Searching journal content for articles similar to McDowell et al. 28 (9): 1272.

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Research: AP-1 subunits converge promiscuously at enhancers to potentiate transcription
- Jungkyun Seo,
- D. Dewran Koçak,
- Luke C. Bartelt,
- Courtney A. Williams,
- Alejandro Barrera,
- Charles A. Gersbach,
- and Timothy E. Reddy
Genome Res. April 2021 31: 538-550; Published in Advance March 5, 2021, doi:10.1101/gr.267898.120
...suggests that canonical AP-1 motifs indiscriminately recruit all AP-1 subunits to genomic sites, which we term AP-1 hotspots. We find that AP-1 hotspots are predictive of cell type–specific gene expression and of genomic responses to glucocorticoid signaling (more so than super-enhancers...
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Research: Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression
- Sarah K. Sasse,
- Margaret Gruca,
- Mary A. Allen,
- Vineela Kadiyala,
- Tengyao Song,
- Fabienne Gally,
- Arnav Gupta,
- Miles A. Pufall,
- Robin D. Dowell,
- and Anthony N. Gerber
Genome Res. November 2019 29: 1753-1765; Published in Advance September 13, 2019, doi:10.1101/gr.248187.119
...repression. Glucocorticoids rapidly induce target genes predominantly through glucocorticoid receptor (GR) interactions with enhancers harboring canonical GR binding sites (GBSs). The consequences of -wide transcriptional induction by the GR include (1) an immediate early wave of repression, characterized...
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Method: Probabilistic association of differentially expressed genes with cis-regulatory elements
- Brian S. Roberts,
- Ashlyn G. Anderson,
- E. Christopher Partridge,
- Gregory M. Cooper,
- and Richard M. Myers
Genome Res. April 2024 34: 620-632; Published in Advance April 17, 2024, doi:10.1101/gr.278598.123
...-change. Regions of NR3C1 signal have been merged in some cases for better visibility at browser scale.We further considered the DegCre results derived from NR3C1 (commonly referred to as the glucocorticoid receptor) ChIP-seq in the McDowell et al. data. In these experiments, cells were treated with dexamethasone...
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Method: A universal framework for detecting cis-regulatory diversity in DNA regions
- Anushua Biswas and
- Leelavati Narlikar
Genome Res. September 2021 31: 1646-1662; Published in Advance July 19, 2021, doi:10.1101/gr.274563.120
...this.GR binds to diverse regions after activationThe human glucocorticoid receptor (GR; encoded by NR3C1) binds to thousands of sites in response to exposure to the glucocorticoid (GC) hormone cortisol. GR is understood to bind primarily to DNase I hypersensitive sites (DHSs) (John et al. 2011...
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Method: Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data
- Kaixuan Luo,
- Jianling Zhong,
- Alexias Safi,
- Linda K. Hong,
- Alok K. Tewari,
- Lingyun Song,
- Timothy E. Reddy,
- Li Ma,
- Gregory E. Crawford,
- and Alexander J. Hartemink
Genome Res. June 2022 32: 1183-1198; Published in Advance May 24, 2022, doi:10.1101/gr.272203.120
...Nuclear hormone receptors are TFs specifically activated in response to hormone exposure. Once activated, they bind to specific hormone response elements (HREs) where they regulate gene expression, often in conjunction with the binding of cofactors and remodeling of the chromatin structure. Glucocorticoid (GC...
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Method: Correcting signal biases and detecting regulatory elements in STARR-seq data
- Young-Sook Kim,
- Graham D. Johnson,
- Jungkyun Seo,
- Alejandro Barrera,
- Thomas N. Cowart,
- William H. Majoros,
- Alejandro Ochoa,
- Andrew S. Allen,
- and Timothy E. Reddy
Genome Res. May 2021 31: 877-889; Published in Advance March 15, 2021, doi:10.1101/gr.269209.120
...for clearer visual identification of elements with activating or repressive regulatory effects. For example, a region near the PER1 gene that is well known to have activating regulatory activity in response activation of the glucocorticoid receptor (NR3C1) (Reddy et al. 2012; Johnson et al. 2018) showed much...
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