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Research article
Xiaofei Zhang
Corresponding Author
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Background: Duck hepatitis A virus type 3 (DHAV-3) is one of the most harmful pathogens in the duck industry. However, the molecular mechanism underlying DHAV-3 infection in ducklings is remain poorly understood. To elucidate the genetic regulatory network for miRNA-mRNA and the signaling pathways involved in DHAV-3 infection in ducklings, we conducted global miRNA and mRNA expression profiling of duckling liver tissues infected with lethal DHAV-3 using high-throughput sequencing. Results: We found 156 differentially expressed miRNAs (DEMs) and 7717 differentially expressed miRNAs (DEGs) between mock-infected and DHAV-3-infected duckling livers. A total of 19,606 miRNA-mRNA pairs with negatively correlated expression patterns were identified in miRNA-mRNA networks constructed on the basis of these DEMs and DEGs. Moreover, immune-related pathways including the cytokine-cytokine receptor interaction, apoptosis, Toll-like receptor, Jak-STAT, and RIG-I-like receptor signaling pathway were significantly enriched through analyzing functions of mRNAs in the network in response to DHAV-3 infection. Besides, apl-miR-32-5p, apl-miR-125-5p, apl-miR-128-3p, apl-miR-460-5p, and novel-m0012-3p were identified as potential regulators in the immune-related signaling pathways during the DHAV-3 infection. Conclusions: To our knowledge, this is the first report on integrated analysis of miRNA-seq and mRNA-seq in DHAV-3-infected ducklings. The results indicated the important roles of miRNAs in regulating immune response genes and revealed the immune related miRNA-mRNA regulation network in the DHAV-3-infected duckling liver. Our findings may provide valuable information to further investigate the roles of miRNAs and their target genes in DHAV-3 replication and pathogenesis; additionally, they may offer clues for further understanding host-virus interactions.
Keywords
Duck hepatitis A virus type 3, miRNA-seq, mRNA-seq, miRNA-mRNA network, Innate immune response, Host-virus interactions
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Received 03 Dec, 2019
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On 03 Dec, 2019
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Received 03 Dec, 2019
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On 04 Oct, 2019
Review #3 received
Received 03 Oct, 2019
Review #2 received
Received 29 Sep, 2019
Reviewer #3 agreed
On 23 Sep, 2019
Review #1 received
Received 23 Sep, 2019
Reviewer #2 agreed
On 14 Sep, 2019
Reviewer #1 agreed
On 13 Sep, 2019
Reviewers invited
Invitations sent on 12 Sep, 2019
Editor assigned
On 11 Sep, 2019
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On 10 Sep, 2019
Editor invited
On 10 Sep, 2019
No comments provided
Editorial decision: Revise before sending to peer reviewers
On 26 Aug, 2019
Editor invited
On 20 Aug, 2019
Submission checks complete
On 19 Aug, 2019
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On 29 Jul, 2019
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A new preprint design is coming!
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See the published version of this preprint at BMC Genomics.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Xiaofei Zhang
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Genomics.
No community comments so far
Review #3 received
Received 09 Dec, 2019
Reviewers invited
Invitations sent on 03 Dec, 2019
Reviewer #1 agreed
On 03 Dec, 2019
Reviewer #2 agreed
On 03 Dec, 2019
Review #1 received
Received 03 Dec, 2019
Reviewer #3 agreed
On 03 Dec, 2019
Review #2 received
Received 03 Dec, 2019
Editor assigned
On 02 Dec, 2019
Editor invited
On 01 Dec, 2019
Submission checks complete
On 01 Dec, 2019
Version 2
Posted 15 Oct, 2019
No comments provided
Editorial decision: Major revision
On 04 Oct, 2019
Review #3 received
Received 03 Oct, 2019
Review #2 received
Received 29 Sep, 2019
Reviewer #3 agreed
On 23 Sep, 2019
Review #1 received
Received 23 Sep, 2019
Reviewer #2 agreed
On 14 Sep, 2019
Reviewer #1 agreed
On 13 Sep, 2019
Reviewers invited
Invitations sent on 12 Sep, 2019
Editor assigned
On 11 Sep, 2019
Submission checks complete
On 10 Sep, 2019
Editor invited
On 10 Sep, 2019
No comments provided
Editorial decision: Revise before sending to peer reviewers
On 26 Aug, 2019
Editor invited
On 20 Aug, 2019
Submission checks complete
On 19 Aug, 2019
Editor assigned
On 29 Jul, 2019
First submitted
On 25 Jul, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Genomics.
Background: Duck hepatitis A virus type 3 (DHAV-3) is one of the most harmful pathogens in the duck industry. However, the molecular mechanism underlying DHAV-3 infection in ducklings is remain poorly understood. To elucidate the genetic regulatory network for miRNA-mRNA and the signaling pathways involved in DHAV-3 infection in ducklings, we conducted global miRNA and mRNA expression profiling of duckling liver tissues infected with lethal DHAV-3 using high-throughput sequencing. Results: We found 156 differentially expressed miRNAs (DEMs) and 7717 differentially expressed miRNAs (DEGs) between mock-infected and DHAV-3-infected duckling livers. A total of 19,606 miRNA-mRNA pairs with negatively correlated expression patterns were identified in miRNA-mRNA networks constructed on the basis of these DEMs and DEGs. Moreover, immune-related pathways including the cytokine-cytokine receptor interaction, apoptosis, Toll-like receptor, Jak-STAT, and RIG-I-like receptor signaling pathway were significantly enriched through analyzing functions of mRNAs in the network in response to DHAV-3 infection. Besides, apl-miR-32-5p, apl-miR-125-5p, apl-miR-128-3p, apl-miR-460-5p, and novel-m0012-3p were identified as potential regulators in the immune-related signaling pathways during the DHAV-3 infection. Conclusions: To our knowledge, this is the first report on integrated analysis of miRNA-seq and mRNA-seq in DHAV-3-infected ducklings. The results indicated the important roles of miRNAs in regulating immune response genes and revealed the immune related miRNA-mRNA regulation network in the DHAV-3-infected duckling liver. Our findings may provide valuable information to further investigate the roles of miRNAs and their target genes in DHAV-3 replication and pathogenesis; additionally, they may offer clues for further understanding host-virus interactions.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
This is a list of supplementary files associated with this preprint. Click to download.
- Additionalfile13.xlsx
- Additionalfile4.xlsx
- NC3RsARRIVEGuidelinesChecklist.docx
- Additionalfile8.png
- Additionalfile9.xlsx
- Additionalfile10.xlsx
- Additionalfile12.xlsx
- Additionalfile7.xlsx
- Additionalfile3.xlsx
- Additionalfile5.xlsx
- Additionalfile6.xlsx
- Additionalfile2.xlsx
- Additionalfile1.xlsx
- Additionalfile11.pdf
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