Integrated Analysis of lncRNA and circRNA Mediated ceRNA Regulatory Networks in Skin Reveals Innate Immunity Differences Between Wild-Type and Yellow Mutant Rainbow Trout (Oncorhynchus mykiss)

Wu, Shenji; Huang, Jinxin; Li, Yongjuan; Liu, Zhe; Zhao, Lu

doi:10.3389/fimmu.2022.802731

Cited by 10 publications

(8 citation statements)

References 93 publications

(107 reference statements)

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“…2, MSTRG.32014.1, and .29012.1 in regulating at least two immune-related genes (IFIH1, DHIRF). Interferon, CD, and HSP genes were also expressed in our study[ 12 ] …”

supporting

confidence: 64%

“…Gene Ontology and Databank (KEGG) pathways associated with innate immunity, such as NAD+ADP-ribosyltransferase activity, immune response to bacterial infection, and RIG-I receptor signaling, including NOD-like receptor signaling and phagosomal KEGG pathways, are depicted. In addition, the role of long non-coding RNAs (lncRNAs) MSTRG.11484.2, MSTRG.32014.1, and MSTRG.29012.1 in the regulation of at least three immunerelated genes (IFIH1, DHIRF) was determined [ 12 ] .…”

Section: Q-rt-pcr This Researchmentioning

confidence: 99%

“…In addition, the role of long non-coding RNAs (lncRNAs) MSTRG.11484.2, MSTRG.32014.1, and MSTRG.29012.1 in the regulation of at least three immune-related genes (IFIH1, DHIRF) was determined. [ 12 ] . In another study, liver tissues from rainbow trout were sampled and analyzed using RNA-seq technology under heat stress (24 °C) and control conditions (18 °C).…”

Section: Introductionmentioning

confidence: 99%

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Identification and Expression Analysis of Long Noncoding RNAs in Response to Infection with VHSV in Rainbow Trout

Tavakoli alamouti,

Rahimi Mianji,

Nejati Javaremi

et al. 2024

Preprint

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Viral contamination in the aquaculture industry is a significant challenge that requires further research. Emerging evidence suggests that long noncoding RNAs (lncRNAs) play a role in regulating various biological processes, including immunity. However, most studies have focused on model organisms, and little is known about non-coding RNAs in the immune response to viral hemorrhagic septicemia (VHS) in rainbow trout. In this study, we investigated the listing of non-coding RNAs (ncRNAs) in rainbow trout challenged with VHS virus. We explored their potential role in defense-like responses based on transcriptomic analysis of the virus-treated and control groups. As a result of this research, 4207 lncRNAs were identified, of which 182 lncRNAs were differentially expressed between treated and untreated samples. Among 7753 lncRNA transcripts, 1920 were novel intergenic (class code “u”), and 3748 transcripts were potentially novel isoform of lncRNAs. Gene ontology analysis revealed biological pathways associated with the stress response and immune signaling. Pairs of genes such as TP63-MSTRG.62, IL10-MSTRG.9783, IL10-MSTRG.9784, TK1-MSTRG.22826, and MSTRG.17881-GLI1 showed cis interactions, while DOCK10-MSTRG.30015, MSTRG.36357-LOC101268921, and MSTRG.34190-ENPP2 showed trans interactions. In this study, the role of lncRNAs in regulating the expression of the target genes was clearly identified. This finding is consistent with the regulatory processes of immune system responses mediated by cytokines, as well as the regulation of oxygen levels in response to viral infection. The information presented here highlights the various regulatory mechanisms of lncRNAs in the expression of immune system genes in fish treated with VHS virus.

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“…2, MSTRG.32014.1, and .29012.1 in regulating at least two immune-related genes (IFIH1, DHIRF). Interferon, CD, and HSP genes were also expressed in our study[ 12 ] …”

supporting

confidence: 64%

Section: Q-rt-pcr This Researchmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Identification and Expression Analysis of Long Noncoding RNAs in Response to Infection with VHSV in Rainbow Trout

Tavakoli alamouti,

Rahimi Mianji,

Nejati Javaremi

et al. 2024

Preprint

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“…Immune-related ceRNAs may regulate the acute heat stress-induced response mainly by the MAPK signaling pathway ( 77 ). In addition, comparing the whole transcriptome of skin in wild-type rainbow trout, a total of 1630 lncRNAs, 50 miRNAs and 2448 mRNAs were differentially expressed in the skin of yellow mutant rainbow trout, which involved numerous key innate immune-related signaling pathways ( 78 ). In the immune-related lncRNA-mediated ceRNA network, the lncRNAs MSTRG.11484.2, MSTRG.32014.1 and MSTRG.29012.1 together with PC-5p-43254_34, PC-3p-28352_70 and bta-miR-11987_L-1R-1_1 ss8TA were identified to regulate at least 3 immune-related genes, interferon-induced helicase C domain-containing protein 1 (ifih1), DEXH (Asp-Glu-X-His) box polypeptide 58 (dhx58) and irf3 ( 78 ).…”

Section: The Regulatory Roles Of the Lncrna-mirna-mrna Axis In Teleos...mentioning

confidence: 99%

The potential regulatory role of the lncRNA-miRNA-mRNA axis in teleost fish

Zhou

Leng²,

Wang³

et al. 2023

Front. Immunol.

