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Gene Network Transitions in Embryos Depend Upon Interactions between a Pioneer Transcription Factor and Core Histones

ABSTRACT: Gene Network Transitions in Embryos Depend Upon Interactions between a Pioneer Transcription Factor and Core Histones

PROVIDER: PRJNA555189 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9701880.fastq.gz	Fastqsanger.gz
	SRR9701890_1.fastq.gz	Fastqsanger.gz
	SRR9701890_2.fastq.gz	Fastqsanger.gz
	SRR9701900_1.fastq.gz	Fastqsanger.gz
	SRR9701900_2.fastq.gz	Fastqsanger.gz

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Gene Network Transitions in Embryos Depend Upon Interactions between a Pioneer Transcription Factor and Core Histones [ATAC-Seq]

Project description:Gene network transitions in embryos and fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. But a gap has remained in understanding how molecular interactions with the nucleosome, beyond interactions with the DNA helix, contribute to the chromatin opening phenomenon. Here we identified a short alpha-helical region, conserved among FoxA pioneer factors and separated from the DNA binding domain, that interacts with core histones and is necessary for chromatin opening in vitro. The same domain is necessary for chromatin opening in early mouse embryos and for normal embryonic development and viability. Thus, local opening of chromatin by interactions between pioneer factors and core histones is crucial for genetic programming.

2020-01-22 | GSE134464 | GEO

Gene Network Transitions in Embryos Depend Upon Interactions between a Pioneer Transcription Factor and Core Histones [RNA-Seq]

2020-01-22 | GSE134463 | GEO

Gene Network Transitions in Embryos Depend Upon Interactions between a Pioneer Transcription Factor and Core Histones [ATAC-Seq]

Project description:Gene Network Transitions in Embryos Depend Upon Interactions between a Pioneer Transcription Factor and Core Histones [ATAC-Seq]

| PRJNA555197 | ENA

Gene Network Transitions in Embryos Depend Upon Interactions between a Pioneer Transcription Factor and Core Histones [RNA-Seq]

Project description:Gene Network Transitions in Embryos Depend Upon Interactions between a Pioneer Transcription Factor and Core Histones [RNA-Seq]

| PRJNA555196 | ENA

Gene network transitions in embryos depend upon interactions between a pioneer transcription factor and core histones.

Project description:Gene network transitions in embryos and other fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. However, a gap has remained in understanding how molecular interactions with the nucleosome contribute to the chromatin-opening phenomenon. Here we identified a short α-helical region, conserved among FOXA pioneer factors, that interacts with core histones and contributes to chromatin opening in vitro. The same domain is involved in chromatin opening in early mouse embryos for normal development. Thus, local opening of chromatin by interactions between pioneer factors and core histones promotes genetic programming.

| S-EPMC7901023 | biostudies-literature

Novel nucleosomal particles containing core histones and linker DNA but no histone H1

Project description:The nucleosome plays a central role in genome regulation. Traditional methods for mapping nucleosomes depend on the resistance of the nucleosome core to micrococcal nuclease (MNase). However, the lengths of the protected DNA fragments are heterogeneous, limiting the accuracy of nucleosome position information. To resolve this problem, we removed residual linker DNA by simultaneous digestion of yeast chromatin with MNase and exonuclease III (ExoIII). Paired-end sequencing of mono-nucleosomes revealed not only core particles (145-147 bp), but also intermediate particles in which ~8 bp project from one side (154 bp) or both sides (161 bp) of the nucleosome core. We term these particles "pseudo-chromatosomes" because they are present in yeast lacking linker histone. They are also observed after MNase-ExoIII digestion of chromatin reconstituted using recombinant core histones. We propose that the pseudo-chromatosome provides a DNA framework to facilitate H1 binding. Comparison of budding yeast nucleosome sequences obtained using micrococcal nuclease (MNase-seq) and MNase + exonuclease III (ExoIII) (MNase-ExoIII-seq): wild type cells and hho1-null cells. Nucleosome sequences from native chromatin and H1-depleted chromatin from mouse liver. Nucleosome sequences from a plasmid reconstituted into nucleosomes using recombinant yeast histones or native chicken erythrocyte histones.

2015-09-23 | E-GEOD-65889 | biostudies-arrayexpress

Gene Network Transitions in Embryos Depend Upon Interactions between a Pioneer Transcription Factor and Core Histones

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

2020-01-20 | GSE134465 | GEO

Pioneer transcription factor FoxA maintains an open nucleosome configuration for tissue-specific gene activation [MNase-Seq]

Project description:Nuclear DNA is wrapped around core histones to form nucleosomes, which constrains how transcription factors bind to gene regulatory sequences. Pioneer transcription factors have the special ability to bind target DNA on nucleosomes and initiate gene regulatory events, often leading to a local opening of chromatin. Yet the nucleosomal status of such open chromatin, e.g., at active enhancers, is not clear. Here we develop a combination of low and high levels of MNase digestion along with core histone ChIP-seq to assess the presence of nucleosomes at enhancers and promoters in mouse liver. We find that liver-specific enhancers retain preferentially MNase-accessible nucleosomes, with factors bound, substantially more than ubiquitous enhancers. Furthermore, the pioneer factor FoxA2 is required to keep enhancer nucleosomes accessible in chromatin at active liver genes. Thus, nucleosomes are not exclusively repressive to gene regulation when they are retained with, and exposed by, pioneer factors.

2018-05-30 | GSE71947 | GEO

Pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation [ChIP-seq]

Project description:Nuclear DNA is wrapped around core histones to form nucleosomes, which constrains how transcription factors bind to gene regulatory sequences. Pioneer transcription factors have the special ability to bind target DNA on nucleosomes and initiate gene regulatory events, often leading to a local opening of chromatin. Yet the nucleosomal configuration of such open chromatin and the basis for chromatin opening is unclear. Here we combine low and high levels of MNase digestion along with core histone ChIP-seq to assess the presence of nucleosomes at enhancers and promoters in mouse liver. We find that the pioneer factor FoxA displaces linker histone H1, thereby keeping enhancer nucleosomes accessible in chromatin and helping other transcription factors bind. MNase-accessible nucleosomes, bound by transcription factors, are retained substantially more at liver-specific enhancers than promoters and tissue-ubiquitous enhancers. Thus, nucleosomes are not exclusively repressive to gene regulation when they are retained with, and exposed by, pioneer factors.

2016-04-08 | GSE77670 | GEO

Cell-type-specific chromatin occupancy by the pioneer factor Zelda drives key developmental transitions in Drosophila

Project description:During early Drosophila embryogenesis, the essential pioneer factor Zelda defines hundreds of cis-regulatory regions and in doing so reprograms the zygotic transcriptome. While Zelda is essential later in development, it is unclear how the ability of Zelda to define cis-regulatory regions is shaped by cell-type specific chromatin architecture established during differentiation. Asymmetric division of neural stem cells (neuroblasts) in the fly brain provide an excellent paradigm for investigating the cell-type specific functions of this pioneer factor. Zelda is expressed in neuroblasts, and we show that Zelda synergistically functions with Notch to maintain neuroblasts in an undifferentiated state. Zelda misexpression can reprogram progenitor cells to neuroblasts, but this capacity is limited by transcriptional repressors critical for progenitor commitment. Zelda genomic occupancy in neuroblasts is reorganized as compared to the embryo, despite sharing many target genes in these two developmental stages. This reorganization is likely driven by differences in chromatin accessibility and cofactor availability. We propose that Zelda regulates essential transitions in the neuroblasts and embryo through a shared gene regulatory network by defining cell-type specific enhancers.

2021-11-05 | GSE150931 | GEO

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