@article{71a124cb8a3f41998e0a02dc295dbdb7,
title = "PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and RNA polymerase pause release at select gene targets",
abstract = "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.",
keywords = "ATAC-seq, PAX3, PAX3-FOXO1, PRO-seq, chromatin remodeling, differentiation, enhancer, rhabdomyosarcoma, t(2;13)(q35;q14), therapeutics",
author = "Susu Zhang and Jing Wang and Qi Liu and McDonald, {W. Hayes} and Bomber, {Monica L.} and Layden, {Hillary M.} and Jacob Ellis and Borinstein, {Scott C.} and Hiebert, {Scott W.} and Stengel, {Kristy R.}",
note = "Funding Information: We especially thank members of the Hiebert lab for helpful discussions, reagents, and advice. We thank the Flow Cytometry, Chemical Synthesis, and Genome Sciences Shared Resources for services and support. We thank Dr. Javed Khan (NCI) for the gift of Rh4 cells. This work was supported by a St. Baldrick{\textquoteright}s Research Grant with generous support from Rachael Chaffin{\textquoteright}s Research Fund , The V Foundation Grant ID #: T2021-005 , the T. J. Martell Foundation , the Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation , the Edward P. Evans Foundation , National Institutes of Health grants ( R01-CA164605 , R01-CA255446 , and T32-CA009582-36 to S.W.H., and R35-GM147213 to K.R.S.), and as well as core services performed through Vanderbilt Digestive Disease Research grant ( NIDDK P30DK58404 ), the Vanderbilt-Ingram Cancer Center support grant ( NCI P30CA68485 ), and a grant from the National Center for Advancing Translational Sciences ( 2 UL1 TR000445-06 ). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH . Funding Information: The authors declare no competing interests, although Scott Hiebert received research funding from Incyte Inc. through the Vanderbilt-Incyte Alliance. These funds did not support this work. Scott Hiebert is also a scientific advisor for the Edward P. Evans Foundation. Publisher Copyright: {\textcopyright} 2022 Elsevier Inc.",
year = "2022",
month = dec,
day = "1",
doi = "10.1016/j.molcel.2022.10.025",
language = "English (US)",
volume = "82",
pages = "4428--4442.e7",
journal = "Molecular Cell",
issn = "1097-2765",
publisher = "Cell Press",
number = "23",
}