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Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling [RNA-seq]

ABSTRACT: Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling [RNA-seq]

PROVIDER: PRJNA1180068 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31173640_1.fastq.gz	Fastqsanger.gz
	SRR31173640_2.fastq.gz	Fastqsanger.gz
	SRR31173641_1.fastq.gz	Fastqsanger.gz
	SRR31173641_2.fastq.gz	Fastqsanger.gz
	SRR31173642_1.fastq.gz	Fastqsanger.gz

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Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling

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Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling [CUTnRUN]

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Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling [ATAC-seq]

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Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling [CUTnRUN]

Project description:The mechanistic details by which pioneer transcription factors interact with partner transcription factors and chromatin modification/remodeling enzymes to activate enhancers remains an emerging area of study. Here, we utilize inducible expression of the pioneer factor GATA3 and study cofactor association and structural alterations in local chromatin. ATAC-seq analysis and footprinting revealed co-occurrence of GATA3 with other transcription factors, including AP-1, in newly accessible chromatin. GATA3 and AP-1 co-localize at primed enhancers with p300 and BRG1 where nucleosome positioning is responsive to GATA3 location, not to AP-1. Genetic inhibition of AP-1 binding alters chromatin opening at some, but not most, GATA3-bound loci. Pharmacologic inhibition of SWI/SNF ATPase function results in loss of GATA3-dependent chromatin accessibility, binding, and alterations in local chromatin architecture. We conclude that GATA3-dependent gains in chromatin accessibility require chromatin remodeling and that accessibility at some loci is facilitated by a partner transcription factor, in this case AP-1.

2025-06-16 | GSE280701 | GEO

Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling [RNA-seq]

2025-06-16 | GSE280704 | GEO

Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling [ATAC-seq]

2025-06-16 | GSE280565 | GEO

Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-06-16 | GSE280731 | GEO

Interaction of the pioneer transcription factor GATA3 with nucleosomes

Project description:We developed a high-resolution nucleosome mapping method to explore nucleosome positioning around GATA3 binding sites during GATA3-mediated mesenchymal-to-epithelial transition. We found specific correlations between nucleosome positioning and pioneering activities of GATA3.

2020-04-17 | GSE137794 | GEO

Precise control of GATA3 expression in CD4+ T cell differentiation via selective activation of primed enhancers

Project description:GATA3 is a master regulator with expression that must be precisely controlled during differentiation of naïve CD4+ T cells into diverse subtypes to ensure correct immune responses. The regulatory landscape of GATA3 is complex with dozens of potential enhancers in different states. Here, we use thousands of tiling deletions to systematically map regulatory sequences that affect GATA3 expression. We identify and characterize 34 regulatory sequences in naïve CD4+ T cells, including 4 active enhancers and, unexpectedly, 10 primed enhancers. Focusing on the differentiation of naïve CD4+ T cells into T helper 2 cells where GATA3 expression is highest, we find that upregulation of GATA3 is achieved by retaining active enhancers and activating poised and primed enhancers, including one which harbors candidate causal genetic variants for allergic diseases.

2023-02-24 | GSE190860 | GEO

ILC2 development requires GATA3-related super-enhancers after lineage commitment

Project description:This SuperSeries is composed of the SubSeries listed below. Group 2 innate lymphoid cells (ILC2) are a subset of innate lymphocytes that produce type 2 cytokines, including IL-4, IL-5, and IL-13. GATA3 being a critical transcription factor for ILC2 development at multiple stages. However, when and how GATA3 is induced to the levels required for ILC2 development remains elusive. Herein, we identified ILC2-specific tandem GATA3-related super-enhancers (G3SE) that induce high GATA3 in ILC2-committed precursors. G3SE-deficient mice exhibit ILC2 loss in the BM, lung, liver, and small intestine, a slight ILC1 increase, and no difference in ILC3, LTi, NK cells, nor Th2 cells. Single-cell RNA-sequencing revealed that GATA3 induction in late ILC2-committed precursors depends on G3SEs and is required for the transition to mature ILC2. Cnot6l, part of the CCR4-Not deadenylase complex, is a possible GATA3 target during ILC2 development. Our findings indicate a novel regulatory mechanism for GATA3 expression during ILC2 development.

2024-05-14 | GSE218155 | GEO

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