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Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation

ABSTRACT: Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation

PROVIDER: PRJNA1105930 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28834079_1.fastq.gz	Fastqsanger.gz
	SRR28834079_2.fastq.gz	Fastqsanger.gz
	SRR28834080_1.fastq.gz	Fastqsanger.gz
	SRR28834080_2.fastq.gz	Fastqsanger.gz
	SRR28834081_1.fastq.gz	Fastqsanger.gz

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Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation (microarray)

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Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation (ChIP-Seq)

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Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation (microarray)

Project description:Transcription factor (TF)-cofactor (COF) interactions define dynamic, cell-specific networks that govern gene expression; however, these networks are understudied due to a lack of methods for high-throughput profiling of DNA-bound TF-COF complexes. Here we describe the Cofactor Recruitment (CoRec) method for rapid profiling of cell-specific TF-COF complexes. We define a lysine acetyltransferase (KAT)-TF network in resting and stimulated T cells. We find promiscuous recruitment of KATs for many TFs and that 35% of KAT-TF interactions are condition specific. KAT-TF interactions identify NF-κB as a primary regulator of acutely induced H3K27ac. Finally, we find that heterotypic clustering of CBP/P300-recruiting TFs is a strong predictor of total promoter H3K27ac. Our data supports clustering of TF sites that broadly recruit KATs as a mechanism for widespread co-occurring histone acetylation marks. CoRec can be readily applied to different cell systems and provides a powerful approach to define TF-COF networks impacting chromatin state and gene regulation.

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Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation (ChIP-Seq)

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Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation

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

2024-06-30 | GSE266127 | GEO

FHL5 cofactor mediates vascular disease risk by regulating smooth muscle cell transcriptional networks

Project description:FHL5 cofactor mediates vascular disease risk by regulating smooth muscle cell transcriptional networks

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Absolute quantification of protein production reveals principles underlying protein synthesis rates

Project description:A quantitative view of cellular functions requires precise measures of the rates of biomolecule production, especially proteins-the direct effectors of biological processes. Here we present a genome-wide approach, based on ribosome profiling, for measuring absolute protein synthesis rates. The resultant E. coli dataset transforms our understanding of the extent to which protein synthesis is precisely controlled to optimize function and efficiency. For example, members of multi-protein complexes are made in precise proportion to their stoichiometry, whereas components of functional modules are produced differentially according to their hierarchical role. Estimates of absolute protein abundance also reveal principles used to optimize design. These include how the level of different types of transcription factors is optimized for rapid response, and how a metabolic pathway (methionine biosynthesis) balances production cost with activity requirements. More broadly, our studies reveal how general principles, important both for understanding natural systems and for synthesizing new ones, emerge from global quantitative analyses of protein synthesis. 4 samples of E. coli ribosome profiling and mRNA-seq, including biological replicates

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