Searching journal content for articles similar to Starick et al. 25 (6): 825.

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  1. Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
    • Kevin Moyung,
    • Yulong Li,
    • Heather K. MacAlpine,
    • Alexander J. Hartemink,
    • and David M. MacAlpine
    Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
    ...occupancy across the (Li et al. 2007; Rando and Winston 2012). Although prior studies have provided valuable insights into transcriptional regulation by focusing individually on nucleosome positioning or TF binding (van Bakel et al. 2013; Kemmeren et al. 2014), the ability to characterize the precise...
  2. Research: Glucocorticoid receptor quaternary structure drives chromatin occupancy and transcriptional outcome
    • Ville Paakinaho,
    • Thomas A. Johnson,
    • Diego M. Presman,
    • and Gordon L. Hager
    Genome Res. August 2019 29: 1223-1234; Published in Advance July 23, 2019, doi:10.1101/gr.244814.118
    ...that the receptor likely binds DNA as a dimer owing to the palindromic nature of the GRE consensus motif (Evans 1988). The further characterization of the crystal structure of the DNA-binding domain (DBD) fragment appeared to confirm this theory (Luisi et al. 1991). This line of research continued in the 1990s...
  3. Research: Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding
    • Ian C. McDowell,
    • Alejandro Barrera,
    • Anthony M. D'Ippolito,
    • Christopher M. Vockley,
    • Linda K. Hong,
    • Sarah M. Leichter,
    • Luke C. Bartelt,
    • William H. Majoros,
    • Lingyun Song,
    • Alexias Safi,
    • D. Dewran Koçak,
    • Charles A. Gersbach,
    • Alexander J. Hartemink,
    • Gregory E. Crawford,
    • Barbara E. Engelhardt,
    • and Timothy E. Reddy
    Genome Res. September 2018 28: 1272-1284; Published in Advance August 10, 2018, doi:10.1101/gr.233346.117
    ...in the model. Overwhelmingly, the most predictive DNA binding motif for changes in enhancer activation across the time course was the GR binding motif (Fig. 5F). Most of the other motifs positively predictive for enhancer activation were for factors that have been shown to participate with GR in genomic...
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  4. 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
    .... 5A). Although TOP was trained on human data, it could equally be trained and applied in other organisms. As an example, we were able to successfully predict quantitative Reb1 occupancy (ChIP-exo) in the yeast from DNase-seq data (Supplemental Fig. S18). As a resource for the community, we provide...
  5. Research: Genomic redistribution of GR monomers and dimers mediates transcriptional response to exogenous glucocorticoid in vivo
    • Hee-Woong Lim,
    • N. Henriette Uhlenhaut,
    • Alexander Rauch,
    • Juliane Weiner,
    • Sabine Hübner,
    • Norbert Hübner,
    • Kyoung-Jae Won,
    • Mitchell A. Lazar,
    • Jan Tuckermann,
    • and David J. Steger
    Genome Res. June 2015 25: 836-844; Published in Advance May 8, 2015, doi:10.1101/gr.188581.114
    ...and repression, are mediated by the glucocorticoid receptor (GR), which is known to bind as a homodimer to a palindromic DNA sequence. Using ChIP-exo in mouse liver under endogenous corticosterone exposure, we report here that monomeric GR interaction with a half-site motif is more prevalent than homodimer...
  6. Method: Fast decoding cell type–specific transcription factor binding landscape at single-nucleotide resolution
    • Hongyang Li and
    • Yuanfang Guan
    Genome Res. April 2021 31: 721-731; Published in Advance March 19, 2021, doi:10.1101/gr.269613.120
    ...the predictive performance of Leopard at single-base resolution, we further trained and evaluated Leopard models using ChIP-exo data, including CTCF in HeLa-S3 (Rhee and Pugh 2011); NR2F2, Estrogen Receptor (ER), and EP300 in MCF-7 (Serandour et al. 2013); and Glucocorticoid Receptor (GR) in IMR-90 and K562...
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