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NextPBM - A platform to study cell-specific transcription factor binding and cooperativity [ChIP-Seq]

ABSTRACT: NextPBM - A platform to study cell-specific transcription factor binding and cooperativity [ChIP-Seq]

PROVIDER: PRJNA510375 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8329540.fastq.gz	Fastqsanger.gz
	SRR8329550.fastq.gz	Fastqsanger.gz
	SRR8329541.fastq.gz	Fastqsanger.gz
	SRR8329551.fastq.gz	Fastqsanger.gz
	SRR8329542.fastq.gz	Fastqsanger.gz

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NextPBM - A platform to study cell-specific transcription factor binding and cooperativity

Project description:NextPBM - A platform to study cell-specific transcription factor binding and cooperativity

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NextPBM - A platform to study cell-specific transcription factor binding and cooperativity [array]

Project description:NextPBM - A platform to study cell-specific transcription factor binding and cooperativity [array]

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NextPBM - A platform to study cell-specific transcription factor binding and cooperativity [array]

Project description:High-throughput (HT) in vitro methods for measuring protein-DNA binding have become invaluable for characterizing transcription factor (TF) complexes and modeling gene regulation. However, current methods do not utilize endogenous proteins and, therefore, do not quantify the impact of cell-specific post-translational modifications (PTMs) and cooperative cofactors. We introduce the HT nextPBM (nuclear extract protein-binding microarray) approach to study DNA binding of native cellular TFs that accounts for PTMs and cell-specific cofactors. We integrate immune-depletion and phosphatase-treatment steps into our nextPBM pipeline to characterize the impact of cofactors and phosphorylation on TF binding. We analyze binding of PU.1/SPI1 and IRF8 from human monocytes, delineate DNA-sequence determinants for their cooperativity, and show how PU.1 affinity correlates with enhancer status and the presence of cooperative and collaborative cofactors. We describe how nextPBMs, and our accompanying computational framework, can be used to discover cell-specific cofactors, screen for synthetic cooperative DNA elements, and characterize TF cooperativity at single-nucleotide resolution.

2018-12-18 | GSE123946 | GEO

NextPBM - A platform to study cell-specific transcription factor binding and cooperativity [ChIP-Seq]

Project description:We analyzed binding of PU.1/SPI1 and IRF8 from human monocytes, delineate DNA-sequence determinants for their cooperativity using nextPBM, and show how PU.1 affinity correlates with enhancer status and the presence of cooperative and collaborative factors (C/EBPa)

2018-12-18 | GSE123872 | GEO

NextPBM: a platform to study cell-specific transcription factor binding and cooperativity.

Project description:High-throughput (HT) in vitro methods for measuring protein-DNA binding have become invaluable for characterizing transcription factor (TF) complexes and modeling gene regulation. However, current methods do not utilize endogenous proteins and, therefore, do not quantify the impact of cell-specific post-translational modifications (PTMs) and cooperative cofactors. We introduce the HT nextPBM (nuclear extract protein-binding microarray) approach to study DNA binding of native cellular TFs that accounts for PTMs and cell-specific cofactors. We integrate immune-depletion and phosphatase treatment steps into our nextPBM pipeline to characterize the impact of cofactors and phosphorylation on TF binding. We analyze binding of PU.1/SPI1 and IRF8 from human monocytes, delineate DNA-sequence determinants for their cooperativity, and show how PU.1 affinity correlates with enhancer status and the presence of cooperative and collaborative cofactors. We describe how nextPBMs, and our accompanying computational framework, can be used to discover cell-specific cofactors, screen for synthetic cooperative DNA elements, and characterize TF cooperativity.

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NextPBM - A platform to study cell-specific transcription factor binding and cooperativity

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

2018-12-18 | GSE123947 | GEO

Transcription factor cooperativity in early adipogenic hotspots and super-enhancers

Project description:Here we have used a combination of advanced proteomics and genomics approaches to investigate the extent and mechanisms of transcription factor cross-talk at genomic hotspots. We identify ~12,000 transcription factor hotspots in the early phase of adipogenesis, and we find evidence of both simultaneous and sequential binding of transcription factors at these regions. We demonstrate for the first time that hotspots are highly enriched in large super-enhancer regions and that these drive the early adipogenic reprogramming of gene expression. Our results indicate that cooperativity between transcription factors at the level of hotspots as well as super-enhancers is very important for enhancer activity and transcriptional reprogramming. Thus, hotspots and super-enhancers constitute important regulatory hubs integrating external stimuli on chromatin. Genome-wide profiling of transcription factor and co-factor binding, epigenomic marks, and gene expression in 3T3-L1 pre-adipocytes.

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