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Background: Avian infectious bronchitis virus (IBV) is a gammacoronavirus that severely affects the poultry industry worldwide. Long non-coding RNAs (lncRNAs), a subset of non-coding RNAs with a length of more than 200 nucleotides, have been recently recognized as pivotal factors in the pathogenesis of viral infections. However, little is known about the function of lncRNAs in host cultured cells in response to IBV infection.
Results: We used next-generation high throughput sequencing to reveal the expression profiles of mRNAs and lncRNAs in IBV-infected HD11 cells. Compared with the uninfected cells, we identified 153 differently expressed (DE) mRNAs (106 up-regulated mRNAs, 47 down-regulated mRNAs) and 181 DE lncRNAs (59 up-regulated lncRNAs, 122 down-regulated lncRNAs) in IBV-infected HD11 cells. Moreover, gene ontology (GO) and pathway enrichment analyses indicated that DE mRNAs and lncRNAs were mainly involved in cellular innate immunity, amino acid metabolism, and nucleic acid metabolism. In addition, 2,640 novel chicken lncRNAs were identified, and a competitive endogenous RNA (ceRNAs) network centered on gga-miR-30d and miR-146a-5p was established.
Conclusions: The present study identified the expression profiles of mRNAs and lncRNAs during IBV infection and provides new insights into the pathogenesis of IBV.
Keywords
IBV, lncRNA, HD11, coronavirus, chicken, gga-miR-30d, miR-146a-5p
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This is a list of supplementary files associated with this preprint. Click to download.
- Additionalfile1.xlsx
Additional file 1: Differentially expressed mRNA. xlsx
- Additionalfile1.xlsx
Additional file 1: Differentially expressed mRNA. xlsx
- Additionalfile2.xlsx
Additional file 2: Differentially expressed lncRNA. xlsx
- Additionalfile2.xlsx
Additional file 2: Differentially expressed lncRNA. xlsx
- Additionalfile3.xlsx
Additional file 3: Cis-target lncRNA prediction. xlsx
- Additionalfile3.xlsx
Additional file 3: Cis-target lncRNA prediction. xlsx
- Additionalfile4.xlsx
Additional file 4: Trans-target lncRNA prediction. xlsx
- Additionalfile4.xlsx
Additional file 4: Trans-target lncRNA prediction. xlsx
- Additionalfile5.xlsx
Additional file 5: Immune related lncRNAs. xlsx
- Additionalfile5.xlsx
Additional file 5: Immune related lncRNAs. xlsx
- Additionalfile6.xlsx
Additional file 6: lncRNA-miRNA-mRNA network. xlsx
- Additionalfile6.xlsx
Additional file 6: lncRNA-miRNA-mRNA network. xlsx
- Additionalfile11.xlsx
Additional file 11: Immune related lncRNAs . xlsx
- Additionalfile11.xlsx
Additional file 11: Immune related lncRNAs . xlsx
- Additionalfile12.txt
Additional file 12: Prediction of lncRNAs targeting gga miR 30d. xlsx
- Additionalfile12.txt
Additional file 12: Prediction of lncRNAs targeting gga miR 30d. xlsx
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CURRENT STATUS: Published
View the published article at BMC Genomics.
No community comments so far
Editorial decision: Accept
On 27 Dec, 2020
Editor assigned
On 25 Dec, 2020
Submission checks complete
On 25 Dec, 2020
Editor invited
On 25 Dec, 2020
Version (no preprint)
Posted 21 Dec, 2020
Editorial decision: Minor revision
On 21 Dec, 2020
Editor assigned
On 20 Dec, 2020
Submission checks complete
On 20 Dec, 2020
Editor invited
On 20 Dec, 2020
This version was not preprinted
Version 2
Posted 02 Dec, 2020
No comments provided
Editorial decision: Minor revision
On 14 Dec, 2020
Review #1 received
Received 01 Dec, 2020
Review #2 received
Received 01 Dec, 2020
Reviewer #2 agreed
On 24 Nov, 2020
Reviewers invited
Invitations sent on 23 Nov, 2020
Reviewer #1 agreed
On 23 Nov, 2020
Editor assigned
On 17 Nov, 2020
Submission checks complete
On 17 Nov, 2020
Editor invited
On 17 Nov, 2020
No comments provided
Review #3 received
Received 29 Sep, 2020
Editorial decision: Major revision
On 29 Sep, 2020
Review #2 received
Received 28 Sep, 2020
Reviewer #3 agreed
On 09 Sep, 2020
Review #1 received
Received 09 Sep, 2020
Reviewer #1 agreed
On 07 Sep, 2020
Reviewer #2 agreed
On 07 Sep, 2020
Reviewers invited
Invitations sent on 05 Sep, 2020
Editor assigned
On 01 Sep, 2020
Submission checks complete
On 31 Aug, 2020
Editor invited
On 31 Aug, 2020
First submitted
On 29 Aug, 2020
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PDF Downloads: ...
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Subject Areas
Epigenetics & Genomics
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A new preprint design is coming!
