Genome-wide identification, evolution of chromobox family genes and their expression in Nile tilapia

Liu, Xingyong; Zhang, Xianbo; Li, Minghui; Zheng, Shuqing; Liu, Zhilong; Cheng, Yunying; Wang, Deshou

doi:10.1016/j.cbpb.2016.09.001

Cited by 7 publications

(4 citation statements)

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“…We also found downregulation of genes of the polycomb group, which are also repressors of the gene transcription machinery, in particular, the polycomb homologue 1 ( epc1 ) and two chromobox genes ( cbx4 and cbx5 ). In mammals, the role of the cbx2 in sex determination and differentiation has been shown [ 85 , 86 ], whereas in Nile tilapia it was demonstrated that the expression of cbx1b , cbx3a and cbx5 was sexually dimorphic in the gonads [ 87 ].…”

Section: Discussionmentioning

confidence: 99%

Treatment with a DNA methyltransferase inhibitor feminizes zebrafish and induces long-term expression changes in the gonads

Ribas

Vanezis

Imués

et al. 2017

Epigenetics & Chromatin

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BackgroundThe role of epigenetic modifications such as DNA methylation during vertebrate sexual development is far from being clear. Using the zebrafish model, we tested the effects of one of the most common DNA methyltransferase (dnmt) inhibitor, 5-aza-2′-deoxycytidine (5-aza-dC), which is approved for the treatment of acute myeloid leukaemia and is under active investigation for the treatment of solid tumours. Several dose–response experiments were carried out during two periods, including not only the very first days of development (0–6 days post-fertilization, dpf), as done in previous studies, but also, and as a novelty, the period of gonadal development (10–30 dpf).ResultsEarly treatment with 5-aza-dC altered embryonic development, delayed hatching and increased teratology and mortality, as expected. The most striking result, however, was an increase in the number of females, suggesting that alterations induced by 5-aza-dC treatment can affect sexual development as well. Results were confirmed when treatment coincided with gonadal development. In addition, we also found that the adult gonadal transcriptome of 5-aza-dC-exposed females included significant changes in the expression of key reproduction-related genes (e.g. cyp11a1, esr2b and figla), and that several pro-female-related pathways such as the Fanconi anaemia or the Wnt signalling pathways were downregulated. Furthermore, an overall inhibition of genes implicated in epigenetic regulatory mechanisms (e.g. dnmt1, dicer, cbx4) was also observed.ConclusionsTaken together, our results indicate that treatment with a DNA methylation inhibitor can also alter the sexual development in zebrafish, with permanent alterations of the adult gonadal transcriptome, at least in females. Our results show the importance of DNA methylation for proper control of sexual development, open new avenues for the potential control of sex ratios in fish (aquaculture, population control) and call attention to possibly hidden long-term effects of dnmt therapy when used, for example, in the treatment of prepuberal children affected by some types of cancer.Electronic supplementary materialThe online version of this article (10.1186/s13072-017-0168-7) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Treatment with a DNA methyltransferase inhibitor feminizes zebrafish and induces long-term expression changes in the gonads

Ribas

Vanezis

Imués

et al. 2017

Epigenetics & Chromatin

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“…The hypoxia tolerance of tilapia is higher than other farmed fish, and some tilapia can tolerate a hypoxia environment with dissolved oxygen below 0.5 mg/L for a short period (Teichert DR, et al, 1997;Stickney RR, 2000;Lim CE, et al, 2006), which makes it a suitable model species to study hypoxia stress in an aquatic habitat. Nile tilapia was chosen in this study not only because of its great hypoxia tolerance, but also the availability of its genome database (Chen XW, et al, 2017;Li HL, et al, 2017;Liu XY, et al, 2017). Therefore, the objective of this study was to explore the metabolic response of Nile tilapia to acute and chronic hypoxia stress and mechanism for fish to cope with acute ACCEPTED MANUSCRIPT…”

