Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos)

Lu, Chao; Xing, Yanling; Cai, Han; Shi, Yangguang; Liu, Jinhua; Huang, Yinhua

doi:10.1186/s12864-018-5422-2

Cited by 11 publications

(8 citation statements)

References 36 publications

(43 reference statements)

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“…Accumulated studies demonstrated that viral infection can alter lncRNA expression profile of host (44), including infectious bronchitis virus infection of primary dendritic cells (45), H5N1 influenza viruses infection of ducks (46), and Porcine reproductive and respiratory syndrome virus infection of endometrial epithelial cells (47). In our study, the change of lncRNA expression profile was also observed in DEFs in response to DTMUV infection.…”

Section: Discussionsupporting

confidence: 70%

Differently Expression Analysis and Function Prediction of Long Non-coding RNAs in Duck Embryo Fibroblast Cells Infected by Duck Tembusu Virus

Lin

Yang

et al. 2020

Front. Immunol.

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Duck Tembusu virus (DTMUV), the causative agent of egg-drop syndrome, has caused substantial economic losses to duck industry. DTMUV infection leads to profound changes of host cells, including transcriptome and proteome. However, the lncRNA expression profile and the biological function of lncRNA have not been revealed. Therefore, DTMUV was used to inoculate duck embryo fibroblast cells (DEFs) for high-throughput RNA-sequencing (RNA-Seq). The results showed that 34 and 339 differently expressed lncRNAs were, respectively, identified at 12 and 24 h post-infection (hpi). To analyze their biological functions, target genes in cis were searched and the regulatory network was formed. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the target genes were strongly associated with immune system, signaling molecular and interaction, endocrine system, and signal transduction. The differently expressed lncRNAs were selected and verified by quantitative real-time polymerase chain reaction (RT-qPCR). Our study, for the first time, analyzed a comprehensive lncRNA expression profile in DEFs following DTMUV infection. The analysis provided a view on the important roles of lncRNAs in gene regulation and DTMUV infection.

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Section: Discussionsupporting

confidence: 70%

Differently Expression Analysis and Function Prediction of Long Non-coding RNAs in Duck Embryo Fibroblast Cells Infected by Duck Tembusu Virus

Lin

Yang

et al. 2020

Front. Immunol.

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“…The majority of lncRNAs in the liver and adrenal glands is located in intergenic regions, which is consistent with previous studies performed in other mammalian [ 49 , 50 ], plant [ 51 , 52 ] and fungal [ 53 , 54 ] species. In addition, previous research showed that animal lncRNAs are shorter and have fewer exons than PCGs [ 55 , 56 ], which is in line with our findings (Fig. 3 b and c).…”

Section: Discussionsupporting

confidence: 93%

Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress

Dou

Schenkel

et al. 2021

BMC Genomics

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Background Heat stress (HS) is a major stress event in the life of an animal, with detrimental upshots in production and health. Long-non-coding RNAs (lncRNAs) play an important role in many biological processes by transcriptional regulation. However, no research has been reported on the characterization and functionality of lncRNAs in heat-stressed rats. Results We studied expression levels of lncRNAs in rats during HS, using strand-specific RNA sequencing. Six rats, three in each of Control (22 ± 1 °C) and H120 (42 °C for 120 min) experimental groups, were used to screen for lncRNAs in their liver and adrenal glands. Totally, 4498 and 7627 putative lncRNAs were identified in liver and adrenal glands of the Control and H120 groups, respectively. The majority of lncRNAs were relatively shorter and contained fewer exons than protein-coding transcripts. In total, 482 (174 up-regulated and 308 down-regulated) and 271 (126 up-regulated and 145 down-regulated) differentially-expressed lncRNAs (DElncRNAs, P < 0.05) were identified in the liver and adrenal glands of the Control and H120 groups, respectively. Furthermore, 1274, 121, and 73 target differentially-expressed genes (DEGs) in the liver were predicted to interact with DElncRNAs based on trans−/cis- and sequence similarity regulatory modes. Functional annotation analyses indicated that these DEGs were mostly significantly enriched in insulin signalling, myeloid leukaemia, and glucagon signalling pathways. Similarly, 437, 73 and 41 target DEGs in the adrenal glands were mostly significantly enriched in the cell cycle (trans-prediction) and lysosome pathways (cis-prediction). The DElncRNAs interacting with DEGs that encode heat shock proteins (HSPs) may play an important role in HS response, which include Hsf4, Dnaja1, Dnajb4, Hsph1 and Hspb1 in the liver, and Dnajb13 and Hspb8 in the adrenal glands. The strand-specific RNA sequencing findings were also further verified through RT-qPCR. Conclusions This study is the first to provide a detailed characterization and functional analysis of expression levels of lncRNAs in liver and adrenal glands of heat-stressed rats, which provides basis for further studies on the biological functions of lncRNAs under heat stress in rats and other mammalian species.

