Deep sequencing of the mouse lung transcriptome reveals distinct long non-coding RNAs expression associated with the high virulence of H5N1 avian influenza virus in mice

ABSTRACT

Long non-coding RNAs (lncRNAs) play multiple key regulatory roles in various biological processes. However, their function in influenza A virus (IAV) pathogenicity remains largely unexplored. Here, using next generation sequencing, we systemically compared the whole-transcriptome response of the mouse lung infected with either the highly pathogenic (A/Chicken/Jiangsu/k0402/2010, CK10) or the nonpathogenic (A/Goose/Jiangsu/k0403/2010, GS10) H5N1 virus. A total of 126 significantly differentially expressed (SDE) lncRNAs from three replicates were identified to be associated with the high virulence of CK10, whereas 94 SDE lncRNAs were related with GS10. Functional category analysis suggested that the SDE lncRNAs-coexpressed mRNAs regulated by CK10 were highly related with aberrant and uncontrolled inflammatory responses. Further canonical pathway analysis also confirmed that these targets were highly enriched for inflammatory-related pathways. Moreover, 9 lncRNAs and 17 lncRNAs-coexpressed mRNAs associated with a large number of targeted genes were successfully verified by qRT-PCR. One targeted lncRNA (NONMMUT011061) that was markedly activated and correlated with a great number of mRNAs was selected for further in-depth analysis, including predication of transcription factors, potential interacting proteins, genomic location, coding ability and construction of the secondary structure. More importantly, NONMMUT011061 was also distinctively stimulated during the highly pathogenic H5N8 virus infection in mice, suggesting a potential universal role of NONMMUT011061 in the pathogenesis of different H5 IAV. Altogether, these results provide a subset of lncRNAs that might play important roles in the pathogenesis of influenza virus and add the lncRNAs to the vast repertoire of host factors utilized by IAV for infection and persistence.

KEYWORDS:

• H5N1 influenza virus
• deep sequencing
• lncRNAs
• innate immune response
• pathogenesis

Disclosure statement

No potential conflict of interest was reported by the authors.

Supplementary material

Supplementary data for this article can be accessed here

Additional information

Funding

This work was supported by the National Key Research and Development Project of China (2016YFD0500202-1 and 2016YFD0501601), by the Jiangsu Provincial Natural Science Foundation of China (BK20150444), by the National Natural Science Foundation of China (31502076), by the Postdoctoral Science Foundation of Jiangsu Province, China (1501015B), by the Special Financial Grant from the China Postdoctoral Science Foundation (2016T90515), by the ‘Qing Lan Project’ of Higher Education Institutions of Jiangsu Province, China, by the ‘High-end talent support program’ of Yangzhou University, China, by the Natural Science Foundation of the Higher Education Institutions of Jiangsu Province, China (15KJB230006), by the Earmarked Fund for China Agriculture Research System (CARS-40) and by A Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

Notes on contributors

Xiufan Liu

Conceived and designed the experiments: JH, ZH and XL. Performed the experiments: JH, ZG, ZH, YL and CM. Analyzed the data: JH, ZH, XW, MG, XL, SH, SC, DP and XJ. Contributed reagents/materials/analysis tools: XW, MG, XL, SH, SC, DP and XJ. Specifically, DP and XJ provided the IPA software and contribute to partial analysis work; XW and MG contribute to the TRANSFAC and UCSC analysis method and analysis; XL and SH involved in providing PhyloCSF and RNAfold WebServer analysis tools and contribute to partial analysis work; SC contributes to the catRAPID algorithm analysis. Wrote the paper: JH, ZH and XL.