Systemic gain and loss of chromatin architecture throughout zebrafish development [Hi-C]
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ABSTRACT:
PROVIDER: PRJNA414425 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development.
| PRJNA414421 | ENA
Project description:Systemic gain and loss of chromatin architecture throughout zebrafish development [4C]
| PRJNA414424 | ENA
Project description:Chromosomes are three-dimensional structures in the nucleus that are organized at multiple levels. Studies in mammals have shown that chromosomes segregate in active and inactive compartments (A and B, resp.). A compartments have high transcription activity, high GC-content and replicate early in S-phase. B compartments on the other hand are transcriptionally inactive, have low CG content are often found at the nuclear periphery. Every compartment is further divided into megabase-sized Topologically Associated Domains (TADs), the functional units of gene regulation. Regions within such a domain preferentially interact with each other. TAD positions are conserved between mouse and human genomes. However, it is unclear if non-mammalian vertebrates also show these organizational features and how these change throughout development. We have generated Hi-C maps for zebrafish embryos and show that the structural features of mammalian genomes (A/B-compartments and TADs) are also found in this species. We find that the genes within TADs show spatial co-expression. Moreover, the order of genes within a TAD is conserved to other vertebrate species. One of the key features of development is the switch from maternally loaded mRNAs to the transcriptional activation of the zygotic genome, known as Zygotic Genome Activation (ZGA). Prior to ZGA we see both TADs and compartments. Paradoxically, after the initiation of transcription, TADs and compartments completely disappear. These features are progressively re-established in the following developmental stages. Our results show that chromosome conformation can be formed independent of transcription. Analysis of active enhancer and promoter marks after ZGA showed that promoters and enhancers are enriched at future TAD-boundaries. Later in time, when TADs are present, the enrichment of active enhancers at the TAD-boundaries is lost. These data suggest that proximal enhancer-promoter interactions are needed for gene regulation when TADs are not in place. The loss of both TADs and compartments represent an interesting avenue for the further study of factors involved in the formation of the structural features of vertebrate chromosomes.
2018-07-01 | GSE105013 | GEO
Project description:Chromosomes are three-dimensional structures in the nucleus that are organized at multiple levels. Studies in mammals have shown that chromosomes segregate in active and inactive compartments (A and B, resp.). A compartments have high transcription activity, high GC-content and replicate early in S-phase. B compartments on the other hand are transcriptionally inactive, have low CG content are often found at the nuclear periphery. Every compartment is further divided into megabase-sized Topologically Associated Domains (TADs), the functional units of gene regulation. Regions within such a domain preferentially interact with each other. TAD positions are conserved between mouse and human genomes. However, it is unclear if non-mammalian vertebrates also show these organizational features and how these change throughout development. We have generated Hi-C maps for zebrafish embryos and show that the structural features of mammalian genomes (A/B-compartments and TADs) are also found in this species. We find that the genes within TADs show spatial co-expression. Moreover, the order of genes within a TAD is conserved to other vertebrate species. One of the key features of development is the switch from maternally loaded mRNAs to the transcriptional activation of the zygotic genome, known as Zygotic Genome Activation (ZGA). Prior to ZGA we see both TADs and compartments. Paradoxically, after the initiation of transcription, TADs and compartments completely disappear. These features are progressively re-established in the following developmental stages. Our results show that chromosome conformation can be formed independent of transcription. Analysis of active enhancer and promoter marks after ZGA showed that promoters and enhancers are enriched at future TAD-boundaries. Later in time, when TADs are present, the enrichment of active enhancers at the TAD-boundaries is lost. These data suggest that proximal enhancer-promoter interactions are needed for gene regulation when TADs are not in place. The loss of both TADs and compartments represent an interesting avenue for the further study of factors involved in the formation of the structural features of vertebrate chromosomes.
2018-07-01 | GSE105014 | GEO
Project description:The spatial organization of chromosomes is critical in establishing gene expression programs. We generated in situ Hi-C maps throughout zebrafish development to gain insight into higher-order chromatin organization and dynamics. Zebrafish chromosomes segregate in active and inactive chromatin (A/B compartments), which are further organized into topologically associating domains (TADs). Zebrafish A/B compartments and TADs have genomic features similar to those of their mammalian counterparts, including evolutionary conservation and enrichment of CTCF binding sites at TAD borders. At the earliest time point, when there is no zygotic transcription, the genome is highly structured. After zygotic genome activation (ZGA), the genome loses structural features, which are re-established throughout early development. Despite the absence of structural features, we see clustering of super-enhancers in the 3D genome. Our results provide insight into vertebrate genome organization and demonstrate that the developing zebrafish embryo is a powerful model system to study the dynamics of nuclear organization.
| S-EPMC6047509 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2018-07-01 | GSE105015 | GEO
Project description:Comparative 3D Genome Architecture in Vertebrates (Hi-C)
| PRJNA704984 | ENA
Project description:Hi-C was performed on SK-N-SH cells to study 3-dimensional chromatin architecture. Two biological replicates were performed, each with roughly 25x10^7 cells.
2015-09-01 | E-GEOD-71072 | biostudies-arrayexpress
Project description:Three-dimensional genome architecture influences the regulation of essential nuclear processes, such as gene transcription. However, how 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. This analysis shows a correlation between genome size and chromosome length that affects chromosomal territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through vertebrate’s evolution. Further, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture.
2022-04-12 | GSE167579 | GEO
Project description:Comprehensive analysis of chromatin architecture is crucial for understanding the gene regulatory programs during development and in disease pathogenesis, yet current methods often inadequately address the unique challenges presented by analysis of heterogeneous tissue samples. Here, we introduce Droplet Hi-C, which employs a commercial microfluidic device for high-throughput, single-cell chromatin conformation profiling in droplets. Using Droplet Hi-C we analyzed the chromatin architecture cells from the mouse cortex and delineated gene regulatory programs in major cortical cell types. Additionally, we used this technique to detect copy number variation (CNV), structural variations (SVs) and the extrachromosomal DNA (ecDNA) in cancer cells, revealing clonal dynamics and other oncogenic events during treatment. We further refined this technique to allow for joint single-cell profiling of chromatin architecture and transcriptome, facilitating a more comprehensive exploration of the links between chromatin architecture and gene expression in both normal tissues and tumors. Thus, Droplet Hi-C not only addresses critical gaps in chromatin analysis of heterogeneous tissues but also emerges as a versatile tool enhancing our understanding of gene regulation in health and disease.
2024-09-04 | GSE253407 | GEO