Developmental features of DNA methylation during activation of the embryonic zebrafish genome
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ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE33236 | GEO | 2012/07/06
SECONDARY ACCESSION(S): PRJNA149411
REPOSITORIES: GEO
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Project description:Zygotic genome activation (ZGA) occurs at the mid-blastula transition (MBT) in zebrafish and is a period of chromatin remodeling. Genome-scale gametic demethylation and remethylation occurs after fertilization, during blastula stages, but how ZGA relates to promoter DNA methylation states is unknown. Using methylated DNA immunoprecipitation coupled to high-density microarray hybridization (MeDIP-ChIP), we characterize genome-wide promoter DNA methylation dynamics before, during and after ZGA onset, in relation changes in post-translational histone modification and gene expression (Series GSE22830). A Kolmogorov-Smirnov (KS) test was applied with P <= 0.01 to identify methylation peaks. MeDIP-chip experiments were performed on24 hpf zebrafish embryos and sperm. Samples were lysed and proteins digested by proteinase k treatment. DNA was extracted with phenol-chloroform-isoamylalcohol and ethanol precipitation. The DNA was RNAse treated and sonicated to fragment lengths between 300-1000 bp. From each stage, duplicate immuneoprecipitations were performed using anti-5-methylcytosine antibody (10 ng/M-BM-5l; Mab-006-100; Diagenode) coupled to Dynabeads M-280 sheep anti-mouse IgG (Invitrogen). MeDIP and input DNA (150 ng each) were amplified (WGA-2; Sigma-Aldrich), cleaned up, eluted and processed for array hybridization. MeDIP and input DNA were labeled and co-hybridized onto the Nimbegen promoter arrays. The array covers 15 kb of upstream regulatory sequence and 5 kb downstream of the TSS of all zebrafish genes. A Kolmogorov-Smirnov (KS) test was applied with P <= 0.01 to identify methylation peaks.
2012-07-05 | E-GEOD-33236 | biostudies-arrayexpress
Project description:Early zebrafish embryo development proceeds first from a maternally transcribed and stored mRNAs, and zygotic gene activation (ZGA) is initiated at the mid-blastula transition (MBT; 1000-cell stage), 3.3 h post-fertilization. Very little is known on how the zygotic genome is programmed for transcriptional activation at the MBT. To start addressing this issue, we have mapped by ChIP-chip genome-wide promoter histone methylation (H3K4me3, H3K9me3, H3K27me3, H3K36me3) and RNA Pol II profiles before ZGA (256-cell stage; 2.5 hpf), during ZGA (MBT; 3.5 hpf)) and after ZGA (Post-MBT; 5.3 hpf) . We used a custom 2.1M probe HD promoter array (Nimblegen) for ChIP and input DNA hybridization. Peak detection was done using MA2C with P=10e-4 as cutoff. ChIP-chip experiments were performed from chromatin prepared by sonication after formaldehyde cross-linking, from embryos are the indicated developmental stages and ChIP DNA was hybridized onto the aforementioned Nimbegen promoter arrays.
2011-12-02 | E-GEOD-27314 | biostudies-arrayexpress
Project description:Early zebrafish embryo development proceeds first from a maternally transcribed and stored mRNAs, and zygotic gene activation (ZGA) is initiated at the mid-blastula transition (MBT; 1000-cell stage), 3.3 h post-fertilization. Very little is known on how the zygotic genome is programmed for transcriptional activation at the MBT. To start addressing this issue, we have mapped by ChIP-chip genome-wide promoter histone methylation (H3K4me3, H3K9me3, H3K27me3, H3K36me3) and RNA Pol II profiles before ZGA (256-cell stage; 2.5 hpf), during ZGA (MBT; 3.5 hpf)) and after ZGA (Post-MBT; 5.3 hpf) . We used a custom 2.1M probe HD promoter array (Nimblegen) for ChIP and input DNA hybridization. Peak detection was done using MA2C with P=10e-4 as cutoff.
2011-12-02 | GSE27314 | GEO
Project description:We describe that during early zebrafish development, DNA methylation has little influence on enhancer activity, and that hypo-methylation is a unique feature of primed enhancers, whereas active enhancers are generally hyper-methylated. Hypo-methylated enhancers (hypo-enhancers) are enriched close to important transcription factors (TFs) that act later in development, are specifically de-methylated before the mid blastula transition (MBT), and reside in a unique epigenetic environment. Finally, we demonstrate that hypo-enhancers are functionally active later in development and that they are physically associated with the transcriptional start site (TSS) of target-genes, irrespective of target-gene activity.
2015-11-06 | GSE74616 | GEO
Project description:We describe that during early zebrafish development, DNA methylation has little influence on enhancer activity, and that hypo-methylation is a unique feature of primed enhancers, whereas active enhancers are generally hyper-methylated. Hypo-methylated enhancers (hypo-enhancers) are enriched close to important transcription factors (TFs) that act later in development, are specifically de-methylated before the mid blastula transition (MBT), and reside in a unique epigenetic environment. Finally, we demonstrate that hypo-enhancers are functionally active later in development and that they are physically associated with the transcriptional start site (TSS) of target-genes, irrespective of target-gene activity.
2015-11-06 | GSE74231 | GEO
Project description:We describe that during early zebrafish development, DNA methylation has little influence on enhancer activity, and that hypo-methylation is a unique feature of primed enhancers, whereas active enhancers are generally hyper-methylated. Hypo-methylated enhancers (hypo-enhancers) are enriched close to important transcription factors (TFs) that act later in development, are specifically de-methylated before the mid blastula transition (MBT), and reside in a unique epigenetic environment. Finally, we demonstrate that hypo-enhancers are functionally active later in development and that they are physically associated with the transcriptional start site (TSS) of target-genes, irrespective of target-gene activity. We performed 6 different 4C-Seq experiment at two different timepoints and in adult brain.
