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PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE183281 | GEO | 2022/12/14

REPOSITORIES: GEO

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PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and RNA polymerase pause release at select gene targets.

Project description:Transcriptional control is a highly dynamic process that changes rapidly in response to various cellular and extracellular cues, making it difficult to define the mechanism of transcription factor function using slow genetic methods. We used a chemical-genetic approach to rapidly degrade a canonical transcriptional activator, PAX3-FOXO1, to define the mechanism by which it regulates gene expression programs. By coupling rapid protein degradation with the analysis of nascent transcription over short time courses and integrating CUT&RUN, ATAC-seq, and eRNA analysis with deep proteomic analysis, we defined PAX3-FOXO1 function at a small network of direct transcriptional targets. PAX3-FOXO1 degradation impaired RNA polymerase pause release and transcription elongation at most regulated gene targets. Moreover, the activity of PAX3-FOXO1 at enhancers controlling this core network was surprisingly selective, affecting single elements in super-enhancers. This combinatorial analysis indicated that PAX3-FOXO1 was continuously required to maintain chromatin accessibility and enhancer architecture at regulated enhancers.

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PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [Cut & Run]

Project description:This study aim to in-depth understand the function of a transcription factor fusion protein that drives the development of a highly aggressive pediatric malignancy. After engineered the endogenous PAX3-FOXO1 locus, we use chemical genetics to rapidly degrade the protein. This comprehensive, detailed, and accurate study with deep genomic analyses and deep proteomics provide a detailed mechanism by which PAX3-FOXO1 maintains an oncogenic transcriptional regulatory network.

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