H3K4me3 and H3K27me3 modification profiling in early zebrafish embryo
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA434216 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6729440_1.fastq.gz | Fastqsanger.gz | |||
| SRR6729440_2.fastq.gz | Fastqsanger.gz | |||
| SRR6729450_1.fastq.gz | Fastqsanger.gz | |||
| SRR6729450_2.fastq.gz | Fastqsanger.gz | |||
| SRR6729460_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 57 |
Similar Datasets
Project description:Multicellular organism requires concise gene regulation during ontogeny and epigenetic modifications, such as DNA methylation and histone modification, facilitate the concise regulation. The conservative reprogramming patterns of DNA methylation in vertebrates have been well described but knowledge of how histone modifications are passed on to zygote from gametes are limited and conservations of histone modifications are not clear.We profiled H3K4me3/H3K27me3 modifications in gametes and early embryos in zebrafish and find out that patterns in gene promoter regions have been largely set to either bivalent or active states in gametes and then passed on to zygote. Bivalent states are partially maintained and active states are restored to match sperm’s pattern. But repressive H3K27me3 modifications as well as stage specific modifications in promoter regions are discarded. Prior to zygotic genome activation, patterns of genes that initialize ZGA have been converted to non-repressive states to coordinate gene expression. Histone modification in hyper methylated promoter peaks are erased independent of DNA methylome reprogramming. Comparative analysis revealed that functions of bivalent and active genes passed on from gametes are conserved in vertebrates and gene age preferences by bivalent and active histone modifications are also confirmed in vertebrates.
2019-04-17 | GSE110663 | GEO
Project description:The perturbations of ER homeostasis lead to the development of a condition referred to as ER stress. However, the repressive trimethylation on histone H3 lysine 27 (H3k27me3) under ER stress remains largely elusive. Here, we identify a critical role for H3k27me3 to impact the expression of Crytochrome 1 (Cry1). To examine the effect of ER stress on histone modification, MEFs were treated with vehicle 2μg/ml tunicamycin for 6 h. The cell lysate were collected and ChIP-seq assays were performed with the primary H3k27me3 or H3k4me3 antibody. When compared to the Vehicle group, the tunicamycin treatment reduced the 23,008 H3k27me3 peaks. In line with the roles of H3k27me3 in the regulation of gene transcriptions, annotation of the peak in genomic positions to the cloest genes indicated that many peaks were positioned after the transcription start site. Cry1 is one of the most regulated genes. However, the tunicamycin treatment slightly reduced H3k4me3 modification in MEFs. There are only 3109 peaks were decreased by the tunicamycin treatment. These data suggest ER stress selectively regulated H3k27me3 modification in the hisone 3 and reactivate Cry1 gene expression in MEFs.
2021-05-01 | GSE131068 | GEO
Project description:Histone modifications play critical roles in regulating developmental genes expression during embryo development in mammals1,2. However, genome-wide analysis of histone modifications in pre-implantation embryos has been impeded by technical difficulties and the scarcity of required materials. Here, by using a small-scale chromatin immunoprecipitation sequencing (ChIP-seq) method3, for the first time, we mapped the genome-wide profile of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 trimethylation (H3K27me3), associated with gene activation and repression respectively, in mouse pre-implantation embryos. We found that the establishment of H3K4me3 mark occurs much more rapidly than that of H3K27me3 following fertilization. Furthermore, H3K4me3 and H3K27me3 possess distinct features in sequence preference and dynamics in pre-implantation embryos. Although most H3K4me3 signature constantly exists on transcription start site (TSS) region, the breadth of H3K4me3 domain is of high-dynamic feature. Interestingly, the broad H3K4me3 peak (wider than 5kb) is associated with higher transcription activity and cell identity not only in pre-implantation embryos but also in the process of deriving embryonic stem cells (ESCs) from the inner cell mass (ICM) and trophoblast stem cells (TSCs) from the trophectoderm (TE). Unlike those observed in ESCs, we found that the bivalency (containing both H3K4me3 and H3K27me3) is unstable and not frequently observed in early cleavage stage embryos until the morula to blastocyst transition. Taken all together, our study provides a genome-wide map of H3K4me3 and H3K27me3 modifications in pre-implantation embryos, which offers us opportunities to further understand the epigenetic regulation mechanism in early embryo development.
