Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development.
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ABSTRACT:
PROVIDER: PRJNA414421 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Systemic gain and loss of chromatin architecture throughout zebrafish development [4C]
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Project description:Systemic gain and loss of chromatin architecture throughout zebrafish development [Hi-C]
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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: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:This SuperSeries is composed of the SubSeries listed below.
2018-07-01 | GSE105015 | 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 | GSE105013 | GEO
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Project description:Defining the structural and functional changes in the nervous system underlying learning and memory represents a major challenge for modern neuroscience. Although changes in neuronal activity following memory formation have been studied [B. F. Grewe et al., Nature 543, 670-675 (2017); M. T. Rogan, U. V. Stäubli, J. E. LeDoux, Nature 390, 604-607 (1997)], the underlying structural changes at the synapse level remain poorly understood. Here, we capture synaptic changes in the midlarval zebrafish brain that occur during associative memory formation by imaging excitatory synapses labeled with recombinant probes using selective plane illumination microscopy. Imaging the same subjects before and after classical conditioning at single-synapse resolution provides an unbiased mapping of synaptic changes accompanying memory formation. In control animals and animals that failed to learn the task, there were no significant changes in the spatial patterns of synapses in the pallium, which contains the equivalent of the mammalian amygdala and is essential for associative learning in teleost fish [M. Portavella, J. P. Vargas, B. Torres, C. Salas, Brain Res. Bull 57, 397-399 (2002)]. In zebrafish that formed memories, we saw a dramatic increase in the number of synapses in the ventrolateral pallium, which contains neurons active during memory formation and retrieval. Concurrently, synapse loss predominated in the dorsomedial pallium. Surprisingly, we did not observe significant changes in the intensity of synaptic labeling, a proxy for synaptic strength, with memory formation in any region of the pallium. Our results suggest that memory formation due to classical conditioning is associated with reciprocal changes in synapse numbers in the pallium.
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2018-01-11 | PXD007859 | Pride