Identification of microRNA expression profiles in the gill, intestine and hepatic caecum of Branchiostoma belcheri

Liao, Xin; Liu, Yang; Chen, Xi; Chen, Jun-Yuan

doi:10.1007/s13238-016-0365-3

Cited by 4 publications

(3 citation statements)

References 15 publications

(16 reference statements)

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“…Based on the expression profiles of miRNAs, Liao et al. (2017) found regulationary functions of miRNAs in digestive and immune-related organs: gill, intestine, and hepatic caecum ( 18 ). Meanwhile, IL-1 receptor-associated kinase 4 (IRAK4) was identified and validated, which can be targeted by miR-203, thus inhibiting the activation of nuclear factor κB (NF-κB) signaling pathway ( 19 ).…”

Section: Introductionmentioning

confidence: 99%

Integrated Analysis of circRNA-miRNA-mRNA Regulatory Networks in the Intestine of Sebastes schlegelii Following Edwardsiella tarda Challenge

Cao

et al. 2021

Front. Immunol.

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Sebastes schlegelii, an important aquaculture species, has been widely cultured in East Asian countries. With the increase in the cultivation scale, various diseases have become major threats to the industry. Evidence has shown that non-coding RNAs (ncRNAs) have remarkable functions in the interactions between pathogens and their hosts. However, little is known about the mechanisms of circular RNAs (circRNAs) and coding RNAs in the process of preventing pathogen infection in the intestine in teleosts. In this study, we aimed to uncover the global landscape of mRNAs, circRNAs, and microRNAs (miRNAs) in response to Edwardsiella tarda infection at different time points (0, 2, 6, 12, and 24 h) and to construct regulatory networks for exploring the immune regulatory mechanism in the intestine of S. schlegelii. In total, 1,794 mRNAs, 87 circRNAs, and 79 miRNAs were differentially expressed. The differentially expressed RNAs were quantitatively validated using qRT-PCR. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that most of the differentially expressed mRNA genes and the target genes of ncRNAs were related to immune signaling pathways, such as the NF-κB signal pathway, pathogen recognition receptors related to signaling pathways (Toll-like receptors and Nod-like receptors), and the chemokine signaling pathway. Based on these differentially expressed genes, 624 circRNA-miRNA pairs and 2,694 miRNA-mRNA pairs were predicted using the miRanda software. Integrated analyses generated 25 circRNA-miRNA-mRNA interaction networks. In a novel_circ_0004195/novel-530/IκB interaction network, novel_530 was upregulated, while its two targets, novel_circ_0004195 and IκB, were downregulated after E. tarda infection. In addition, two circRNA-miRNA-mRNA networks related to apoptosis (novel_circ_0003210/novel_152/apoptosis-stimulating of p53 protein 1) and interleukin (novel_circ_0001907/novel_127/interleukin-1 receptor type 2) were also identified in our study. We thus speculated that the downstream NF-κB signaling pathway, p53 signaling pathway, and apoptosis pathway might play vital roles in the immune response in the intestine of S. schlegelii. This study revealed a landscape of RNAs in the intestine of S. schlegelii during E. tarda infection and provided clues for further study on the immune mechanisms and signaling networks based on the circRNA-miRNA-mRNA axis in S. schlegelii.

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Section: Introductionmentioning

confidence: 99%

Integrated Analysis of circRNA-miRNA-mRNA Regulatory Networks in the Intestine of Sebastes schlegelii Following Edwardsiella tarda Challenge

Cao

et al. 2021

Front. Immunol.

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“…However, amphioxus lacks lymphoid organs and has no free circulating blood cells (Moller and Philpott 1973;Yuan et al 2015a). Instead, its digestive organs, including the gill, intestine and hepatic cecum, are regarded as sites of continuous immunological interaction and thus act as the major player of defense against infection (Gao and Zhang 2018;Huang et al 2011b;Liao et al 2017;Tao and Xu 2016). The hepatic cecum not only serves as a physical barrier but is also an integrator of the immune system.…”

Section: Introductionmentioning

confidence: 99%

Hepatic cecum: a key integrator of immunity in amphioxus

Zhang

et al. 2021

Mar Life Sci Technol

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The vertebrate liver is regarded as an organ essential to the regulation of immunity and inflammation as well as being central to the metabolism of nutrients. Here, we discuss the functions that the hepatic cecum of amphioxus plays in the regulation of immunity and inflammation, and the molecular basis of this. It is apparent that the hepatic cecum performs important roles in the immunity of amphioxus including immune surveillance, clearance of pathogens and acute phase response. Therefore, the hepatic cecum, like the vertebrate liver, is an organ functioning as a key integrator of immunity in amphioxus.

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“…Thus, the body of literature suggests that miRNAs may be key regulatory molecules for the regional and specific function formation of different organs in amphioxus. So far, only miRNA expression profiles in three digestive and immune-related organs, gill, intestine, and hepatic cecum, have been obtained using microarray technology based on nucleic acid hybridization (Liao et al, 2017a). However, only three organ types were used, and microarray based on nonsequencing technology is not feasible for the identification of novel molecules in different organs (Gao et al, 2011), possibly hindering a systematic and accurate discovery and function analysis of organ-specific expressed genes.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Transcriptomic Analysis of MicroRNAs Across Various Amphioxus Organs Using Deep Sequencing

et al. 2019

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Amphioxus is the closest living invertebrate proxy of the vertebrate ancestor. Systematic gene identification and expression profile analysis of amphioxus organs are thus important for clarifying the molecular mechanisms of organ function formation and further understanding the evolutionary origin of organs and genes in vertebrates. The precise regulation of microRNAs (miRNAs) is crucial for the functional specification and differentiation of organs. In particular, those miRNAs that are expressed specifically in organs (OSMs) play key roles in organ identity, differentiation, and function. In this study, the genome-wide miRNA transcriptome was analyzed in eight organs of adult amphioxus Branchiostoma belcheri using deep sequencing. A total of 167 known miRNAs and 23 novel miRNAs (named novel_mir), including 139 conserved miRNAs, were discovered, and 79 of these were identified as OSMs. Additionally, analyses of the expression patterns of eight randomly selected known miRNAs demonstrated the accuracy of the miRNA deep sequencing that was used in this study. Furthermore, potentially OSM-regulated genes were predicted for each organ type. Functional enrichment of these predicted targets, as well as further functional analyses of known OSMs, was conducted. We found that the OSMs were potentially to be involved in organ-specific functions, such as epidermis development, gonad development, muscle cell development, proteolysis, lipid metabolism, and generation of neurons. Moreover, OSMs with non–organ-specific functions were detected and primarily include those related to innate immunity and response to stimuli. These findings provide insights into the regulatory roles of OSMs in various amphioxus organs.

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Identification of microRNA expression profiles in the gill, intestine and hepatic caecum of Branchiostoma belcheri

Cited by 4 publications

References 15 publications

Integrated Analysis of circRNA-miRNA-mRNA Regulatory Networks in the Intestine of Sebastes schlegelii Following Edwardsiella tarda Challenge

Integrated Analysis of circRNA-miRNA-mRNA Regulatory Networks in the Intestine of Sebastes schlegelii Following Edwardsiella tarda Challenge

Hepatic cecum: a key integrator of immunity in amphioxus

Genome-Wide Identification and Transcriptomic Analysis of MicroRNAs Across Various Amphioxus Organs Using Deep Sequencing

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