We have improved readability, clarity, accessibility, and opportunities for engagement.
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
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
Editorial decision: Accept
On 27 Dec, 2020
Editor assigned
On 25 Dec, 2020
Submission checks complete
On 25 Dec, 2020
Editor invited
On 25 Dec, 2020
Version (no preprint)
Posted 21 Dec, 2020
Editorial decision: Minor revision
On 21 Dec, 2020
Editor assigned
On 20 Dec, 2020
Submission checks complete
On 20 Dec, 2020
Editor invited
On 20 Dec, 2020
This version was not preprinted
Version 2
Posted 02 Dec, 2020
No comments provided
Editorial decision: Minor revision
On 14 Dec, 2020
Review #1 received
Received 01 Dec, 2020
Review #2 received
Received 01 Dec, 2020
Reviewer #2 agreed
On 24 Nov, 2020
Reviewers invited
Invitations sent on 23 Nov, 2020
Reviewer #1 agreed
On 23 Nov, 2020
Editor assigned
On 17 Nov, 2020
Submission checks complete
On 17 Nov, 2020
Editor invited
On 17 Nov, 2020
No comments provided
Review #3 received
Received 29 Sep, 2020
Editorial decision: Major revision
On 29 Sep, 2020
Review #2 received
Received 28 Sep, 2020
Reviewer #3 agreed
On 09 Sep, 2020
Review #1 received
Received 09 Sep, 2020
Reviewer #1 agreed
On 07 Sep, 2020
Reviewer #2 agreed
On 07 Sep, 2020
Reviewers invited
Invitations sent on 05 Sep, 2020
Editor assigned
On 01 Sep, 2020
Submission checks complete
On 31 Aug, 2020
Editor invited
On 31 Aug, 2020
First submitted
On 29 Aug, 2020
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: Avian infectious bronchitis virus (IBV) is a gammacoronavirus that severely affects the poultry industry worldwide. Long non-coding RNAs (lncRNAs), a subset of non-coding RNAs with a length of more than 200 nucleotides, have been recently recognized as pivotal factors in the pathogenesis of viral infections. However, little is known about the function of lncRNAs in host cultured cells in response to IBV infection.
Results: We used next-generation high throughput sequencing to reveal the expression profiles of mRNAs and lncRNAs in IBV-infected HD11 cells. Compared with the uninfected cells, we identified 153 differently expressed (DE) mRNAs (106 up-regulated mRNAs, 47 down-regulated mRNAs) and 181 DE lncRNAs (59 up-regulated lncRNAs, 122 down-regulated lncRNAs) in IBV-infected HD11 cells. Moreover, gene ontology (GO) and pathway enrichment analyses indicated that DE mRNAs and lncRNAs were mainly involved in cellular innate immunity, amino acid metabolism, and nucleic acid metabolism. In addition, 2,640 novel chicken lncRNAs were identified, and a competitive endogenous RNA (ceRNAs) network centered on gga-miR-30d and miR-146a-5p was established.
Conclusions: The present study identified the expression profiles of mRNAs and lncRNAs during IBV infection and provides new insights into the pathogenesis of IBV.
Figure 1
Figure 1
Figure 2
Figure 2
Figure 3
Figure 3
Figure 4
Figure 4
Figure 5
Figure 5
Figure 6
Figure 6
Figure 7
Figure 7
Figure 8
Figure 8
Figure 9
Figure 9
This is a list of supplementary files associated with this preprint. Click to download.
- Additionalfile1.xlsx
Additional file 1: Differentially expressed mRNA. xlsx
- Additionalfile1.xlsx
Additional file 1: Differentially expressed mRNA. xlsx
- Additionalfile2.xlsx
Additional file 2: Differentially expressed lncRNA. xlsx
- Additionalfile2.xlsx
Additional file 2: Differentially expressed lncRNA. xlsx
- Additionalfile3.xlsx
Additional file 3: Cis-target lncRNA prediction. xlsx
- Additionalfile3.xlsx
Additional file 3: Cis-target lncRNA prediction. xlsx
- Additionalfile4.xlsx
Additional file 4: Trans-target lncRNA prediction. xlsx
- Additionalfile4.xlsx
Additional file 4: Trans-target lncRNA prediction. xlsx
- Additionalfile5.xlsx
Additional file 5: Immune related lncRNAs. xlsx
- Additionalfile5.xlsx
Additional file 5: Immune related lncRNAs. xlsx
- Additionalfile6.xlsx
Additional file 6: lncRNA-miRNA-mRNA network. xlsx
- Additionalfile6.xlsx
Additional file 6: lncRNA-miRNA-mRNA network. xlsx
- Additionalfile11.xlsx
Additional file 11: Immune related lncRNAs . xlsx
- Additionalfile11.xlsx
Additional file 11: Immune related lncRNAs . xlsx
- Additionalfile12.txt
Additional file 12: Prediction of lncRNAs targeting gga miR 30d. xlsx
- Additionalfile12.txt
Additional file 12: Prediction of lncRNAs targeting gga miR 30d. xlsx
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