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Research article
xin yang
Key Laboratory of Bio Resources and Eco Environment, Ministry of Education, College of Life Science, 7 Sichuan University, Chengdu 610064, China 8 2 Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Avian infectious bronchitis virus (IBV) is a gammacoronavirus that seriously affects the world's poultry industry Long non coding RNAs (lncRNAs), a subset of non coding RNAs greater than 200 nucleotides in length, have been recently recognized as pivotal factors during the pathogenesis of viral infection. However, how lncRNAs in host cul tured cells respond to IBV infection was little known. Herein, we detected the expression profiles of the mRNAs and lncRNAs in IBV infected HD11 cells.
Results: By RNA seq, 2640 novel lncRNAs were identified, and 181 lncRNAs (59 up regulated lncRNAs , 122 down regulated lncRNAs) exhibited significant difference in expression levels in IBV infected HD11 cells compared with the uninfected. Based on the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) data bases, the significant diff erentially expressed (DE) lncRNAs, such as MSTRG.25416.43, MSTRG.6458.31, MSTRG.14220.1 and MSTRG.21445.2, were mainly involved in the regulation of cellular innate immunity and amino acid, nucleic acid metabolism. In addition, 30 DE lncRNAs were screened out, and these lncRNAs may interact with gga miR 30d to regulate IBV replication.
Conclusions:
Our results provided novel insights into the functions of lncRNAs and the possible pathogenic mechanism following IBV infection.
Keywords
IBV, lncRNA, HD11, Coronavirus, chicken, gga miR 30d, RNA seq
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
The full text of this article is available to read as a PDF.
This is a list of supplementary files associated with this preprint. Click to download.
- Additionalfile10figure7.pdf
Additional file 10: Figure7. The i nteraction network of ten DE lncRNAs and immune related targets in 525 IBV infected chicken HD11 cells. The red node denotes lncRNA and the blue node represents immune related 526 gene. pdf 527 Additional file 11:
- Additionalfile9figure6.pdf
Additional file 9: Figure 6. Validation of RNA seq data by quantitative real time PCR (qPCR). qPCR results of 522 selected mRNAs (A) and lncRNAs (B) in chicken HD11 cells infected by IBV. *p < 0.05, **p < 0.01. pdf
- Additionalfile7figure5.pdf
Additional file 7: Figure 5 . The GO and KEGG enrichment analyses (A) The top 10 G O BP, 5 GO MF and 5 516 GO CC terms of DEGs. (B) The top 20 KEGG terms of DEGs. (C) The top 10 GO BP, 5 GO MF and 5 GO CC 517 terms of the target genes of DE lncRNAs. (D) The KEGG terms of the target genes of DE lncRNAs. pdf
- Additionalfile6figure4.pdf
Additional file 6: Figure 4. Co expression network of DE lncRNA mRNA based on Pearson’s correlation 512 coefficient. The top 10 DE lncRNAs and their 50 most frequently altered relative mRNAs with 174 connection 513 edges in IBV infected HD11 cells. The red node denotes lncRNA and the blue node represents genes. pdf
- Additionalfile3figure3.pdf
Additional file 3: Figure 3. Differentially expressed genes ( DEGs and differentially expressed ( DE lncRNAs 503 analysis . Exp (IBV infected HD11 cells) vs CK (mock infected HD11 cells) (A, C) H eat map and M A map for 504 mRNAs expression in control and IBV stimulated avian HD11 cells at 36 h post infection. (B, D) Heat map and 505 M A map for lncRNAs in control and IBV stimulated avian HD11 cells at 36 h post infection. pdf
- Additionalfile2figure2.pdf
Additional file 2: Figure 2. Novel lncRNAs prediction and characterization. (A) Three different colored circles 496 represent three different lncRNA prediction software. The overlapping areas of the Venn diagrams represent the 497 numb er of the most credible newly identified lncRNAs. (B) Distribution of the number of transcript in the 498 lncRNAs and mRNAs in chicken HD11 cells. (C) Distribution of the number of exons in the lncRNAs and 499 mRNAs in chicken HD11 cells. (D) Distribution of trans cript lengths in the lncRNAs and mRNAs in chicken 500 HD11 cells. pdf
- additionalfile1figure1.pdf
Additional file 1: Figure 1 Indirect Immunofluorescence Assay (IFA) of HD11 cells infected by IBV. Cells were 491 fixed at indicate time, and virally infected cells were visualized by immunofluorescence (IF) staining of IBV N 492 protein (red). Cell nuclei were visualized by DAPI staining. Merge is an overlap of DAPI and NP (amplification: 493 200x). pdf
- Additionalfile8table1.pdf
Additional file 8: Table 1. Primers for qPCR pdf
- Additionalfile13figure8.pdf
Additional file 13: Figure 8. The interaction network of gga miR 30d and related lncRNAs in IBV infected HD11 532 cells. The red node denotes lncRNAs. The yellow node denotes microRNA and the blue node represen ts gene. pdf
- Additionalfile12.txt
Additional file 12: Prediction of lncRNAs targeting gga miR 30d. xlsx
- Additionalfile11.xlsx
Additional file 11: Immune related lncRNAs . xlsx
- Additionalfile5.xlsx
Additional file 5: Trans target lncRNA prediction xlsx
- Additionalfile4.xlsx
Additional file 4: Cis target lncRNA prediction xlsx
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Editorial decision: Major revision
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Received 28 Sep, 2020
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Received 09 Sep, 2020
Reviewer #1 agreed
On 07 Sep, 2020
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On 07 Sep, 2020
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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
xin yang
Key Laboratory of Bio Resources and Eco Environment, Ministry of Education, College of Life Science, 7 Sichuan University, Chengdu 610064, China 8 2 Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu 610064, China
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
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
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
Version 1
Posted 08 Sep, 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 seriously affects the world's poultry industry Long non coding RNAs (lncRNAs), a subset of non coding RNAs greater than 200 nucleotides in length, have been recently recognized as pivotal factors during the pathogenesis of viral infection. However, how lncRNAs in host cul tured cells respond to IBV infection was little known. Herein, we detected the expression profiles of the mRNAs and lncRNAs in IBV infected HD11 cells.