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Research over the past two decades has confirmed that noncoding RNAs (ncRNAs), which are abundant in cells from yeast to vertebrates, are no longer “junk” transcripts but functional regulators that can mediate various cellular and physiological processes. The dysregulation of ncRNAs is closely related to the imbalance of cellular homeostasis and the occurrence and development of various diseases. In mammals, ncRNAs, such as long noncoding RNAs (lncRNAs) and microRNAs (miRNAs), have been shown to serve as biomarkers and intervention targets in growth, development, immunity, and disease progression. The regulatory functions of lncRNAs on gene expression are usually mediated by crosstalk with miRNAs. The most predominant mode of lncRNA-miRNA crosstalk is the lncRNA-miRNA-mRNA axis, in which lncRNAs act as competing endogenous RNAs (ceRNAs). Compared to mammals, little attention has been given to the role and mechanism of the lncRNA-miRNA-mRNA axis in teleost species. In this review, we provide current knowledge about the teleost lncRNA-miRNA-mRNA axis, focusing on its physiological and pathological regulation in growth and development, reproduction, skeletal muscle, immunity to bacterial and viral infections, and other stress-related immune responses. Herein, we also explored the potential application of the lncRNA-miRNA-mRNA axis in the aquaculture industry. These findings contribute to an enhanced understanding of ncRNA and ncRNA-ncRNA crosstalk in fish biology to improve aquaculture productivity, fish health and quality.

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“…Recently, ceRNA (circRNA–miRNA–mRNA) has been reported to play an important role in cell proliferation, cell differentiation, ECM synthesis and degradation, immune response, and growth and development [ 16 , 17 , 18 , 19 , 20 ]. Studies have shown that the circ-0005526/miR-142-5p/TCF4, circ-UBE2G1/miR-373/HIF-1α, circ-0000423/miR-27b-3p/MMP-13, and circ-SEC24A/miR-26b-5p/DNMT3A regulatory axis can promote inflammatory factor-induced chondrocytes apoptosis and extracellular matrix degradation [ 18 , 21 , 22 , 23 ].…”

Section: Introductionmentioning

confidence: 99%

Integration Analysis of circRNA–miRNA–mRNA and Identification of Critical Networks in Valgus-Varus Deformity (Gallus gallus)

Cai

et al. 2023

Genes

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Valgus-valgus deformity (VVD) is a common leg deformity in broilers with inward or outward deviation of the tibiotarsus and tarsometatarsus. The competing endogenous RNA (ceRNA) network plays an essential role in the study of leg disease. However, its role in the etiology and pathogenesis of VVD remains unclear. Here, based on case (VVD) and control (normal) group design, we performed analyses of differentially expressed circRNAs (DEcircRNAs), differentially expressed miRNAs (DEmiRNAs) and differentially expressed mRNAs (DEmRNAs). Transcriptome data derived 86 DEcircRNAs, 13 DEmiRNAs and 410 DEmRNAs. Functional analysis showed that DEmRNAs were significantly enriched in cell cycle, apoptosis, ECM-receptor interaction, FoxO signaling pathway and protein processing synthesis. DEcirc/miRNA-associated DEmRNAs were associated with skeletal and muscle growth and development pathways, including mTOR, Wnt, and VEGF signaling pathways. Subsequently, a circRNA–miRNA–mRNA regulatory network was constructed based on the ceRNA hypothesis, including 8 circRNAs, 6 miRNAs, and 31 mRNAs, which were significantly enriched in the skeletal developmental pathway. Finally, two key mRNAs (CDC20 and CTNNB1) and their regulatory axes were screened by the PPI network and cytohubba. The expression levels of CDC20 and CTNNB1 in cartilage and seven other tissues were also quantified by qPCR. In conclusion, we analyzed the functions of DEmRNA, DEcircRNA and DEmiRNA and constructed the hub ceRNA regulatory axis, and obtained two hub genes, CDC20 and CTNNB1. The study more deeply explored the etiology and pathogenesis of VVD and lays the foundation for further study of the role of the ceRNA network on skeletal development.

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Integrated Analysis of lncRNA and circRNA Mediated ceRNA Regulatory Networks in Skin Reveals Innate Immunity Differences Between Wild-Type and Yellow Mutant Rainbow Trout (Oncorhynchus mykiss)

Cited by 10 publications

References 93 publications

Identification and Expression Analysis of Long Noncoding RNAs in Response to Infection with VHSV in Rainbow Trout

Identification and Expression Analysis of Long Noncoding RNAs in Response to Infection with VHSV in Rainbow Trout

The potential regulatory role of the lncRNA-miRNA-mRNA axis in teleost fish

Integration Analysis of circRNA–miRNA–mRNA and Identification of Critical Networks in Valgus-Varus Deformity (Gallus gallus)

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