Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia

Wan, Zi Yi; Xia, Jun; Lin, Grace; Wang, Le; Lin, Valerie Chun Ling; Yue, Gen Hua

doi:10.1038/srep35903

Cited by 74 publications

(73 citation statements)

References 53 publications

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“…We compared the genome-wide methylation patterns between the control and leucine programming zebra sh. The methylation level of CpGs in zebra sh liver was above 70%, similar to those found in zebra sh and tilapia [46][47]. The total DNA methylation level of CHG and CHH methylation types in sh of the leucine programming group was higher than those of the control group.…”

Section: Discussionsupporting

confidence: 76%

Early Leucine Programming on Protein Utilization and mTOR Signaling by DNA Methylation in Zebrafish (Danio Rerio)

Zhu

Wang

et al. 2020

Preprint

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Background: Early nutritional programming affects a series of metabolism, growth and development in mammals. Fish also exhibit the developmental plasticity by early nutritional programming. However, little is known about the effect of early amino acid programming on growth and metabolism. Methods: In the present study, zebrafish (Danio rerio) was used as the experimental animal to study whether early leucine stimulation can programmatically affect the mechanistic target of rapamycin (mTOR) signaling pathway, growth and metabolism in the later life, and to undercover the mechanism of epigenetic regulation. Zebrafish larvas at 3 days post hatching (dph) were raised with 1.0% leucine from 3 to 13 dph during the critical developmental stage, then back to normal water for 70 days (83 dph). Results: The growth performance and crude protein content of zebrafish in the early leucine programming group were increased, and consistent with the activation of the mTOR signaling pathway and the high expression of genes involved in the metabolism of amino acid and glycolipid. Furthermore, we compared the DNA methylation profiles between the control and leucine-stimulated zebrafish, and found that the methylation levels of CG-differentially methylated regions (DMGs) and CHH-DMGs of genes involved in mTOR signaling pathway were different between the two groups. With quantitative PCR analysis, the decreased methylation levels of CG type of Growth factor receptor-bound protein 10 (Grb10), eukaryotic translation initiation factor 4E (eIF4E) and mTOR genes of mTOR signaling pathway in the leucine programming group, might contribute to the enhanced gene expression. Conclusions: The early leucine programming could improve the protein synthesis and growth, which might be attributed to the methylation of genes in mTOR pathway and the expression of genes involved in protein synthesis and glycolipid metabolism in zebrafish. These results could be beneficial for better understanding of the epigenetic regulatory mechanism of early nutritional programming.

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Section: Discussionsupporting

confidence: 76%

Early Leucine Programming on Protein Utilization and mTOR Signaling by DNA Methylation in Zebrafish (Danio Rerio)

Zhu

Wang

et al. 2020

Preprint

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“…In tilapia, genome-wide methylation analysis identified sexually dimorphic methylated regions throughout specific genomic regions (Wan et al, 2016) as well as in the zebrafish's brain, global methylation differences were found between males and females (Chatterjee et al, 2016). Both studies pointed out the importance of the sexual dimorphic methylation patterns in fish.…”

Section: Discussionmentioning

confidence: 99%

Immune genes, IL1β and Casp9, show sexual dimorphic methylation patterns in zebrafish gonads

Caballero‐Huertas

Moraleda-Prados

Joly

et al. 2020

Fish & Shellfish Immunology

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Highlights  DNA methylation profiles of two immune genes IL1 and Casp9 present sexual dimorphism in adult gonad of zebrafish with higher methylation levels in the testes when compared to the ovaries.  Sex-biased differences in methylation profiles need to be taken into account when analyzing immune responses in fish.  IL1 gene expression differs between ovaries and testes, being higher in male gonadal tissue.  An inverse, although not significant, correlation was found between DNA methylation and gene expression levels,  IL1 and Casp9 might be two potential epimarkers to predict sexual dimorphic DNA methylation profiles in fish gonads.

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“…Read coverage was normalized between samples. A minimum of five reads in all samples were required at a CpG site for that site to be analysed (Walker et al., ; Wan et al., ). Sites that were in the 99.9th percentile of coverage were also removed from the analysis to account for potential PCR bias.…”

Section: Methodsmentioning

confidence: 99%

Genome‐wide DNA methylation signatures of infection status in Trinidadian guppies (Poecilia reticulata)

Pérez‐Jvostov

Blondel

et al. 2018

Molecular Ecology

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Epigenetic modification, especially DNA methylation, can play an important role in mediating gene regulatory response to environmental stressors and may be a key process affecting phenotypic plasticity and adaptation. Parasites are potent stressors with profound physiological and ecological effects on their hosts, yet it remains unclear how parasites influence host methylation patterns. Here, we used a well-studied host-parasite system, the guppy Poecilia reticulata and its ectoparasitic monogenean Gyrodactylus turnbulli to gain mechanistic insight into the dynamics of DNA methylation in host-parasite interactions. To explore this, we quantitatively measured genome-wide DNA methylation in guppy skin tissue using reduced representation bisulphite sequencing and characterized differential methylation patterns in guppies during distinct phases of infection. We identified 365, 313, and 741 differentially methylated regions (DMRs) between infected and control fish in early infection, peak infection and recovery phases, respectively. The magnitude of the methylation difference was moderate in DMRs, with an average of 29% (early infection), 27% (peak infection) and 30% (recovery) differential methylation per DMR. Approximately 50% of DMRs overlapped with CpG islands, and over half of the DMRs overlapped with gene bodies, several of which encode proteins relevant to immune response. These findings provide the first evidence of an epigenetic signature of infection by ectoparasites and demonstrate the changing relationship between epigenetic variation and immune response in distinct phases of infection.

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Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia

Cited by 74 publications

References 53 publications

Early Leucine Programming on Protein Utilization and mTOR Signaling by DNA Methylation in Zebrafish (Danio Rerio)

Early Leucine Programming on Protein Utilization and mTOR Signaling by DNA Methylation in Zebrafish (Danio Rerio)

Immune genes, IL1β and Casp9, show sexual dimorphic methylation patterns in zebrafish gonads

Genome‐wide DNA methylation signatures of infection status in Trinidadian guppies (Poecilia reticulata)

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