Gonadal DNA methylomes of half-smooth tongue sole Cynoglossus semilaevis
Ontology highlight
ABSTRACT:
ORGANISM(S): Cynoglossus semilaevis
PROVIDER: GSE41129 | GEO | 2014/01/23
SECONDARY ACCESSION(S): PRJNA175873
REPOSITORIES: GEO
Similar Datasets
Project description:Environmental sex determination (ESD) occurs in divergent, phylogenetically unrelated taxa, and in some species co-occurs with genetic sex determination (GSD) mechanisms. Although epigenetic regulation in response to environmental effects has long been proposed to be associated with ESD, a systemic analysis on epigenetic regulation of ESD is still lacking. Using half-smooth tongue sole (Cynoglossus semilaevis) as a model – a marine fish which has both ZW chromosomal GSD and temperature-dependent ESD – we investigated the role of DNA methylation in transition from GSD to ESD by comparing gonadal DNA methylomes of parental females, parental pseudo-males, F1 females, F1 pseudo-males and normal males. To assess the gonadal DNA methylome patterns across different sexual types of tongue sole, we carried out BS-seq on bisulfite converted DNA extracted from adult gonads of parental females, parental pseudo-males, and F1 pseudo-males and females from a cross between a parental pseudo-male and a normal female. We also sampled normal male individuals as a control for the normal male DNA methylation pattern. For each of the five samples, two biological replicates were utilized, with each replicate being pooled by five fish. The phenotype and genotype of each selected fish was identified by the histological analysis and PCR validation using the W chromosome specific marker. DNA were isolated from five pooled gonads of the same replicate, then 5 ?g DNA was used to do the bisulfite conversion and BS-seq. The bisulfite conversion of sample DNA was carried out using a modified NH4HSO3-based protocol (Hayatsu et al. 2006). The paired-end library construction and sequencing were carried out using Illumina HiSeq 2000, according to the manufacturer’s instructions (Illumina). We also mixed 25 ng cl857 Sam7 Lambda DNA in each sample to use as conversion quality control for each library.
2014-01-23 | E-GEOD-41129 | biostudies-arrayexpress
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.
2015-08-27 | E-GEOD-72386 | biostudies-arrayexpress
Project description:In our study, differential male nucleus events and development behaviors were revealed from the fertilized eggs in response to the sperm from males of genotypic sex determination (GSD) and temperature-dependent sex determination (TSD) in gibel carp. When the eggs of maternal fish were fertilized by the sperm from males of GSD, the fertilized egg encountered similar sexual reproduction events and behaviors. However, when the eggs of maternal fish were fertilized by the sperm from males of TSD, a typical process of gynogenesis was observed. To reveal the underlying molecular mechanism of differential sperm nucleus development behaviors in the fertilized eggs, iTRAQ-based quantitative semen proteomics were performed on three semen samples from three males of GSD and three semen samples from three males of TSD respectively.
2018-06-14 | PXD008919 | Pride
Project description:Transcriptome analysis of gastrocnemius muscle RNA samples from exercise and sedentary ancestries Early life and pre-conception environmental stimuli can affect adult health-related phenotypes. Exercise training is an environmental stimulus affecting many systems throughout the body and appears to alter offspring phenotypes. The aim of this study was to examine the influence of parental exercise training, or “exercise ancestry,” on morphological and metabolic phenotypes in multiple generations of mouse offspring. F0 C57BL/6 mice were exposed to voluntary exercise or sedentary lifestyle and bred with like-exposed mates to produce an F1 generation. F1 mice of both ancestries were sedentary and sacrificed at 8 wk or bred with littermates to produce an F2 generation, which was also sedentary and sacrificed at 8 wk. Small, but broad generation- and sex-specific effects of exercise ancestry were observed for body mass, fat and muscle mass, serum insulin, glucose tolerance, and muscle gene expression. F1 EX females were heavier than F1 SED females, but F1 SED females had higher absolute tibialis anterior and omental fat masses. Serum insulin was lower in F1 SED females compared to F1 EX females. F2 EX females had impaired glucose tolerance compared to F2 SED females. Analysis of skeletal muscle mRNA levels revealed several generation- and sex-specific differences in mRNA levels for multiple genes, especially those related to metabolic genes (e.g., F1 EX males had lower mRNA levels of Hk2, Ppard, Ppargc1α, Adipoq, and Scd1 than F1 SED males). These results provide preliminary evidence that parental exercise training can influence health-related phenotypes in mouse offspring.
