu Lin4,2, Raymond T Chung2. 1. College of Animal Science and Technology, Southwest University, Chongqing, China. 2. Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA. 3. Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China. 4. Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China. 5. Department of Infectious Disease, Anhui Provincial Hospital, Anhui Medical University, Hefei, China. 6. Soonchunhyang University College of Medicine, Cheonan Hospital, Dongnamgu Cheonan, Republic of Korea. 7. Department of Microbiology, College of Basic Medical Science, Chongqing Medical University, Chongqing, China. 8. Department of Infectious Disease, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China. 9. Department of Infectious Disease, Chongqing Medical University, Chongqing, China. 10. Division of Hepatobiliary, Department of Internal Medicine and Hepatitis Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
Abstract
Long noncoding RNAs (lncRNAs) play a critical role in the regulation of many important cellular processes. However, the mechanisms by which lncRNAs regulate viral infection and host immune responses are not well understood. We sought to explore lncRNA regulation of hepatitis C virus (HCV) infection and interferon response. We performed RNA sequencing (RNAseq) in Huh7.5.1 cells with or without interferon alpha (IFNα) treatment. Clustered regularly interspaced short palindromic repeats/Cas9 guide RNA (gRNA) was used to knock out selected genes. The promoter clones were constructed, and the activity of related interferon-stimulated genes (ISGs) were detected by the secrete-pair dual luminescence assay. We constructed the full-length and four deletion mutants of an interferon-induced lncRNA RP11-288L9.4 (lncRNA-IFI6) based on predicted secondary structure. Selected gene mRNAs and their proteins, together with HCV infection, in Huh7.5.1 cells and primary human hepatocytes (PHHs) were monitored by quantitative real-time PCR (qRT-PCR) and western blot. We obtained 7,901 lncRNAs from RNAseq. A total of 1,062 host-encoded lncRNAs were significantly differentially regulated by IFNα treatment. We found that lncRNA-IFI6 gRNA significantly inhibited HCV infection compared with negative gRNA control. The expression of the antiviral ISG IFI6 was significantly increased following lncRNA-IFI6 gRNA editing compared with negative gRNA control in Japanese fulminant hepatitis 1 (JFH1)-infected Huh7.5.1 cells and PHHs. We observed that lncRNA-IFI6 regulation of HCV was independent of Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling. lncRNA-IFI6 negatively regulated IFI6 promoter function through histone modification. Overexpression of the truncated spatial domain or full-length lncRNA-IFI6 inhibited IFI6 expression and increased HCV replication. Conclusion: A lncRNA, lncRNA-IFI6, regulates antiviral innate immunity in the JFH1 HCV infection model. lncRNA-IFI6 regulates HCV infection independently of the JAK-STAT pathway. lncRNA-IFI6 exerts its regulatory function via promoter activation and histone modification of IFI6 through its spatial domain.
Long noncoding RNAs (lncRNAs) play a critical role in the regulation of many important cellular processes. However, the mechanisms by which lncRNAs regulate viral infection and host immune responses are not well understood. We sought to explore lncRNA regulation of hepatitis C virus (HCV) infection and interferon response. We performed RNA sequencing (RNAseq) in Huh7.5.1 cells with or without interferon alpha (IFNα) treatment. Clustered regularly interspaced short palindromic repeats/Cas9 guide RNA (gRNA) was used to knock out selected genes. The promoter clones were constructed, and the activity of related interferon-stimulated genes (ISGs) were detected by the secrete-pair dual luminescence assay. We constructed the full-length and four deletion mutants of an interferon-induced lncRNA RP11-288L9.4 (lncRNA-IFI6) based on predicted secondary structure. Selected gene mRNAs and their proteins, together with HCV infection, in Huh7.5.1 cells and primary human hepatocytes (PHHs) were monitored by quantitative real-time PCR (qRT-PCR) and western blot. We obtained 7,901 lncRNAs from RNAseq. A total of 1,062 host-encoded lncRNAs were significantly differentially regulated by IFNα treatment. We found that lncRNA-IFI6 gRNA significantly inhibited HCV infection compared with negative gRNA control. The expression of the antiviral ISG IFI6 was significantly increased following lncRNA-IFI6 gRNA editing compared with negative gRNA control in Japanese fulminant hepatitis 1 (JFH1)-infected Huh7.5.1 cells and PHHs. We observed that lncRNA-IFI6 regulation of HCV was independent of Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling. lncRNA-IFI6 negatively regulated IFI6 promoter function through histone modification. Overexpression of the truncated spatial domain or full-length lncRNA-IFI6 inhibited IFI6 expression and increased HCV replication. Conclusion: A lncRNA, lncRNA-IFI6, regulates antiviral innate immunity in the JFH1 HCV infection model. lncRNA-IFI6 regulates HCV infection independently of the JAK-STAT pathway. lncRNA-IFI6 exerts its regulatory function via promoter activation and histone modification of IFI6 through its spatial domain.
Authors: Wenyu Lin; Wei-Lun Tsai; Run-Xuan Shao; Guoyang Wu; Lee F Peng; Lydia L Barlow; Woo Jin Chung; Leiliang Zhang; Hong Zhao; Jae-Young Jang; Raymond T Chung Journal: Gastroenterology Date: 2010-03-12 Impact factor: 22.682
Authors: Y Itsui; N Sakamoto; M Kurosaki; N Kanazawa; Y Tanabe; T Koyama; Y Takeda; M Nakagawa; S Kakinuma; Y Sekine; S Maekawa; N Enomoto; M Watanabe Journal: J Viral Hepat Date: 2006-10 Impact factor: 3.728
Authors: M J de Veer; M Holko; M Frevel; E Walker; S Der; J M Paranjape; R H Silverman; B R Williams Journal: J Leukoc Biol Date: 2001-06 Impact factor: 4.962
Authors: Wenyu Lin; Won Hyeok Choe; Yoichi Hiasa; Yoshitaka Kamegaya; Jason T Blackard; Emmett V Schmidt; Raymond T Chung Journal: Gastroenterology Date: 2005-04 Impact factor: 22.682
Authors: Glenn Randall; Limin Chen; Maryline Panis; Andrew K Fischer; Brett D Lindenbach; Jing Sun; Jenny Heathcote; Charles M Rice; Aled M Edwards; Ian D McGilvray Journal: Gastroenterology Date: 2006-08-22 Impact factor: 22.682
Authors: Michael W Fried; Mitchell L Shiffman; K Rajender Reddy; Coleman Smith; George Marinos; Fernando L Gonçales; Dieter Häussinger; Moises Diago; Giampiero Carosi; Daniel Dhumeaux; Antonio Craxi; Amy Lin; Joseph Hoffman; Jian Yu Journal: N Engl J Med Date: 2002-09-26 Impact factor: 91.245
Authors: Stephanos J Hadziyannis; Hoel Sette; Timothy R Morgan; Vijayan Balan; Moises Diago; Patrick Marcellin; Giuliano Ramadori; Henry Bodenheimer; David Bernstein; Mario Rizzetto; Stefan Zeuzem; Paul J Pockros; Amy Lin; Andrew M Ackrill Journal: Ann Intern Med Date: 2004-03-02 Impact factor: 25.391