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3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [ChIP-seq]

ABSTRACT: 3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [ChIP-seq]

PROVIDER: PRJNA976618 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24745559_1.fastq.gz	Fastqsanger.gz
	SRR24745559_2.fastq.gz	Fastqsanger.gz
	SRR24745560_1.fastq.gz	Fastqsanger.gz
	SRR24745560_2.fastq.gz	Fastqsanger.gz

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3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis

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3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [ChIA-PET]

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3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [ATAC-seq]

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3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [ChIP-seq]

Project description:Analyses of the regulatory repertoire showed that distal active cis-regulatory elements (CREs) are linked to their target genes through long-range chromatin interactions with increased expression, and poised CREs are linked to their target genes through long-range chromatin interactions with depressed expression. Furthermore, we demonstrated that transcription factor MYC2 is critical for chromatin spatial organization, and proposed that MYC2 occupancy and MYC2-mediated chromatin interactions coordinately facilitate transcription within the framework of 3D chromatin architecture. An analysis of functionally related gene-defined chromatin connectivity networks revealed that genes implicated in flowering-time control are functionally compartmentalized into separate subdomains via their spatial activity in the leaf or shoot apical meristem, linking active mark- or H3K27me3-associated chromatin conformation to coordinated gene expression. The results showed that the guiding principle for modulating gene transcription in Arabidopsis includes not only the linear juxtaposition, but also the long-range chromatin interactions.

2023-07-10 | GSE233526 | GEO

3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [ATAC-seq]

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3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [ChIA-PET]

2023-07-10 | GSE233527 | GEO

3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [RNA-seq]

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3D regulatory landscape of human naive pluripotency [ChIAPET]

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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