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Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors

ABSTRACT: Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors

PROVIDER: PRJNA244744 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1239520.fastq.gz	Fastqsanger.gz
	SRR1239521.fastq.gz	Fastqsanger.gz
	SRR1239518.fastq.gz	Fastqsanger.gz
	SRR1239519.fastq.gz	Fastqsanger.gz

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Similar Datasets

Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors [ChIP-seq]

Project description:Cell type-specific master transcription factors (MTFs) play vital roles in defining cell identity and function. However, the roles ubiquitous factors play in the specification of cell identity remain underappreciated. Here we show that all three subunits of the ubiquitous heterotrimeric CCAAT-binding NF-Y complex are required for the maintenance of embryonic stem cell (ESC) identity, and establish NF-Y as a novel component of the core pluripotency network. Genome-wide occupancy and transcriptomic analyses in ESCs and neurons reveal that not only does NF-Y regulate genes with housekeeping functions through cell type-invariant promoter-proximal binding, but also genes required for cell identity by binding to cell type-specific enhancers with MTFs. Mechanistically, NF-Y's distinctive DNA-binding mode promotes MTF binding at enhancers by facilitating a permissive chromatin conformation. Our studies unearth a novel function for NF-Y in promoting chromatin accessibility, and suggest that other proteins with analogous structural and DNA-binding properties may function in similar ways. Genome-wide mapping of NF-YA, NF-YB, and NF-YC subunits of the NF-Y complex in mouse ESCs, and microarray gene expression profiling of control knockdown (KD), NF-YA KD, NF-YB KD, NF-YC KD, and NF-YA/NF-YB/NF-YC triple KD ESCs.

2014-08-14 | E-GEOD-56839 | biostudies-arrayexpress

Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors [gene expression]

2014-08-14 | E-GEOD-56838 | biostudies-arrayexpress

Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors [ChIP-seq]

2014-08-14 | GSE56839 | GEO

Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors [gene expression]

2014-08-14 | GSE56838 | GEO

CONSTANS Imparts DNA Sequence Specificity to the Histone Fold NF-YB/NF-YC Dimer

Project description:Nuclear Factor Y (NF-Y) is a heterotrimeric transcription factor that binds CCAAT elements. The NF-Y trimer is composed of a Histone Fold Domain (HFD) dimer (NF-YB/NF-YC) and NF-YA, which confers DNA sequence specificity. NF-YA shares a conserved domain with the CONSTANS, CONSTANS-LIKE, TOC1 (CCT) proteins. We show that CONSTANS (CO/B-BOX PROTEIN1 BBX1), a master flowering regulator, forms a trimer with Arabidopsis thaliana NF-YB2/NF-YC3 to efficiently bind the CORE element of the FLOWERING LOCUS T promoter. Using saturation mutagenesis, electrophoretic mobility shift assays, and RNA-sequencing profiling of co, nf-yb, and nf-yc mutants, we identify CCACA elements as the core NF-CO binding site. CO physically interacts with the same HFD surface required for NF-YA association, as determined by mutations in NF-YB2 and NF-YC9, and tested in vitro and in vivo. The co-7 mutation in the CCT domain, corresponding to an NF-YA arginine directly involved in CCAAT recognition, abolishes NF-CO binding to DNA

2022-06-09 | GSE205675 | GEO

Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors.

Project description:Cell type-specific master transcription factors (TFs) play vital roles in defining cell identity and function. However, the roles ubiquitous factors play in the specification of cell identity remain underappreciated. Here we show that the ubiquitous CCAAT-binding NF-Y complex is required for the maintenance of embryonic stem cell (ESC) identity and is an essential component of the core pluripotency network. Genome-wide studies in ESCs and neurons reveal that NF-Y regulates not only genes with housekeeping functions through cell type-invariant promoter-proximal binding, but also genes required for cell identity by binding to cell type-specific enhancers with master TFs. Mechanistically, NF-Y's distinct DNA-binding mode promotes master/pioneer TF binding at enhancers by facilitating a permissive chromatin conformation. Our studies unearth a conceptually unique function for histone-fold domain (HFD) protein NF-Y in promoting chromatin accessibility and suggest that other HFD proteins with analogous structural and DNA-binding properties may function in similar ways.

| S-EPMC4157648 | biostudies-literature

Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-08-14 | E-GEOD-56840 | biostudies-arrayexpress

CONSTANS Imparts DNA Sequence Specificity to the Histone Fold NF-YB/NF-YC Dimer

Project description:CONSTANS Imparts DNA Sequence Specificity to the Histone Fold NF-YB/NF-YC Dimer

| PRJNA847163 | ENA

Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors

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

2014-08-14 | GSE56840 | GEO

Mus musculus

Project description:Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors [ChIP-seq]

| PRJNA244746 | ENA

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