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“…In human cells, a long noncoding RNA (lncRNA) Lnczc3h7a also contributes to stabilizing the interaction between TRIM25 and RIG-I CARD domains (Lin et al, 2019). Recently, duck lncRNA were analyzed during HPAI and LPAI infection to determine which were differentially expressed and potentially involved in influenza A control (Lu et al, 2019). This study did not assess whether lnczc3h7a is differentially expressed, nor is it known if duck lnczc3h7a can function in the same manner, but this augmentation by lncRNAs may well be conserved.…”

Section: Trim25mentioning

confidence: 99%

Pattern Recognition Receptor Signaling and Innate Responses to Influenza A Viruses in the Mallard Duck, Compared to Humans and Chickens

Campbell

Magor

2020

Front. Cell. Infect. Microbiol.

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Mallard ducks are a natural host and reservoir of avian Influenza A viruses. While most influenza strains can replicate in mallards, the virus typically does not cause substantial disease in this host. Mallards are often resistant to disease caused by highly pathogenic avian influenza viruses, while the same strains can cause severe infection in humans, chickens, and even other species of ducks, resulting in systemic spread of the virus and even death. The differences in influenza detection and antiviral effectors responsible for limiting damage in the mallards are largely unknown. Domestic mallards have an early and robust innate response to infection that seems to limit replication and clear highly pathogenic strains. The regulation and timing of the response to influenza also seems to circumvent damage done by a prolonged or dysregulated immune response. Rapid initiation of innate immune responses depends on viral recognition by pattern recognition receptors (PRRs) expressed in tissues where the virus replicates. RIG-like receptors (RLRs), Toll-like receptors (TLRs), and Nod-like receptors (NLRs) are all important influenza sensors in mammals during infection. Ducks utilize many of the same PRRs to detect influenza, namely RIG-I, TLR7, and TLR3 and their downstream adaptors. Ducks also express many of the same signal transduction proteins including TBK1, TRIF, and TRAF3. Some antiviral effectors expressed downstream of these signaling pathways inhibit influenza replication in ducks. In this review, we summarize the recent advances in our understanding of influenza recognition and response through duck PRRs and their adaptors. We compare basal tissue expression and regulation of these signaling components in birds, to better understand what contributes to influenza resistance in the duck.

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Identification and analysis of long non-coding RNAs in response to H5N1 influenza viruses in duck (Anas platyrhynchos)

Cited by 11 publications

References 36 publications

Differently Expression Analysis and Function Prediction of Long Non-coding RNAs in Duck Embryo Fibroblast Cells Infected by Duck Tembusu Virus

Differently Expression Analysis and Function Prediction of Long Non-coding RNAs in Duck Embryo Fibroblast Cells Infected by Duck Tembusu Virus

Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress

Pattern Recognition Receptor Signaling and Innate Responses to Influenza A Viruses in the Mallard Duck, Compared to Humans and Chickens

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