Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen
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PROVIDER: PRJNA993593 | ENA |
REPOSITORIES: ENA
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Project description:We performed in situ Hi-C experiments to determine the 3D chromatin organization in pig spleen
2023-12-31 | GSE237035 | GEO
Project description:The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intra-chromosome interaction rates than neighboring regions and which represent a dominant local structural feature of genome conformation in A. thaliana. These regions appear as positive strips on two-dimensional representations of chromatin interaction and they are enriched in epigenetic marks H3K27me3, H3.1 and H3.3. We also identify over 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not the dominant feature of A. thaliana genome packing, we found over 1,000 regions that have properties of TAD boundaries, and a similar number of regions similar to the interior of TADs. These insulator-like, TAD-boundary-like, and TAD-interior-like regions show strong enrichment for distinct epigenetic marks, and correlate with gene transcription levels. We conclude that epigenetic modifications, gene density, and transcriptional activity all contribute to shaping the local structure of the A. thaliana nuclear genome.
2014-09-24 | E-MTAB-4438 | biostudies-arrayexpress
Project description:The dynamic three-dimensional organization of the diploid yeast genome
| PRJNA349185 | ENA
Project description:Three-dimensional chromatin re-organization during muscle stem cell aging
| PRJNA883688 | ENA
Project description:Age-related skeletal muscle atrophy or sarcopenia is a significant societal problem that is becoming amplified as the world’s population continues to increase. A critical contributor to sarcopenia is the loss in the number and function of muscle stem cells, which maintain tissue homeostasis and regenerate damage. The molecular mechanisms that govern muscle stem cell aging encompass changes across multiple regulatory layers and are integrated by the three-dimensional organization of the genome. To quantitatively understand how hierarchical chromatin architecture changes during muscle stem cell aging, we generated 3D chromatin conformation maps (Hi-C) and integrated these datasets with multi-omic (chromatin accessibility and transcriptome) profiles from bulk populations and single cells. We observed that muscle stem cells display static behavior at global scales of chromatin organization during aging and extensive rewiring of local contacts at finer scales that were associated with variations in transcription factor binding and aberrant gene expression. These data provide insights into genome topology as a regulator of molecular function in stem cell aging.
2023-02-02 | GSE214047 | GEO
Project description:The budding yeast Saccharomyces cerevisiae is a long-standing model for the three-dimensional organization of eukaryotic genomes1,2, and recent high-throughput chromatin conformation capture (Hi-C)2 methods have allowed systematic and unbiased measurement of this organization. Using polymer modeling, some groups have suggested that yeast genome conformation is simple and dominated by its Rabl-like orientation (anaphase-like polarization)3,4. Others have argued that yeast genome conformation is influenced by homolog pairing in diploids5–7 and environment-induced gene relocalization8–13, but the generality and extent of these phenomena remain unclear14. Here, we perform Hi-C on diverged Saccharomyces hybrid diploids to obtain the first global view of chromosome conformation in diploid budding yeasts. Previous studies of homolog pairing have attempted to control for the Rabl-like orientation14, but genomic analysis combined with polymer modeling reveals underappreciated contributions of the Rabl-like orientation to homolog proximity. After controlling for these features, we observe a residual signature of homolog proximity, particularly in saturated phase. From these same data, we also identify known and unexpected inducible gene repositioning. We observe that GAL1 shifts away from the centromere cluster upon galactose induction, consistent with reports of peripheral relocalization8,15. Surprisingly, under galactose induction and saturated phase, we observe a localized increase in homologous interactions between the HAS1 alleles, mediated by association with nuclear pore complexes. The discovery of this conformational change in such well-studied conditions suggests that our understanding of inducible genome reorganization remains incomplete. Together, these results reveal that the diploid yeast genome displays dynamic and complex 3D organization.
2016-12-05 | GSE88952 | GEO
Project description:Three-dimensional chromatin re-organization during muscle stem cell aging [Hi-C]
| PRJNA883692 | ENA
Project description:Three-dimensional chromatin re-organization during muscle stem cell aging [scATAC-seq]
| PRJNA883691 | ENA
Project description:Age-related skeletal muscle atrophy or sarcopenia is a significant societal problem that is becoming amplified as the world’s population continues to increase. A critical contributor to sarcopenia is the loss in the number and function of muscle stem cells, which maintain tissue homeostasis and regenerate damage. The molecular mechanisms that govern muscle stem cell aging encompass changes across multiple regulatory layers and are integrated by the three-dimensional organization of the genome. To quantitatively understand how hierarchical chromatin architecture changes during muscle stem cell aging, we generated 3D chromatin conformation maps (Hi-C) and integrated these datasets with multi-omic (chromatin accessibility and transcriptome) profiles from bulk populations and single cells. We observed that muscle stem cells display static behavior at global scales of chromatin organization during aging and extensive rewiring of local contacts at finer scales that were associated with variations in transcription factor binding and aberrant gene expression. These data provide insights into genome topology as a regulator of molecular function in stem cell aging.
2023-02-02 | GSE214046 | GEO
Project description:Age-related skeletal muscle atrophy or sarcopenia is a significant societal problem that is becoming amplified as the world’s population continues to increase. A critical contributor to sarcopenia is the loss in the number and function of muscle stem cells, which maintain tissue homeostasis and regenerate damage. The molecular mechanisms that govern muscle stem cell aging encompass changes across multiple regulatory layers and are integrated by the three-dimensional organization of the genome. To quantitatively understand how hierarchical chromatin architecture changes during muscle stem cell aging, we generated 3D chromatin conformation maps (Hi-C) and integrated these datasets with multi-omic (chromatin accessibility and transcriptome) profiles from bulk populations and single cells. We observed that muscle stem cells display static behavior at global scales of chromatin organization during aging and extensive rewiring of local contacts at finer scales that were associated with variations in transcription factor binding and aberrant gene expression. These data provide insights into genome topology as a regulator of molecular function in stem cell aging.
2023-02-02 | GSE214045 | GEO