2012-08-30 | GSE40469 | GEO
Project description:Transcriptome analysis of gastrocnemius muscle RNA samples from exercise and sedentary ancestries Early life and pre-conception environmental stimuli can affect adult health-related phenotypes. Exercise training is an environmental stimulus affecting many systems throughout the body and appears to alter offspring phenotypes. The aim of this study was to examine the influence of parental exercise training, or M-bM-^@M-^\exercise ancestry,M-bM-^@M-^] on morphological and metabolic phenotypes in multiple generations of mouse offspring. F0 C57BL/6 mice were exposed to voluntary exercise or sedentary lifestyle and bred with like-exposed mates to produce an F1 generation. F1 mice of both ancestries were sedentary and sacrificed at 8 wk or bred with littermates to produce an F2 generation, which was also sedentary and sacrificed at 8 wk. Small, but broad generation- and sex-specific effects of exercise ancestry were observed for body mass, fat and muscle mass, serum insulin, glucose tolerance, and muscle gene expression. F1 EX females were heavier than F1 SED females, but F1 SED females had higher absolute tibialis anterior and omental fat masses. Serum insulin was lower in F1 SED females compared to F1 EX females. F2 EX females had impaired glucose tolerance compared to F2 SED females. Analysis of skeletal muscle mRNA levels revealed several generation- and sex-specific differences in mRNA levels for multiple genes, especially those related to metabolic genes (e.g., F1 EX males had lower mRNA levels of Hk2, Ppard, Ppargc1M-NM-1, Adipoq, and Scd1 than F1 SED males). These results provide preliminary evidence that parental exercise training can influence health-related phenotypes in mouse offspring. We analyzed RNA from 10 males each from exercise and sedentary ancestries over 2 generations of offspring (F1 and F2)
2012-08-30 | E-GEOD-40469 | biostudies-arrayexpress
Project description:Gestating F0 generational female rats were transiently exposed to DDT during fetal gonadal sex determination and the incidence of adult onset pathologies was assessed in the subsequent F1, F2, and F3 generations. In addition, sperm differential DNA methylation regions (DMRs) that were associated with specific pathologies in the F3 generation males were investigated. No pathology was observed in the F1 generation DDT lineage males or females compared with F1 generation controls (vehicle exposure). There was an increase of testis disease and early onset puberty in the F2 generation DDT lineage males. The F3 generation DDT males had significant increases in testis disease, prostate disease, and late onset puberty. The F3 generation DDT females had significant increases in ovarian and kidney disease. Both the F3 generation males and females had significant increases in the frequency of obesity and multiple disease. The F3 generation sperm was collected to examine DMRs for the ancestrally exposed DDT male population. Unique sets of DMRs were associated with late onset puberty, kidney disease, and multiple disease pathologies.
