Abstract
Long non-coding RNAs (lncRNAs) play widespread roles in fundamental biological processes, including immune responses. The olive flounder (Paralichthys olivaceus), an important economical flatfish widely cultured in Japan, Korea, and China, is threatened by infectious pathogens, including bacteria, viruses, and parasites. However, the role of lncRNAs in the immune responses of this species against pathogen infections is not well-understood. Therefore, in this study, we aimed to identify lncRNAs in the intestine of olive flounder and evaluate their differential expression profiles during Edwardsiella tarda infection, which is an important zoonotic and intestinal pathogen. A total of 4,445 putative lncRNAs were identified, including 3,975 novel lncRNAs and 470 annotated lncRNAs. These lncRNAs had shorter lengths and fewer exons compared with mRNAs. In total, 115 differentially expressed lncRNAs (DE-lncRNAs) were identified during E. tarda infection. To validate the expression pattern of lncRNAs, six DE-lncRNAs were randomly selected for quantitative real-time PCR. The co-located and co-expressed mRNAs of DE-lncRNAs were predicted, which were used to conduct the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. The target genes of DE-lncRNAs enriched numerous immune-related processes and exhibited a strong correlation with immune-related signaling pathways. To better understand the extensive regulatory functions of lncRNAs, the lncRNA–miRNA–mRNA regulatory networks were constructed, and two potential competing endogenous RNA (ceRNA) networks, LNC_001979-novel_171-Potusc2 and LNC_001979-novel_171-Podad1, were preliminarily identified from the intestine of olive flounders for the first time. In conclusion, this study provides an invaluable annotation and expression profile of lncRNAs in the intestine of olive flounder infected with E. tarda; this forms a basis for further studies on the regulatory function of lncRNAs in the intestinal mucosal immune responses of olive flounder.
Highlights
Long non-coding RNAs are a group of non-coding RNAs that are longer than 200 nucleotides [1]
The clean reads from all the libraries were used to discern the Long non-coding RNAs (lncRNAs)
More complete and unbiased transcriptome datasets were developed, which will help elucidating the function of lncRNAs related to immune responses under pathogen infections in teleosts
Summary
Long non-coding RNAs (lncRNAs) are a group of non-coding RNAs (ncRNAs) that are longer than 200 nucleotides [1]. Studies have shown that lncRNAs play important roles in the regulation of immune responses and host defense against pathogens [5]. Several lncRNAs have been shown to be differentially expressed during microbial component stimulation or pathogen infection [5]. The lncRNAs might regulate the transcription of immune genes by interacting with other complexes. These lncRNAs might play an important role in controlling host–pathogen interactions via regulating the growth and replication of pathogens, or via cellautonomous anti-microbial defense mechanisms. LncRNAs can regulate a variety of biological processes at transcriptional and post-transcriptional levels, such as DNA methylation, histone modification, splicing, transcription, and translation, by interacting with genomic DNA, RNA, proteins, or a combination of these [1]. Several novel findings suggested that lncRNAs can act as miRNA sponges to bind miRNAs competitively to modulate the expression of mRNAs
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