2015-11-06 | E-GEOD-74616 | biostudies-arrayexpress
Project description:We describe that during early zebrafish development, DNA methylation has little influence on enhancer activity, and that hypo-methylation is a unique feature of primed enhancers, whereas active enhancers are generally hyper-methylated. Hypo-methylated enhancers (hypo-enhancers) are enriched close to important transcription factors (TFs) that act later in development, are specifically de-methylated before the mid blastula transition (MBT), and reside in a unique epigenetic environment. Finally, we demonstrate that hypo-enhancers are functionally active later in development and that they are physically associated with the transcriptional start site (TSS) of target-genes, irrespective of target-gene activity. we analyzed 5 novel ChIP-Seq libraries where we used the following AB (H3K27ac,H3K4me1,H3K4me2 and H3K27ac) and an Atac-Seq library.
2015-11-06 | E-GEOD-74231 | biostudies-arrayexpress
Project description:Upon fertilization, the embryonic genome remains transcriptionally inactive until the mid-blastula transition. Zygotic genome activation (ZGA) of vertebrate embryos has been extensively studied using nucleic acid-based strategies, but proteomics data are still scarce, impeding the full mechanistic understanding of how ZGA is executed during the maternal-to-zygotic transition (MZT). Here, we performed quantitative proteomics to decipher the proteome landscape of zebrafish embryos during the MZT, quantifying nearly 5,000 proteins across four embryonic stages. The stage-specific clustering based on protein expression pattern revealed that helicases (i.e., eif4a2 and ruvbl1) facilitate pluripotency factors (i.e., nanog, pou5f3, ctcf, and hmga1) triggering ZGA in zebrafish, accompanied by the maternal product decay with P-bodies and ubiquitin dependent proteolytic pathway. Dozens of transcription factors show wave-like expression patterns during MZT, implying their diverse functions in triggering the ZGA and modulating differentiation for organ development. The combination of morpholino knockdown and quantitative proteomics demonstrated that maternal Nanog is required for proper embryogenesis by regulating 1) interactions with other pluripotency factors, 2) F-actin band formation, 3) cell cycle checkpoints and 4) maternal product degradation. This study represents the most systematic proteomics survey of developmentally regulated proteins and their expression profiles accompanying MZT in zebrafish, which is a valuable proteome resource for understanding ZGA.
2024-05-01 | PXD036678 | Pride
Project description:Samples from 20 children with B-cell precursor ALL, comprising ten with high hyperdiploidy and ten with the ETV6/RUNX1 fusion, were included in the study. Four µg of methylated and input fraction DNA were analyzed with a classic MeDIP assay and subsequent microarray hybridization using the NimbleGen CpG Island-Plus-Promoter Array (Roche NimbleGen, Madison, WI).<br><br>This array platform covers all 28,226 UCSC-annotated CpG islands and promoter regions for all RefSeq genes, including 385,000 probes of 50-75mer length per array, with an upstream and downstream promoter tiling of 800 bp and 200 bp, respectively. Signal intensity data were extracted from the scanned images. Each feature on the array has a corresponding log2 ratio, which is the ratio of the input signals for the methylated DNA and the input fraction DNA. The log2 ratio was scaled in order to center the ratio data around zero by subtracting the bi-weight mean for the log2 ratio values for all features on the array from each log2 ratio value. A modified ACME algorithm, where a fixed-length window (750 bp) is placed around each consecutive probe, and the one-sided Kolmogorov-Smirnov test were then applied on the scaled log2 ratio data to determine whether the probes were drawn from a significantly more positive distribution (peak) of intensity log2 ratios than the other probes in the array. The resulting score for each probe is the -log10 p-value from the windowed Kolmogorov-Smirnov test around that probe. Peak data were generated by searching for probes above a p-value minimum cut-off (-log10) of 2.<br><br>Peaks within 500 bp of each other were merged. Each annotated gene was subsequently searched for peaks appearing in a specified promoter region around the transcription start site. The region searched was design-specific, spanning from 5 kb upstream to 1 kb downstream of the transcription start site. Genes that had at least two probes with peaks above the p-value minimum cut-off were considered to have significant CpG island methylation scores for hypermethylation.
2009-09-19 | E-MTAB-144 | biostudies-arrayexpress
Project description:During animal development, a fertilized egg is initially under the control of maternal products and only starts zygotic transcription after several cell divisions. In animals such as Xenopus, zebrafish and Drosophila, a massive increase in zygotic transcription occurs during the mid-blastula transition (MBT), when cells shift from rapid, synchronous cell divisions without gap phases to prolonged asynchronous divisions. Before MBT, only a few so-called pre-MBT genes are expressed. How transcription is set up during these early stages is poorly understood. For example, paused RNA Polymerase (Pol II) is frequently found at developmental control genes in mammalian embryonic stem cells and Drosophila embryos but when Pol II pausing is first established in the embryo is unknown. We have analyzed the genome-wide Pol II occupancy during the maternal-to-zygotic transition in hand-staged Drosophila embryos. The results show that massive Pol II recruitment and pausing is established during MBT. The ~100 genes that are transcribed before MBT are particularly short, consistent with a need for rapid transcription during these early cell divisions. Remarkably, most of these genes are transcribed without Pol II pausing and this correlates with a TATA-enriched promoter type. This suggests that distinct strategies are used for activation in the early Drosophila embryo and this may reflect general dynamic properties of promoters used throughout development. Mnase-seq in staged Drosophila embryos
2013-07-26 | E-GEOD-41686 | biostudies-arrayexpress