Project description:H3K9Ac ChIP-Seq was conducted to investigate whether loss of sinhcaf increases the histone acetylation in the promoter region of kinesin family genes.Increased H3K9Ac ChIP-Seq peaks upon sinhcaf loss were detected in the kif26ab promoter region.
Project description:DNA methylation undergoes dynamic changes during development and cell differentiation. Recent genome-wide studies discovered that tissue-specific differentially methylated regions (DMRs) often overlap tissue-specific distal cis-regulatory elements. However, developmental DNA methylation dynamics of the majority of the genomic CpGs outside gene promoters and CpG islands has not been extensively characterized. Here we generate and compare comprehensive DNA methylome maps of zebrafish developing embryos. From these maps, we identify thousands of developmental stage-specific DMRs (dsDMRs) across zebrafish developmental stages. The dsDMRs contain evolutionarily conserved sequences, are associated with developmental genes and are marked with active enhancer histone posttranslational modifications. Their methylation pattern correlates much stronger than promoter methylation with expression of putative target genes. When tested in vivo using a transgenic zebrafish assay, 20 out of 20 selected candidate dsDMRs exhibit functional enhancer activities. Our data suggest that developmental enhancers are a major target of DNA methylation changes during embryogenesis. MRE profiles of sperm and 2.5-hpf, 3.5-hpf, 4.5-hpf, 6-hpf and 24-hpf embryos were generated using Illumina HiSeq sequencing.
Project description:DNA methylation undergoes dynamic changes during development and cell differentiation. Recent genome-wide studies discovered that tissue-specific differentially methylated regions (DMRs) often overlap tissue-specific distal cis-regulatory elements. However, developmental DNA methylation dynamics of the majority of the genomic CpGs outside gene promoters and CpG islands has not been extensively characterized. Here we generate and compare comprehensive DNA methylome maps of zebrafish developing embryos. From these maps, we identify thousands of developmental stage-specific DMRs (dsDMRs) across zebrafish developmental stages. The dsDMRs contain evolutionarily conserved sequences, are associated with developmental genes and are marked with active enhancer histone posttranslational modifications. Their methylation pattern correlates much stronger than promoter methylation with expression of putative target genes. When tested in vivo using a transgenic zebrafish assay, 20 out of 20 selected candidate dsDMRs exhibit functional enhancer activities. Our data suggest that developmental enhancers are a major target of DNA methylation changes during embryogenesis. MeDIP profiles of sperm and 2.5-hpf, 3.5-hpf, 4.5-hpf, 6-hpf and 24-hpf embryos were generated using Illumina HiSeq sequencing.
Project description:zebrafish embryos proteome for slbp2 KO F3 and wild type at 2.5hpf and 3.5hpf, three replicates for every sample. There are 12 samples in total. Then we analyse the different expressed genes and hope to find out clue which result in serious phenotype of slbp2 KO F3.
Project description:This SuperSeries is composed of the following subset Series: GSE26707: Zebrafish 27hpf embryos: hdac1 mutant (hi1618) vs sibling GSE26708: Zebrafish embryos: hdac1 Morphants vs Standard control morphants GSE26709: Zebrafish embryos: hdac1 Morphants vs Standard control morphants at 12, 18 and 27 hpf Refer to individual Series
Project description:DNA methylation undergoes dynamic changes during development and cell differentiation. Recent genome-wide studies discovered that tissue-specific differentially methylated regions (DMRs) often overlap tissue-specific distal cis-regulatory elements. However, developmental DNA methylation dynamics of the majority of the genomic CpGs outside gene promoters and CpG islands has not been extensively characterized. Here we generate and compare comprehensive DNA methylome maps of zebrafish developing embryos. From these maps, we identify thousands of developmental stage-specific DMRs (dsDMRs) across zebrafish developmental stages. The dsDMRs contain evolutionarily conserved sequences, are associated with developmental genes and are marked with active enhancer histone posttranslational modifications. Their methylation pattern correlates much stronger than promoter methylation with expression of putative target genes. When tested in vivo using a transgenic zebrafish assay, 20 out of 20 selected candidate dsDMRs exhibit functional enhancer activities. Our data suggest that developmental enhancers are a major target of DNA methylation changes during embryogenesis.
Project description:DNA methylation undergoes dynamic changes during development and cell differentiation. Recent genome-wide studies discovered that tissue-specific differentially methylated regions (DMRs) often overlap tissue-specific distal cis-regulatory elements. However, developmental DNA methylation dynamics of the majority of the genomic CpGs outside gene promoters and CpG islands has not been extensively characterized. Here we generate and compare comprehensive DNA methylome maps of zebrafish developing embryos. From these maps, we identify thousands of developmental stage-specific DMRs (dsDMRs) across zebrafish developmental stages. The dsDMRs contain evolutionarily conserved sequences, are associated with developmental genes and are marked with active enhancer histone posttranslational modifications. Their methylation pattern correlates much stronger than promoter methylation with expression of putative target genes. When tested in vivo using a transgenic zebrafish assay, 20 out of 20 selected candidate dsDMRs exhibit functional enhancer activities. Our data suggest that developmental enhancers are a major target of DNA methylation changes during embryogenesis.
Project description:Somatic cell nuclear transfer (SCNT) enables gaining of totipotency by reprogramming nuclei of terminally differentiated donor cell. Recent studies have clearly demonstrated that intervention of epigenetic networks can significantly elevate both in vitro and in vivo development potential of NT embryos. Specifically, trichostatin A (TSA), a kind of histone deacetylase inhibitors (HDACi), was proved to functionally works during cloning in various mammal systems. However, how it modulates histone acylation lacks careful illustration. Here, we systematically evaluate the effect and limitation of TSA during SCNT embryo development by generating genome-wide H3K9ac maps. In addition, a Dux-dependent 2-cell (2C) activation deficiency is observed in SCNT embryos as compared with their natural fertilized counterparts. Strikingly, a refined Dux supplement can successfully assist SCNT embryos in overcoming the 2C activation defect and further promotes the overall cloning efficiency. Together, our study for the first time reveals the regulation mechanism of histone marker H3K9ac in SCNT and provides the new insight of Dux during embryogenesis.
Project description:Transcriptional profiling of hdac1 mutant zebrafish in comparison to their sibling embryos. Embryos resulting from a cross between heterozygous hdac1 mutant zebrafish (hi1618/+) where cultured together then mutants separated from the siblings one the basis of phenotype and RNA extracted from the two groups at 27hpf was compared in a two-colour hybridisation.