2016-09-15 | GSE73952 | GEO
Project description:Although studies of the differentiation from mouse embryonic stem (ES) cells to vascular endothelial cells (ECs) provide an excellent model for investigating the molecular mechanisms underlying vascular development, temporal dynamics of gene expression and chromatin modifications have not been well studied. Herein, using transcriptomic and epigenomic analyses based on the H3K4me3 and H3K27me3 modifications at a genome-wide scale, we analyzed the EC differentiation steps from ES cells and crucial epigenetic modifications unique to ECs. We determined that Gata2, Fli1, Sox7, and Sox18 are master regulators of EC induced following expression of the hemangioblast commitment pioneer factor, Etv2. These master regulator gene loci were repressed by H3K27me3 under the mesoderm period, but rapidly transitioned to the histone modification switching from H3K27me3 to H3K4me3 after treatment with vascular endothelial growth factor (VEGF). SiRNA knockdown experiments indicated that these regulators are indispensable not only for proper EC differentiation but also for blocking the commitment to other closely aligned lineages. Collectively, our detailed epigenetic analysis might provide an advanced model for understanding temporal regulation of chromatin signature and resulting gene expression profiles during EC commitment. These studies would lead the future development of methods to amplify the vascular endothelium for regenerative medicine.
2017-02-13 | GSE94828 | GEO
Project description:Examination of H3K27me3 histone modification in A549 cell line H3K27me3 ChiP-Seq
2015-12-11 | E-GEOD-75903 | biostudies-arrayexpress
Project description:Arabidopsis telomeric repeat binding factors (TRBs) can bind telomeric DNA sequences to protect telomeres from degradation. TRBs can also recruit Polycomb Repressive Complex 2 (PRC2) to deposit tri-methylation of H3 lysine 27 (H3K27me3) over certain target loci. Here, we demonstrate that TRBs also associate and colocalize with JUMONJI14 (JMJ14) and trigger H3K4me3 demethylation at some loci. The trb1/2/3 triple mutant and the jmj14-1 mutant show an increased level of H3K4me3 over TRB and JMJ14 binding sites, resulting in up-regulation of their target genes. Furthermore, tethering TRBs to the promoter region of genes with an artificial zinc finger (TRB-ZF) successfully triggers target gene silencing, as well as H3K27me3 deposition, and H3K4me3 removal. Interestingly, JMJ14 is predominantly recruited to ZF off-target sites with low levels of H3K4me3, which is accompanied with TRB-ZFs triggered H3K4me3 removal at these loci. These results suggest that TRB proteins coordinate PRC2 and JMJ14 activities to repress target genes via H3K27me3 deposition and H3K4me3 removal.
2023-02-22 | MSV000091349 | MassIVE
Project description:Reprogramming of histone modification regulates gene expression and mammal preimplantation development. Trimethylation of lysine 4 on histone 3 (H3K4me3) has unique landscape in mouse oocytes and early embryos. However, the dynamics and function of H3K4me3 in livestock embryos remain unclear. To address how it is reprogrammed in domestic animals, we profiled changes of H3K4me3 during bovine early embryo development. Notably, the overall signal of H3K4me3 decreased during embryonic genome activation (EGA). By utilizing ultra-low-input native ChIP-seq (ULI-NChIP-seq) technology, we observed widespread broad H3K4me3 domains in oocytes and embryos. The signal of broad H3K4me3 began to decrease after fertilization and was lowest after EGA. Along with the removal of broad H3K4me3, deposition of H3K4me3 at promoter regions enhanced gradually. Besides, the transcriptional activity and signal of promoter H3K4me3 showed positive correlation after the erasure of broad H3K4me3 at 16-cell stage. Moreover, knocking down of demethylases KDM5A, KDM5B and KDM5C caused EGA delay and blastocyst formation failure. RNA-seq analysis revealed 47.8% down-regulated genes in knockdown embryos at 8/16-cell stage were EGA genes, and 63.1% of up-regulated genes were maternal transcripts. Particularly, the positive correlation between transcriptional activity and promoter H3K4me3 during EGA was restrained when knocking down of KDM5A, KDM5B and KDM5C. Overall, our work initiatively mapped the genomic reprogramming of H3K4me3 during bovine preimplantation development, and KDM5A/B/C played roles in modulating oocyte-to-embryonic transition (OET) through timely erasure of broad H3K4me3 domains far away from promoters.
