3D regulatory chromosome landscape of human pluripotent cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Richard Young
PROVIDER: E-GEOD-69647 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The control of cell identity is orchestrated by transcriptional and chromatin regulators in the context of specific chromosome structures. With the recent isolation of human naive embryonic stem cells (ESCs) representative of the ground state of pluripotency, it is possible to deduce this regulatory landscape in one of the earliest stages of human development. Here we generate cohesin ChIA-PET chromatin interaction data in naive and primed human ESCs and use it to reconstruct and compare the 3D regulatory landscapes of these two stages of early human development. The results reveal shared and stage-specific regulatory landscapes of topological domains and their subdomains, which consist of CTCF-CTCF/cohesin loops and enhancer-promoter/cohesin loops. The enhancer-promoter loop data reveal that genes with key roles in pluripotency are nearly always regulated by one or more super-enhancers, and show that these genes tend to occur in insulated neighborhoods. Our results reveal the key features of the 3D regulatory landscape of early human cells that form the foundation for embryonic development. ChIA_PET data against SMC1 from naive and primed human embroynic stem cells.
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Project description:The control of cell identity is orchestrated by transcriptional and chromatin regulators in the context of specific chromosome structures. With the recent isolation of human naive embryonic stem cells (ESCs) representative of the ground state of pluripotency, it is possible to deduce this regulatory landscape in one of the earliest stages of human development. Here we generate cohesin ChIA-PET chromatin interaction data in naive and primed human ESCs and use it to reconstruct and compare the 3D regulatory landscapes of these two stages of early human development. The results reveal shared and stage-specific regulatory landscapes of topological domains and their subdomains, which consist of CTCF-CTCF/cohesin loops and enhancer-promoter/cohesin loops. The enhancer-promoter loop data reveal that genes with key roles in pluripotency are nearly always regulated by one or more super-enhancers, and show that these genes tend to occur in insulated neighborhoods. Our results reveal the key features of the 3D regulatory landscape of early human cells that form the foundation for embryonic development. ChIP-seq data from naive and primed human embroynic stem cells.
2015-11-22 | E-GEOD-69646 | biostudies-arrayexpress
Project description:The control of cell identity is orchestrated by transcriptional and chromatin regulators in the context of specific chromosome structures. With the recent isolation of human naive embryonic stem cells (ESCs) representative of the ground state of pluripotency, it is possible to deduce this regulatory landscape in one of the earliest stages of human development. Here we generate cohesin ChIA-PET chromatin interaction data in naive and primed human ESCs and use it to reconstruct and compare the 3D regulatory landscapes of these two stages of early human development. The results reveal shared and stage-specific regulatory landscapes of topological domains and their subdomains, which consist of CTCF-CTCF/cohesin loops and enhancer-promoter/cohesin loops. The enhancer-promoter loop data reveal that genes with key roles in pluripotency are nearly always regulated by one or more super-enhancers, and show that these genes tend to occur in insulated neighborhoods. Our results reveal the key features of the 3D regulatory landscape of early human cells that form the foundation for embryonic development. Polyadenylated RNA-seq from naive and primed human embroynic stem cells.
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Project description:Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing, we mapped long-range chromatin interactions associated with RNA polymerase II in three different mouse cell lines and uncovered widespread promoter-centered interactions. These interactions further aggregated into higher-order clusters, in which proximal and distant genes are engaged through enhancer-promoter interactions. Comparative analyses of different cell lines imply that cell specific enhancer interactions are dynamic among different cell specific transcription, and suggest significant enrichment of enhancer-promoter interactions for cell specific manner. Overall, our study provides novel insights into the three-dimensional basis of transcription activity in mouse cells. RNA polymerase II (RNAPII) guided chromatin interactions were discovered by Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing, in order to study genome-wise the enhancer-promoter interactions. Three cell lines, namely mouse embryonic stem cell E14, Neural stem cell NS5 and neuroshpere cells were grown under standard culture conditions and harvested at log phase. Harvested cells were cross-linked using 1% formaldehyde followed by neutralization with 0.2M glycine. Chromatin was isolated and subjected to ChIA-PET protocol as described in Fullwood et al, 2009. The ChIA-PET sequence reads were processed and analyzed using ChIA-PET Tool (Li et al, 2010)
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Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
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