Whole genome bisulfite sequencing from four stages of zebrafish sperm development
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB86143 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR14656966_1.fastq.gz | Fastqsanger.gz | |||
| ERR14656966_2.fastq.gz | Fastqsanger.gz | |||
| ERR14656967_1.fastq.gz | Fastqsanger.gz | |||
| ERR14656967_2.fastq.gz | Fastqsanger.gz | |||
| ERR14656968_1.fastq.gz | Fastqsanger.gz |
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Project description:Nucleosome arrangement in promoter regions has been shown to play an important role in gene regulation. Genome wide studies in yeast, flies, worms, mammalian ES and transformed cell lines have found well positioned nucleosomes with an area of nucleosome depletion flanking transcription start sites. This Nucleosome arrangement has been shown to be dependent on sequence (cis-regulatory factors), DNA binding factors (trans-regulatory factors) and ATP-dependant chromatin modifiers. However, little is understood about how the nascent embryonic genome positions nucleosomes during development. This is particularly intriguing since the embryonic genome undergoes a whole scale rechromatinization event upon fusion of sperm and oocyte. Using four stages of early embryonic zebrafish development we map nucleosome positions at the promoter region of 34 zebrafish hox genes. We find that nucleosome arrangement at the hox promoters is a dynamic process which happens over several stages. We also find evidence that trans-regulatory factors play a greater role in nucleosome positioning over cis-regulatory elements. Finally we provide evidence that transcriptional activation is the driving force behind the arrangement of nucleosomes at the promoters of hox gene during early development.
2013-12-09 | GSE43756 | GEO
Project description:Nucleosome arrangement in promoter regions has been shown to play an important role in gene regulation. Genome wide studies in yeast, flies, worms, mammalian ES and transformed cell lines have found well positioned nucleosomes with an area of nucleosome depletion flanking transcription start sites. This Nucleosome arrangement has been shown to be dependent on sequence (cis-regulatory factors), DNA binding factors (trans-regulatory factors) and ATP-dependant chromatin modifiers. However, little is understood about how the nascent embryonic genome positions nucleosomes during development. This is particularly intriguing since the embryonic genome undergoes a whole scale rechromatinization event upon fusion of sperm and oocyte. Using four stages of early embryonic zebrafish development we map nucleosome positions at the promoter region of 34 zebrafish hox genes. We find that nucleosome arrangement at the hox promoters is a dynamic process which happens over several stages. We also find evidence that trans-regulatory factors play a greater role in nucleosome positioning over cis-regulatory elements. Finally we provide evidence that transcriptional activation is the driving force behind the arrangement of nucleosomes at the promoters of hox gene during early development. Four tissue types: 2, 4, 6, and 9 hours post fertilzation embryos. Two treatments: Untreated (WT), and Retinoic Acid treated embryos(RA).
2013-12-09 | E-GEOD-43756 | biostudies-arrayexpress
Project description:Medaka sperm methylomes were sequenced using whole genome bisulfite sequencing (WGBS)
2019-04-23 | GSE128797 | GEO
Project description:Bisulfite sequencing of medaka sperm methylomes
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Project description:5-methylcytosine is a major epigenetic modification sometimes called "the fifth nucleotide". However, our knowledge of how offspring inherit the DNA methylome from parents is limited. We generated nine single-base resolution DNA methylomes including zebrafish gametes and early embryos. The oocyte methylome is significantly hypo-methylated compared to sperm. Strikingly, the paternal DNA methylation pattern is maintained throughout early embryogenesis. The maternal DNA methylation pattern is maintained until the 16-cell stage. Then, the oocyte methylome is gradually discarded through cell division, and progressively reprogrammed to a pattern similar to that of the sperm methylome. The passive demethylation rate and the de novo methylation rate are similar in the maternal DNA. By the midblastula stage, the embryo?s methylome is virtually identical to the sperm methylome. Moreover, inheritance of the sperm methylome facilitates the epigenetic regulation of embryogenesis. Therefore, besides DNA sequences, sperm DNA methylome is also inherited in zebrafish early embryos. hMeDIP-seq is performed in sperm,2-cell,16-cell,1k-cell and a input control sample 4 new samples are added to GSE44075. RNA-seq is performed in sperm, egg,1k-cell, germring samples .hMeDIP-seq is performed in sperm,2-cell,16-cell,1k-cell and a input control sample 10 new samples are added to GSE44075. Bisulfite-seq is performed for nine samples : sperm, egg,16-cell,32-cell,64-cell,128-cell,1k-cell , Germring and testis. TAB-seq is performed for one sample , 32-cell.
2013-05-20 | E-GEOD-44075 | biostudies-arrayexpress
Project description:We report the application of whole genome bisulfite sequencing technology for high-throughput profiling of DNA methylation in mice sperm at young and aging stages. By obtaining over 500 billion bases of sequence from genomic DNA, we generated genome-wide methylation-state maps of sperm from young and aging stages. We find that 2984 differetial methylation regions(DMR) in whole genome, including 916 DMR in promoter regions betweenin sperm from young and aging stages. 591 of DMR in promoter regions were significantly hypomethylated (~59.82%) and 397 significantly hypermethylated (~40.18%) in sperm of old males.