2018-07-31 | GSE114032 | GEO
Project description:We sought to evaluate the brain gene expression profiles of male courtship display. To assess male display and courtship behavior, we designed a courtship preference assay. We evaluated social interactions between males and females using a 40 gallon tank design with a ‘rock’ habitat at one end and ‘sand’ at the other, separated by glass bottom. When parental rock species (Petrotilapia nigra (TaxId 526958), Maylandia zebra (TaxId 106582), Labeotropheus feulliborni) are placed in this tank paradigm, males court females over the rocks. Males of sand species (Mchenga conophorus, Aulonocara baenschi (TaxId 143496), Tramitichromis intermedius (TaxId 323801)) court females over sand and construct species appropriate bowers. When single rock x sand F1 males were placed in this set up with F1 females, males invariably courted females over the ‘rock’ habitat, suggesting genetic dominance. When two rock x sand F1 males were allowed to compete for F1 females in this tank paradigm, something interesting happened. One male, typically the larger, courted females over the rock habitat, and the other simultaneously constructed bowers to court females in the sand. We detected no difference in GSI (gonadal somatic index) between F1 males behaving as ‘socially rock’ vs. ‘socially sand.’ This observation of divergent behavior among interacting F1 brothers suggests an interaction between the genome and the social environment in these males.
2021-07-02 | GSE122500 | GEO
Project description:Females of Chinese tongue sole (Cynoglossus semilaevis) grow 2-4 times faster and bigger than males, but some genetic females can sex reverse into phenotypic males (called pseudomales, ZW karyotype) that presents similar slow growth to normal males. Pseudomales could only produce Z-type sperm, of which the inheritance epigenetic pattern makes their offspring tend to be pseudomales. In this study, to explore the potential mechanism underlying sperm defect (W sperm absence) of pseudomales, we compared the proteomic profiles of pseudomale and male semen samples.
2024-11-07 | PXD057604 |
Project description:Metabolism in males and females is distinct. Differences are usually linked to sexual reproduction, with circulating signals (e.g. hormones) playing major roles. By contrast, sex differences prior to sexual maturity and intrinsic to individual metabolic tissues are less understood. We analyzed Drosophila melanogaster larvae and find that males store more fat than females, the opposite of the sexual dimorphism in adults. We show that metabolic differences are intrinsic to the major fat storage tissue, including many differences in the expression of metabolic genes. Our previous work identified fat storage roles for Spenito (Nito), a conserved RNA-binding protein and regulator of sex determination. Nito knockdown specifically in the fat storage tissue abolished fat differences between males and females. We further show that Nito is required for sex-specific expression of the master regulator of sex determination, Sex-lethal (Sxl). “Feminization” of fat storage cells via tissue-specific overexpression of a Sxl target gene made larvae lean, reduced the fat differences between males and females, and induced female-like metabolic gene expression. Altogether, this study supports a model in which Nito autonomously controls sexual dimorphisms and differential expression of metabolic genes in fat cells in part through its regulation of the sex determination pathway.
2023-04-25 | GSE229991 | GEO
Project description:We investigated parent-of-origin and allele-specific expression effects on obesity and hepatic gene expression in reciprocal crosses between the Berlin Fat Mouse Inbred line (BFMI) and C57Bl/6NCrl (B6N). We sequenced mRNA extracted from liver tissue of 10 M. Musculus individuals. 4 liver samples were collected from 10 week old inbred strains (1 male and 1 female Berlin Fat Mouse Inbred line (BFMI), 1 male and 1 female C57Bl/6NCrl (B6N)) and 6 liver samples collected from 10 week old F1 males using a reciprocal cross design (3 paternal BFMI (patBFMI) vs 3 maternal BFMI (matBFMI)). Reciprocal crosses were generated from the Berlin Fat Mouse Inbred line BFMI860-12/Hber (BFMI) and C57BL/6NCrl (B6N). Seven BFMI males were mated with seven B6N females and six B6N males with six BFMI860 females to generate 48 F1 animals (deemed patBFMI and matBFMI, respectively). Each reciprocal F1 offspring groups consisted of 12 males and 12 females. From these animals three F1 males from three BFMI females and three F1 males from three B6N females were used for RNA-seq measurements. One high fat diet raised male and female from each inbred parental strain (BFMI and B6N) were used as parental strain control animals and measured via RNA-seq as well.
2015-11-11 | E-GEOD-74889 | biostudies-arrayexpress