Body colour is an important economic trait for commercial fishes. Recently, a new colour morph displaying market-favoured yellow skin (termed as yellow-mutant, YM) of northern snakehead (Channa argus) was discovered in China. We confirmed that YM snakehead is an albino with complete loss of melanin in the skin and eyes by histological and ultrastructural observations, and inherited as a recessive Mendelian trait. By applying genomic analysis approaches, in combination with gene knockdown and rescue experiments, we suggested a non-sense mutation inslc45a2(c.383G > A) is the causation for the YM snakehead. Notably, significantly higher levels of key melanogenesis genes (tyr,tyrp1,dctandpmel) and phospho-MITF protein were detected in YM snakehead than those in wild-type individuals, and the underlying mechanism was further investigated by comparative transcriptomic analysis. Results revealed that differential expressed genes involved in pathways like MAPK, WNT and calcium signalling were significantly induced in YM snakehead, which might account for the increased amount of melanogenesis elements, and presumably be stimulated by fibroblast-derived melanogenic factors in a paracrine manner. Our study clarified the genetic basis of colour variation inC. argusand provided the preliminary clue indicating the potential involvement of fibroblasts in pigmentation in fish.

The black rockfish, Sebastes schlegelii, is a typical viviparous teleost, which belongs to the family Scorpaenidae. Due to its high economic and ecological values, S. schlegelii has been widely cultured in East Asian countries. With the enlargement of cultivation scale, bacterial and viral diseases have become the main threats to the farming industry of S. schlegelii, which have resulted in significant economic losses. In this study, Illumina shotgun sequencing, single-molecule real-time (SMRT) sequencing, 10× genomics and high-throughput chromosome conformation capture (Hi-C) technologies were collectively applied to assemble the genome of S. schlegelii. Then, we identified the antimicrobial peptide genes (AMPs) in the S. schlegelii genome. In total, 214 AMPs were identified in the S. schlegelii genome, which can be divided into 33 classes according to the annotation and cataloging of the Antimicrobial Peptides Database (APD3). Among these AMPs, thrombin-derived C-terminal peptide (TCP) was the dominant type, followed by RegIIIgamma and chemokine. The amino acid sequences of the TCP, cgUbiquitin, RegIIIalpha, RegIIIgamma, chemokine shared 32.55%, 42.63%, 29.87%, 28.09%, and 32.15% similarities among the same type in S. schlegelii. Meanwhile, the expression patterns of these AMPs in nine healthy tissues and at different infection time points in intestine were investigated. The results showed that the numbers and types of AMPs that responded to Edwardsiella tarda infection gradually increased as the infection progressed. In addition, we analyzed the phylogenetic relationships of hepcidins in teleost. The identification of AMPs based on the whole genome could provide a comprehensive database of potential AMPs, and benefit for the understanding of the molecular mechanisms of immune responses to E. tarda infection in S. schlegelii. This would further offer insights into an accurate and effective design and development of AMP for aquaculture therapy in the future.

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.

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.

Background/Aims: Cullin 4A (CUL4A) is vital in cell survival, development, growth and cell cycle, it plays an important role in chaperone-mediated ubiquitination and interacts with TP53 in carcinogenesis. However, the clinicopathologic significance of CUL4A expression in colorectal cancer is unknown; in particular, the prognostic value of CUL4A combined with TP53 expression has not been explored. Methods: We analyzed the expression of CUL4A in both public database (Oncomine) and 180 cases of colorectal cancer and paired normal tissues by real-time polymerase chain reaction and western blotting. Colony formation, wound healing, migration and invasion assays and tumorigenesis in nude mice were used to explore the function of CUL4A in CRC proliferation and metastasis in vitro and in vivo. Markers of epithelial to mesenchymal transition (EMT) were evaluated by western blotting. Immunohistochemistry (IHC) was used to analyse the relationship between CUL4A expression and E-cadherin expression. Results: CUL4A and TP53 protein expression was significantly higher in cancerous tissues compared to normal tissues. Significant correlation between CUL4A and TP53 expression was observed. CUL4A expression was an independent prognostic factor for overall survival (OS) and disease-free survival (DFS). Interestingly, patients with tumors that had both CUL4A overexpression and mutant TP53 protein accumulation relapsed and died within a significantly short period after surgery (P < 0.001). Multivariate analysis showed that patients with both CUL4A+ and TP53+ positive tumors had extremely poor OS and DFS. Knockdown of CUL4A by a short interfering RNA (siRNA) significantly suppressed the progression of EMT, proliferation, migration, and invasion of colon cancer cells in vitro and tumor growth in vivo. ZEB1 silencing blocked CUL4A-driven these processes. Conclusion: CUL4A expression correlated positively with the prognosis of colorectal cancer. Mechanistically, ZEB1 was confirmed to mediate the function of CUL4A in regulating the EMT. The assessment of both CUL4A and mutant TP53 expression will be helpful in predicting colon cancer prognosis.