2022-11-28 | GSE141249 | GEO
Project description:To establish contamination profiles, the sperm donors with normal sperm counts were analyzed using an Infinium HumanMethylation450 array. Somatic cell lysis, sperm isolation, DNA extraction, and bisulfite conversion were performed as described by Aston et al. The bisulfite converted sperm DNA was hybridized to Illumina Infinium HumanMethylation450K microarrays at the University of Utah and run as recommended by the manufacturer (Bibikova et al. 2011). Unpaired blood samples were extracted using Qiagen's DNeasy Blood and Tissue kit and bisulfite converted using Zymo's EZ DNA Methylation kit. All procedures were performed according to the instructions of the manufacturer. Four permutations were run on each sample, including pure blood, half blood and half sperm by DNA concentration, half blood and half sperm by cell count, and pure sperm (n = 16). Concentration was normalized using a spectrophotometer. A Makler cell counting chamber was used to count white blood cells and sperm, which were then normalized in a 1:1 ratio.
2023-11-07 | GSE246935 | GEO
Project description:There is a growing body of evidence that inadequate maternal nutrition during gestation can have immediate and life-long effects on offspring. However, little is known about the reproductive effects of maternal gestational nutrition in offspring males. Here, using a sheep model of poor maternal nutrition (restricted- or over-feeding) during gestation, we found that poor maternal gestational nutrition does not affect semen characteristics (i.e. volume, sperm concentration, pH, sperm motility, sperm morphology) and scrotal circumference in offspring. However, by evaluating associations between poor maternal gestational nutrition and altered small non-cording RNAs (sncRNAs) and DNA methylation in offspring sperm, we demonstrated that poor maternal gestational nutrition alters sperm sncRNA composition and expression. Whole genome bisulfite sequencing further identified genomic regions with increased or decreased DNA methylation in sperm in response to poor maternal gestational nutrition. These findings imply that maternal diet-induced epigenetic errors can accumulate in sperm to worsen developmental outcomes of future generations.
2024-04-04 | GSE225924 | GEO
Project description:Fertilisation is based on the tight interaction between sperm and egg and both sperm and egg proteomes are known to evolve and diverge rapidly even between closely related species. Understanding the sperm proteome therefore provides key insights into the mechanisms involved during fertilisation and the fusion between sperm and egg. Despite being a commonly used model organism for reproductive research, very little is currently understood about the zebrafish Danio rerio sperm proteome. We performed in depth proteomics analysis with six pooled samples containing ejaculates from ten males each. We confidently identified 5410 proteins, from which a total of 3900 GeneIDs were generated leading to 1720 Gene Ontology terms. This number of proteins is larger than the number of proteins described in sperm proteomes of other species.
2025-01-27 | PXD056057 | Pride
Project description:In mature human sperm, genes of importance for embryo development (i.e. transcription factors) lack DNA methylation and bear nucleosomes with distinctive histone modifications, suggesting the specialized packaging of these developmental genes in the germline. Here, we explored the tractable zebrafish model and found conceptual conservation as well as several new features. Biochemical and mass spectrometric approaches reveal the zebrafish sperm genome packaged in nucleosomes and histone variants (and not protamine), and we find linker histones high and H4K16ac absent - key factors which may contribute to genome condensation. We examined several activating (H3K4me2/3, H3K14ac, H2AFV) and repressing (H3K27me3, H3K36me3, H3K9me3, hypoacetylation) modifications/compositions genome-wide, and find developmental genes packaged in large blocks of chromatin with coincident activating and repressing marks and DNA hypomethylation, revealing complex ‘multivalent’ chromatin. Notably, genes that acquire DNA methylation in the soma (muscle) are enriched in transcription factors for alternative cell fates. Remarkably, we find H3K36me3 located in ‘silent’ developmental gene promoters, and not present at the 3’ ends of coding regions of genes heavily transcribed during sperm maturation, suggesting different rules for H3K36me3 in the germline and soma. We also reveal the chromatin patterns of transposons, rDNA, and tRNAs. Finally, high levels of H3K4me3 and H3K14ac in sperm are correlated with genes activated in embryos prior to the mid-blastula transition (MBT), whereas multivalent genes are correlated with activation at or after MBT. Taken together, gene sets with particular functions in the embryo are packaged by distinctive types of complex and often atypical chromatin in sperm. [DNA profiling]: H3K4me3, H3K4me2, H3K14ac, H3K36me3, H3K27me3, H3K9me3, and H2AFV ChIP-chip in zebrafish sperm; DNA methylation in zebrafish sperm and muscle by MeDIP-chip. (two replicates and dye-swaps for all experiments). Antibodies: H3K4me3 (Abcam ab8580 and Active Motif 39159), H3K4me2 (Abcam ab7766), H3K14Ac (Upstate 07-353), H2AZ (Abcam ab4174), H3K27me3 (Upstate 07-449), H3K9me3 (Active Motif 39161), H3K36me3 (Abcam ab9050), 5-methylcytidine (Eurogentec BI-MECY-1000). Supplementary files: Processed data files reporting calculated enrichment log2 ratio (mean ChIP/mean Input in the log2 ratio). Note: For analysis, "mean Input" from H3K4me3-rep1 ch1, H3K4me2-rep1 ch2, and H3K36me3-rep2 ch1 for all ChIP eluates. [mRNA profiling]: Transcripts in zebrafish mature sperm using zebrafish expression microarray from Agilent. (two replicates)
2011-01-13 | E-GEOD-26609 | biostudies-arrayexpress