Section: A C C E P T E D Mmentioning

confidence: 99%

Metabolic response of Nile tilapia (Oreochromis niloticus) to acute and chronic hypoxia stress

et al. 2018

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Hypoxia is a critical issue in aquaculture especially in intensive aquaculture systems.Acute hypoxia stress with dissolved oxygen (DO) 0.7±0.1 mg/L for 6 h and chronic hypoxia stress with DO 1.1±0.1 mg/L for 4 weeks were used to investigate the response of nutritional metabolic pathways in Nile tilapia Oreochromis niloticus. Fish in the acute and chronic experiments had different adaptive mechanisms. Upon acute hypoxia stress, the contents of liver glycogen and muscle glycogen were significantly lower, but there was no significant difference in triglycerides (TG). The lactate dehydrogenase (LDH) activities increased after exposure to acute hypoxia stress. The mRNA expression of genes involved in glycolysis and glycogenolysis was significantly up-regulated by acute hypoxia stress. However, the response of fish to long-term hypoxia stress was different from acute hypoxia. Compared with the normoxia treatment, the crude fat in fish decreased in the hypoxia group and TG in the liver and muscle were significantly lower.Beta oxidation of the liver was enhanced in the hypoxia group, while the hepatic glycogen content increased in the hypoxia group. Transcriptomic analysis showed that the expression of genes related to carbohydrate synthesis and lipolysis increased in the hypoxia group, while genes related to carbohydrate catabolism and fat synthesis showed the opposite. This study indicates that fish could utilize carbohydrate as a main energy source during acute hypoxia stress, and metabolize more lipid during long-term hypoxia stress. A high carbohydrate content in the diet may help reduce negative effects from acute hypoxia stress, and an appropriate increase of fat content in the diet may benefit fish growth in a hypoxia environment, e.g., in high-density aquaculture ponds.

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“…However, these will not change the expansion pattern of this family in jawed vertebrates due to whole genome duplication. Interestingly, the duplicated paralogs of brd2 and kmt2b were on LG11 and LG22, respectively, similar to cbx3 , rps19, and rps27-1 [ 47 , 48 ], suggesting possible inter-chromosomal duplication in tilapia. Moreover, uneven chromosomal distribution of BRDs was observed in tilapia, zebrafish, and humans.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of the BRD Family in Nile Tilapia (Oreochromis niloticus)

Zhang

et al. 2022

Animals

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The bromodomain (BRD) proteins specifically recognize the N-acetyllysine motifs, which is a key event in the reading process of epigenetic marks. BRDs are evolutionarily highly conserved. Over recent years, BRDs attracted great interest because of their important roles in biological processes. However, the genome-wide identification of this family was not carried out in many animal groups, in particular, in teleosts. Moreover, the expression patterns were not reported for any of the members in this family, and the role of the BRD family was not extensively studied in fish reproduction. In this study, we identified 16 to 120 BRD genes in 24 representative species. BRDs expanded significantly in vertebrates. Phylogenetic analysis showed that the BRD family was divided into eight subfamilies (I–VIII). Transcriptome analysis showed that BRDs in Nile tilapia (Oreochromis niloticus) exhibited different expression patterns in different tissues, suggesting that these genes may play different roles in growth and development. Gonadal transcriptome analysis showed that most of the BRDs display sexually dimorphic expression in the gonads at 90 and 180 dah (days after hatching), including 21 testis-dominated genes (brdt, brd4a and brd2b, etc.), and nine ovary-dominated genes (brd3b, brd2a and kat2a, etc.). Consistent with transcriptomic data, the results of qRT-PCR and fluorescence in situ hybridization showed that brdt expression was higher in the testis than in the ovary, suggesting its critical role in the spermatogenesis of the tilapia. Male fish treated with JQ1 (BET subfamily inhibitor) displayed abnormal spermatogenesis. The numbers of germ cells were reduced, and the expression of steroidogenic enzyme genes was downregulated, while the expression of apoptosis-promoting genes was elevated in the testis tissue of treated fish. Our data provide insights into the evolution and expression of BRD genes, which is helpful for understanding their critical roles in sex differentiation and gonadal development in teleosts.

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Genome-wide identification, evolution of chromobox family genes and their expression in Nile tilapia

Cited by 7 publications

References 50 publications

Treatment with a DNA methyltransferase inhibitor feminizes zebrafish and induces long-term expression changes in the gonads

Treatment with a DNA methyltransferase inhibitor feminizes zebrafish and induces long-term expression changes in the gonads

Metabolic response of Nile tilapia (Oreochromis niloticus) to acute and chronic hypoxia stress

Genome-Wide Identification and Characterization of the BRD Family in Nile Tilapia (Oreochromis niloticus)

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