2022-03-31 | GSE189100 | GEO
Project description:Reprogramming of histone modification regulates gene expression and mammal preimplantation development. Trimethylation of lysine 4 on histone 3 (H3K4me3) has unique landscape in mouse oocytes and early embryos. However, the dynamics and function of H3K4me3 in livestock embryos remain unclear. To address how it is reprogrammed in domestic animals, we profiled changes of H3K4me3 during bovine early embryo development. Notably, the overall signal of H3K4me3 decreased during embryonic genome activation (EGA). By utilizing ultra-low-input native ChIP-seq (ULI-NChIP-seq) technology, we observed widespread broad H3K4me3 domains in oocytes and embryos. The signal of broad H3K4me3 began to decrease after fertilization and was lowest after EGA. Along with the removal of broad H3K4me3, deposition of H3K4me3 at promoter regions enhanced gradually. Besides, the transcriptional activity and signal of promoter H3K4me3 showed positive correlation after the erasure of broad H3K4me3 at 16-cell stage. Moreover, knocking down of demethylases KDM5A, KDM5B and KDM5C caused EGA delay and blastocyst formation failure. RNA-seq analysis revealed 47.8% down-regulated genes in knockdown embryos at 8/16-cell stage were EGA genes, and 63.1% of up-regulated genes were maternal transcripts. Particularly, the positive correlation between transcriptional activity and promoter H3K4me3 during EGA was restrained when knocking down of KDM5A, KDM5B and KDM5C. Overall, our work initiatively mapped the genomic reprogramming of H3K4me3 during bovine preimplantation development, and KDM5A/B/C played roles in modulating oocyte-to-embryonic transition (OET) through timely erasure of broad H3K4me3 domains far away from promoters.
2022-03-31 | GSE189101 | GEO
Project description:Vernalization, the requirement of long-term exposure to low environmental temperature for flowering, is a typical epigenetic phenomenon in plants. Histone modifications have been analyzed for key vernalization genes, but genome-wide regulation remains unclear. Here, we performed global analysis of histone 3 lysine 4 (H3K4me3) and 27 (H3K27me3) trimethylation with Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) during and after vernalization to obtain complete view of histone modification fluctuation both on whole genome scale and for single genes, even different regions of genes. The critical role of H3K27me3 was revealed. During vernalization H3K27me3 regulation concentrated on a few biological processes, with two essential environmental responses, transcription regulation and anti-stress reactions, being main targets, as indicated by change pattern and GO analysis. The regulation of H3K4me3, however, showed no obvious focus. For gene expression, H3K27me3 is involved in multiple trends of control. H3K4me3, however, mainly focuses on unidirectional regulation. After vernalization most of H3K27me3 changes were kept, but relatively small proportion of H3K4me3 changes could be maintained, as shown by multiple-level analysis, suggesting the active role of H3K27me3 in epigenetic memory. Vernalization-induced histone modification changes were uncovered for VRN3, a gene integrating vernalization/photoperiod signals, suggesting its regulation role at epigenetic level. Memory-related genes were genome-widely identified and a high proportion of them showed quantitative response to vernalization-treatment, suggesting broad existence of this mechanism. Our studies shed new light on epigenetic role of H3K27me3 and VRN3 in vernalization, revealed mechanism underlying epigenetic memory, which helps us to further understand vernalization, a mechanism with great potential in agriculture.
2018-05-22 | GSE93140 | GEO
Project description:A small subgroup of embryonic stem cells (ESCs) exhibit molecular features similar to those of 2-cell (2C) embryos. These so-called 2C-like cells display highly relaxed chromatin architecture and expanded developmental potential. However, it remains elusive whether 2C-like cells and 2-cell embryos share similar epigenetic features. Here, we map the genome-wide profiles of histone H3K4me3 and H3K27me3 in 2C-like cells. We integrated transcriptome and epigenome data to conduct a detailed comparison of 2-cell embryos and 2C-like cells. We found that the majority of genes in 2C-like cells inherit their histone status from ESCs. Among the genes showing a switch in their histone methylation status during 2C-like transitions, only a small number acquire a 2-cell-embryo epigenetic signatures. In contrast, broad H3K4me3 domains display extensive loss in 2C-like cells. Most of differentially expressed genes display decreased H3K4me3 and H3K27me3 levels in 2C-like cells whereas de novo H3K4me3 deposition is closely linked with the expression levels of upregulated 2C-embryo-specific genes. Taken together, our study reveals the unique epigenetic profiles of 2C-like cells, facilitating the further exploration of totipotency in the future.
2021-01-23 | GSE164486 | GEO