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ABSTRACT: DNA hydroxymethylation profiling between divergent phenotypes of captive Nile tilapia

PROVIDER: PRJNA665120 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12695665.fastq.gz	Fastqsanger.gz
	SRR12695666.fastq.gz	Fastqsanger.gz
	SRR12695667.fastq.gz	Fastqsanger.gz
	SRR12695668.fastq.gz	Fastqsanger.gz
	SRR12695669.fastq.gz	Fastqsanger.gz

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Epigenetic mapping of the somatotropic axis reveals differential DNA hydroxymethylation marks with potential implication in growth

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Project description:In fish, the sex determining mechanisms can broadly be classified as genotypic (GSD), temperature-dependent (TSD), or genotypic plus temperature effects (GSD+TE). For the fish species with TSD or GSD+TE, extremely high or low temperature can affect its sex determination and differentiation. For long time, the underlying changes in DNA methylation that occur during high or low temperature induced sex reversal have not been fully clarified. In this study, we used Nile tilapia as a model to perform a genome-wide survey of differences in DNA methylation in female and male gonads between control and high temperature induced groups using methylated DNA immunoprecipitation (MeDIP). We identified the high temperature induction-related differentially methylated regions (DMRs), and performed functional enrichment analysis for genes exhibiting DMR. These identified differentially methylated genes were potentially involved in the connection between environmental temperature and sex reversal in Nile tilapia. In this study, four samples (control females, CF; control males, CM; induced females, IF; induced males, IM) were analyzed.

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Distinct epigenetic profiles at the cytosine modification level define epithelial-to-mesenchymal cell-state transitions

Project description:Genome wide DNA methylation and hydroxymethylation profiling of 6 isolated single cell clones and the parental (SUM149-PT) cell line. The Illumina Infinium Human MethylationEPIC Beadchip was used to obtain DNA methylation and hydroxymethylation profiles across approximately 850,000 CpGs in 6 isolated single cell clones that represent the phenotypes of the epithelial-to-mesenchymal spectrum along with the parental (SUM149-PT) cell line. Isolated single cell clones represent varying phenotypes of the epithelial-to-mesenchymal transition. Detailed isolation and characterization methods can be found in Brown et al, 2021. https://doi.org/10.1101/2021.03.17.434993

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Project description:Commercial production of tilapia relies on monosex cultures of males, which so far proved difficult to maintain in large scale production facilities. Thus, a better understanding of the genetic architecture of the complex trait of sex determination in tilapia is needed.We aimed to detect genes that were differentially expressed by gender at early embryonic development. Artificial fertilization of O. niloticus females with either sex-reversed males (ΔXX) or genetically-modified YY 'supermales' resulted in all-female and all-male embryos, respectively. Pools of all-female and all-male embryos at 2, 5 and 9 days post fertilization were used for custom Agilent eArray. 56 pool samples of Nile tilapia full siblings groups (female or male) at day 2, 5 or 9 post fertilization were subjected to total RNA extraction from whole embryo tissues and hybridized to the custom Agilent array. Each sample was yielded from different cross of artificial fertilization: six dams X five sires. The resulting gender were known based on the sire, sex-reversed males (ΔXX) or genetically-modified YY 'supermales' resulted in all-female and all-male embryos, respectively.

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