RNA Sequencing Reveals circRNA Expression Profiles in Chicken DF1 Cells Infected with H5N1 Influenza Virus
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Cell Culture and Viral Infection
2.2. RNA Sequencing
2.3. Sequencing Data Analysis
2.4. GO and KEGG Pathway Analysis
3. Results
3.1. Characteristics of circRNAs
3.2. Identification of Differentially Expressed circRNAs
3.3. Functional Analysis of the Parental Genes of DE circRNAs
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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CircRNA | Regulation | Gene Symbol | Terms/Pathways | Annotated Database |
---|---|---|---|---|
CIRI_circ_006230 | down | - | ||
CIRI_circ_0013435 | down (6:0); up (12:0; 20:0) | ALKBH8 | ||
CIRI_circ_0011785 | down | - | ||
CIRI_circ_007242 | down | RPL14 | Influenza virus RNA transcription and replication. | Gene cards |
CIRI_circ_002201 | down | - | ||
CIRI_circ_008390 | down | - | ||
CIRI_circ_006022 | down | - | ||
CIRI_circ_008353 | down | CUX1 | Component of nf-munr repressor; binds to the matrix attachment regions (MARs) of the immunoglobulin heavy chain enhancer. Represses T-cell receptor beta enhancer function by binding to MARbeta. | UniProtKB/Swiss-Prot |
CIRI_circ_008531 | up | COL3A1 | ||
CIRI_circ_0011293 | down | CANX | Influenza virus RNA transcription and replication, and the innate immune system. | UniProtKB/Swiss-Prot |
CIRI_circ_003013 | down | COL3A1 | ||
CIRI_circ_008959 | down | - | ||
CIRI_circ_002330 | up | AZIN1 | ||
CIRI_circ_0095 | down (6:0); up (12:0; 20:0) | - | ||
CIRI_circ_005370 | down | - | ||
CIRI_circ_007453 | up | - | ||
CIRI_circ_00136 | down (6:0; 12:0); up (20:0) | - | ||
CIRI_circ_004926 | up | TTC28 | ||
CIRI_circ_005366 | up | AKIRIN2 | Required for the innate immune response. | UniProtKB/Swiss-Prot |
CIRI_circ_0013703 | up | MAFG | ||
CIRI_circ_003547 | up | RPS6KA5 | Activates TLR4 signaling and CNTF signaling. | UniProtKB/Swiss-Prot |
CIRI_circ_003861 | down | VNN2 | ||
CIRI_circ_00491 | down (6:0); up (12:0; 20:0) | DROSHA | ||
CIRI_circ_0013304 | down | IGF1R | ||
CIRI_circ_0014096 | down | - | ||
CIRI_circ_004792 | down | TCP1 | ||
CIRI_circ_0010535 | down | - | ||
CIRI_circ_003044 | up | ATRNL1 | ||
CIRI_circ_008077 | up | - | ||
CIRI_circ_0012305 | up | CD2AP | May play a role in receptor clustering and cytoskeletal polarity in the junction between T-cell and antigen-presenting cell. | UniProtKB/Swiss-Prot |
CIRI_circ_008738 | down | LARGE1 | ||
CIRI_circ_002188 | up | DNAJB6 | ||
CIRI_circ_007562 | up | QKI | HIV Life Cycle and Oncogenic MAPK signaling | GeneCards |
CIRI_circ_002400 | up | TMEM214 | ||
CIRI_circ_009497 | up | MPP6 | ||
CIRI_circ_0014262 | down | - |
Group | Enriched Pathways | Enriched Genes | p-Value |
---|---|---|---|
6-h infected group | Dorsoventral axis formation | 3 | 3.40 × 10−2 |
Focal adhesion | 7 | 3.50 × 10−2 | |
Wnt signaling pathway | 5 | 7.40 × 10−2 | |
FoxO signaling pathway | 5 | 7.60 × 10−2 | |
12-h infected group | Focal adhesion | 11 | 1.20 × 10−2 |
Adherens junction | 6 | 2.20 × 10−2 | |
SNARE interactions in vesicular transport | 4 | 3.10 × 10−2 | |
Tight junction | 6 | 3.40 × 10−2 | |
Cell cycle | 7 | 4.60 × 10−2 | |
Ribosome biogenesis in eukaryotes | 5 | 7.10 × 10−2 | |
ECM–receptor interaction | 5 | 9.50 × 10−2 | |
20-h infected group | MAPK signaling pathway | 20 | 8.60 × 10−4 |
Oocyte meiosis | 12 | 8.90 × 10−4 | |
Endocytosis | 17 | 1.60 × 10−2 | |
Focal adhesion | 15 | 1.80 × 10−2 | |
Adherens junction | 8 | 2.00 × 10−2 | |
Ubiquitin mediated proteolysis | 11 | 2.80 × 10−2 | |
Regulation of actin cytoskeleton | 14 | 2.80 × 10−2 | |
Progesterone-mediated oocyte maturation | 8 | 3.30 × 10−2 | |
Hedgehog signaling pathway | 4 | 5.20 × 10−2 | |
FoxO signaling pathway | 10 | 5.60 × 10−2 | |
mRNA surveillance pathway | 7 | 6.20 × 10−2 | |
Herpes simplex infection | 11 | 6.20 × 10−2 | |
Adrenergic signaling in cardiomyocytes | 9 | 8.70 × 10−2 |
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Chen, L.; Li, G.; Tian, Y.; Zeng, T.; Xu, W.; Gu, T.; Lu, L. RNA Sequencing Reveals circRNA Expression Profiles in Chicken DF1 Cells Infected with H5N1 Influenza Virus. Animals 2022, 12, 158. https://doi.org/10.3390/ani12020158
Chen L, Li G, Tian Y, Zeng T, Xu W, Gu T, Lu L. RNA Sequencing Reveals circRNA Expression Profiles in Chicken DF1 Cells Infected with H5N1 Influenza Virus. Animals. 2022; 12(2):158. https://doi.org/10.3390/ani12020158
Chicago/Turabian StyleChen, Li, Guoqin Li, Yong Tian, Tao Zeng, Wenwu Xu, Tiantian Gu, and Lizhi Lu. 2022. "RNA Sequencing Reveals circRNA Expression Profiles in Chicken DF1 Cells Infected with H5N1 Influenza Virus" Animals 12, no. 2: 158. https://doi.org/10.3390/ani12020158
APA StyleChen, L., Li, G., Tian, Y., Zeng, T., Xu, W., Gu, T., & Lu, L. (2022). RNA Sequencing Reveals circRNA Expression Profiles in Chicken DF1 Cells Infected with H5N1 Influenza Virus. Animals, 12(2), 158. https://doi.org/10.3390/ani12020158