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. 2020 Oct 19;21(1):724.
doi: 10.1186/s12864-020-07129-1.

Genome-wide analysis of differentially expressed mRNAs, lncRNAs, and circRNAs in chicken bursae of Fabricius during infection with very virulent infectious bursal disease virus

Xuewei Huang  1 , Junyan Zhang  1 , Zengsu Liu  1 , Meng Wang  1 , Xiaolong Fan  1 , Li Wang  1   2 , Han Zhou  1   2 , Yanping Jiang  1   2 , Wen Cui  1   2 , Xinyuan Qiao  1   2 , Yigang Xu  1   2 , Yijing Li  1   2 , Lijie Tang  3   4
Affiliations

Genome-wide analysis of differentially expressed mRNAs, lncRNAs, and circRNAs in chicken bursae of Fabricius during infection with very virulent infectious bursal disease virus

Xuewei Huang et al. BMC Genomics. .

Abstract

Background: Infectious bursal disease virus (IBDV) causes acute, highly contagious, immunosuppressive, and lethal infectious disease in young chickens and mainly infects the bursa of Fabricius (BF). To investigate interactions between IBDV and its host, RNA sequencing was applied to analyze the responses of the differentially expressed transcriptional profiles of BF infected by very virulent IBDV (vvIBDV).

Results: In total, 317 upregulated and 94 downregulated mRNAs were found to be significantly differentially expressed in infected chickens, compared to controls. Long non-coding RNA (lncRNA) and circular RNA (circRNA) alterations were identified in IBDV-infected chickens, and significantly different expression was observed in 272 lncRNAs and 143 circRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed to assess the functions of significantly dysregulated genes, which showed that the JAK-STAT signaling pathway, the NOD-like receptor signaling pathway, and apoptosis may be activated by IBDV infection. We predicted interactions between differentially expressed genes and produced lncRNA-mRNA and circRNA-miRNA-mRNA regulator network.

Conclusions: The present study identified the expression profiles of mRNAs, lncRNAs, and circRNAs during vvIBDV infection and provides new insights into the pathogenesis of IBDV and antiviral immunity of the host.

Keywords: Bursa of Fabricius; Infectious bursal disease virus; circRNAs; lncRNAs; mRNAs.

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Conflict of interest statement

The authors have no conflicts of interest to declare.

Figures

Fig. 1
Fig. 1
Screening and classification of lncRNAs in chicken BF. a The novel lncRNAs were mainly classified as intergenic lncRNAs, bidirectional lncRNAs, and sense lncRNAs. b CNCI, CPC, and the SwissProt database were used to analyze the coding potential of the novel lncRNAs. RNAs identified by all three analytical tools were chosen as candidate lncRNAs. c The novel lncRNAs were mainly classified as intergenic lncRNAs, sense lncRNAs, bidirectional lncRNAs, and antisense lncRNAs
Fig. 2
Fig. 2
Venn diagram showing the number of overlapping genes in the IBDV-infected group and the control group. a mRNAs, b lncRNAs, and c circRNAs
Fig. 3
Fig. 3
Histogram of the differentially expressed mRNAs (a), lncRNAs (b) and circRNAs (c) in the two groups. The red and green columns indicate the significantly upregulated and downregulated genes (p < 0.05), respectively
Fig. 4
Fig. 4
Volcano plots of the differentially expressed mRNAs (a), lncRNAs (b), and circRNAs (c). The red and green dots indicate the significantly upregulated and downregulated genes (p < 0.05), respectively. The black dots indicate the genes that were not significantly differentially expressed (p > 0.05)
Fig. 5
Fig. 5
Heatmap of differentially expressed mRNAs (a), lncRNAs (b), and circRNAs (c). The coloration gradient from blue to red indicates low to high expression level. All biological replicates were pooled to identify the DEGs based on a threshold fold change > 2 (mRNAs and circRNAs) or fold change > 1.5 (lncRNAs) at p < 0.05
Fig. 6
Fig. 6
Comparison of mRNA and lncRNA characteristics. a Number of exons in the mRNAs and lncRNAs. b Distribution of transcript lengths in the mRNAs and lncRNAs. The horizontal axis indicates the length of the transcripts, and the vertical axis indicates the abundance. c Number of open reading frames (ORFs) in the mRNAs and lncRNAs
Fig. 7
Fig. 7
Gene ontology (GO) analysis of the differentially expressed mRNAs in IBDV-infected chicken BF. a-c Directed acyclic graph showing the significantly enriched biological processes, cellular components, and molecular functions of the differentially expressed mRNAs. d Number of genes in GO terms are shown in the histogram
Fig. 8
Fig. 8
Gene ontology analysis of the differentially expressed lncRNAs (a) and circRNAs (b) in the two groups. The green, red, and blue column indicate biological processes, cellular components, and molecular functions, respectively
Fig. 9
Fig. 9
Kyoto Encyclopedia of Genes and Genomes pathway enrichment of the differentially expressed mRNAs (a), lncRNAs (b), and circRNAs (c) in the two groups. The vertical axis indicates the pathways, and the horizontal axis represents the Rich factor. The dot size indicates the number of DEGs in the pathway, and the coloration corresponds to the Q-value range
Fig. 10
Fig. 10
LncRNA-mRNA regulatory networks. The red ellipses indicate the differentially expressed lncRNAs, and the green ellipses indicate the differentially expressed mRNAs
Fig. 11
Fig. 11
CircRNA-miRNA-mRNA regulatory networks. The red triangles, blue diamonds, and purple ellipses indicate the differentially expressed circRNA, miRNAs, and mRNAs, respectively
Fig. 12
Fig. 12
Validation of the differentially expressed mRNAs (a), lncRNAs (b), and circRNAs (c) by RT-qPCR. RT-qPCR experiments were performed in triplicate
See this image and copyright information in PMC

References

    1. Li Z, Wang Y, Li X, Li X, Cao H, Zheng SJ. Critical roles of glucocorticoid-induced leucine zipper in infectious bursal disease virus (IBDV)-induced suppression of type I interferon expression and enhancement of IBDV growth in host cells via interaction with VP4. J Virol. 2013;87(2):1221–1231. doi: 10.1128/JVI.02421-12. - DOI - PMC - PubMed
    1. Vukea PR, Willows-Munro S, Horner RF, Coetzer TH. Phylogenetic analysis of the polyprotein coding region of an infectious South African bursal disease virus (IBDV) strain. Infect Genet Evol. 2014;21:279–286. doi: 10.1016/j.meegid.2013.11.017. - DOI - PubMed
    1. McFerran JB, McNulty MS, McKillop ER, Connor TJ, McCracken RM, Collins DS, Allan GM. Isolation and serological studies with infectious bursal disease viruses from fowl, turkeys and ducks: demonstration of a second serotype. Avian Pathol. 1980;9(3):395–404. doi: 10.1080/03079458008418423. - DOI - PubMed
    1. Ruby T, Whittaker C, Withers DR, Chelbi-Alix MK, Morin V, Oudin A, Young JR, Zoorob R. Transcriptional profiling reveals a possible role for the timing of the inflammatory response in determining susceptibility to a viral infection. J Virol. 2006;80(18):9207–9216. doi: 10.1128/JVI.00929-06. - DOI - PMC - PubMed
    1. Becht H, Muller H. Infectious bursal disease--B cell dependent immunodeficiency syndrome in chickens. Behring Inst Mitt. 1991;89:217–225. - PubMed

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