Results: By RNA seq, 2640 novel lncRNAs were identified, and 181 lncRNAs (59 up regulated lncRNAs , 122 down regulated lncRNAs) exhibited significant difference in expression levels in IBV infected HD11 cells compared with the uninfected. Based on the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) data bases, the significant diff erentially expressed (DE) lncRNAs, such as MSTRG.25416.43, MSTRG.6458.31, MSTRG.14220.1 and MSTRG.21445.2, were mainly involved in the regulation of cellular innate immunity and amino acid, nucleic acid metabolism. In addition, 30 DE lncRNAs were screened out, and these lncRNAs may interact with gga miR 30d to regulate IBV replication.
Conclusions:
Our results provided novel insights into the functions of lncRNAs and the possible pathogenic mechanism following IBV infection.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
The full text of this article is available to read as a PDF.
This is a list of supplementary files associated with this preprint. Click to download.
- Additionalfile10figure7.pdf
Additional file 10: Figure7. The i nteraction network of ten DE lncRNAs and immune related targets in 525 IBV infected chicken HD11 cells. The red node denotes lncRNA and the blue node represents immune related 526 gene. pdf 527 Additional file 11:
- Additionalfile9figure6.pdf
Additional file 9: Figure 6. Validation of RNA seq data by quantitative real time PCR (qPCR). qPCR results of 522 selected mRNAs (A) and lncRNAs (B) in chicken HD11 cells infected by IBV. *p < 0.05, **p < 0.01. pdf
- Additionalfile7figure5.pdf
Additional file 7: Figure 5 . The GO and KEGG enrichment analyses (A) The top 10 G O BP, 5 GO MF and 5 516 GO CC terms of DEGs. (B) The top 20 KEGG terms of DEGs. (C) The top 10 GO BP, 5 GO MF and 5 GO CC 517 terms of the target genes of DE lncRNAs. (D) The KEGG terms of the target genes of DE lncRNAs. pdf
- Additionalfile6figure4.pdf
Additional file 6: Figure 4. Co expression network of DE lncRNA mRNA based on Pearson’s correlation 512 coefficient. The top 10 DE lncRNAs and their 50 most frequently altered relative mRNAs with 174 connection 513 edges in IBV infected HD11 cells. The red node denotes lncRNA and the blue node represents genes. pdf
- Additionalfile3figure3.pdf
Additional file 3: Figure 3. Differentially expressed genes ( DEGs and differentially expressed ( DE lncRNAs 503 analysis . Exp (IBV infected HD11 cells) vs CK (mock infected HD11 cells) (A, C) H eat map and M A map for 504 mRNAs expression in control and IBV stimulated avian HD11 cells at 36 h post infection. (B, D) Heat map and 505 M A map for lncRNAs in control and IBV stimulated avian HD11 cells at 36 h post infection. pdf
- Additionalfile2figure2.pdf
Additional file 2: Figure 2. Novel lncRNAs prediction and characterization. (A) Three different colored circles 496 represent three different lncRNA prediction software. The overlapping areas of the Venn diagrams represent the 497 numb er of the most credible newly identified lncRNAs. (B) Distribution of the number of transcript in the 498 lncRNAs and mRNAs in chicken HD11 cells. (C) Distribution of the number of exons in the lncRNAs and 499 mRNAs in chicken HD11 cells. (D) Distribution of trans cript lengths in the lncRNAs and mRNAs in chicken 500 HD11 cells. pdf
- additionalfile1figure1.pdf
Additional file 1: Figure 1 Indirect Immunofluorescence Assay (IFA) of HD11 cells infected by IBV. Cells were 491 fixed at indicate time, and virally infected cells were visualized by immunofluorescence (IF) staining of IBV N 492 protein (red). Cell nuclei were visualized by DAPI staining. Merge is an overlap of DAPI and NP (amplification: 493 200x). pdf
- Additionalfile8table1.pdf
Additional file 8: Table 1. Primers for qPCR pdf
- Additionalfile13figure8.pdf
Additional file 13: Figure 8. The interaction network of gga miR 30d and related lncRNAs in IBV infected HD11 532 cells. The red node denotes lncRNAs. The yellow node denotes microRNA and the blue node represen ts gene. pdf
- Additionalfile12.txt
Additional file 12: Prediction of lncRNAs targeting gga miR 30d. xlsx
- Additionalfile11.xlsx
Additional file 11: Immune related lncRNAs . xlsx
- Additionalfile5.xlsx
Additional file 5: Trans target lncRNA prediction xlsx
- Additionalfile4.xlsx
Additional file 4: Cis target lncRNA prediction xlsx
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