Dynamic exchange at regulatory elements during chromatin remodeling underlies assisted loading mechanism
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The glucocorticoid receptor (GR), like other eukaryotic transcription factors, regulates gene expression by interacting with chromatinized DNA response elements. Photobleaching experiments in living cells indicate that receptors transiently interact with DNA on the time scale of seconds and predict that the response elements may be sparsely occupied on average. Here, we show that the binding of one receptor at the glucocorticoid response element (GRE) does not reduce the steady-state binding of another receptor variant to the same GRE. Mathematical simulations reproduce this noncompetitive state using short GR/GRE residency times and relatively long times between DNA binding events. At many genomic sites where GR binding causes increased chromatin accessibility, concurrent steady-state binding levels for the variant receptor are actually increased, a phenomenon termed assisted loading. Temporally sparse transcription factor-DNA interactions induce local chromatin reorganization, resulting in transient access for binding of secondary regulatory factors.
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Once in the nucleus, liganded glucocorticoid receptors do not bind DNA stably but constantly shuttle between the nucleoplasm and glucocorticoid-responsive elements.
“Once in the nucleus, liganded GRs do not bind to DNA in a stable manner. They rather constantly shuttle between the nucleoplasm and GC-responsive elements (GRE) located in the promoter or enhancer regions of GC-responsive genes (80, 81).”
From The HPA – Immune Axis and the Immunomodulatory Actions of Glucocorticoids in the Brain (2014) · cites this paper as [81]
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The Role of Chromatin during Transcription
Li, B., Carey, M., & Workman, J. L. (2007) · Cell · doi:10.1016/j.cell.2007.01.015 · Cited by 3,503 · see citing works
Genome-Wide Mapping of in Vivo Protein-DNA Interactions
Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science · doi:10.1126/science.1141319 · Cited by 2,927 · see citing works
Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A., et al. (2007) · Nature Methods · doi:10.1038/nmeth1068 · Cited by 1,454 · see citing works
Opening of Compacted Chromatin by Early Developmental Transcription Factors HNF3 (FoxA) and GATA-4
Cirillo, L. A., Lin, F. R., Cuesta, I., Friedman, D., Jarník, M., & Zaret, K. S. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00459-8 · Cited by 1,188 · see citing works
Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
John, S., Sabo, P. J., Thurman, R. E., Sung, M.-H., Biddie, S. C., Johnson, T. A., Hager, G. L., & Stamatoyannopoulos, J. A. (2011) · Nature Genetics · doi:10.1038/ng.759 · Cited by 954 · see citing works
Self-citationThe glucocorticoid receptor: rapid exchange with regulatory sites in living cells
McNally, J. G., Müller, W. G., Walker, D., Wolford, R., & Hager, G. L. (2000) · Science · doi:10.1126/science.287.5456.1262 · Cited by 802 · see citing works
Self-citationGenome-wide analysis of transcription factor binding sites based on ChIP-Seq data
Valouev, A., Johnson, D. S., Sundquist, A., Medina, C., Anton, E., Batzoglou, S., Myers, R. M., & Sidow, A. (2008) · Nature Methods · doi:10.1038/nmeth.1246 · Cited by 695 · see citing works
Payvar, F., DeFranco, D. B., Firestone, G. L., Edgar, B. A., Wränge, Ö., Okret, S., Gustafsson, J.-Å., & Yamamoto, K. R. (1983) · Cell · doi:10.1016/0092-8674(83)90171-x · Cited by 678 · see citing works
In vivo dynamics of RNA polymerase II transcription
Darzacq, X., Shav-Tal, Y., de Turris, V., Brody, Y., Shenoy, S. M., Phair, R. D., & Singer, R. H. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1280 · Cited by 665 · see citing works
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
Hesselberth, J. R., Chen, X., Zhang, Z., Sabo, P. J., Sandstrom, R., Reynolds, A. P., Thurman, R. E., Neph, S., Kuehn, M. S., Noble, W. S., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1313 · Cited by 559 · see citing works
Self-citationSteroid hormone receptors compete for factors that mediate their enhancer function.
Meyer, M., Gronemeyer, H., Turcotte, B., Bocquel, M., Tasset, D., & Chambon, P. (1989) · Cell · doi:10.1016/0092-8674(89)90918-5 · Cited by 542 · see citing works
Genome-wide identification of<i>in vivo</i>protein-DNA binding sites from ChIP-Seq data
Jothi, R., Cuddapah, S., Barski, A., Cui, K., & Zhao, K. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn488 · Cited by 539 · see citing works
Mader, S., Kumar, V., de Verneuil, H., & Chambon, P. (1989) · Nature · doi:10.1038/338271a0 · Cited by 500 · see citing works
Nucleosome dynamics define transcriptional enhancers
He, H. H., Meyer, C. A., Shin, H., Bailey, S. T., Wei, G., Wang, Q., Zhang, Y., Xu, K., Ni, M., Lupien, M., et al. (2010) · Nature Genetics · doi:10.1038/ng.545 · Cited by 476 · see citing works
Predicting expression patterns from regulatory sequence in Drosophila segmentation
Segal, E., Raveh-Sadka, T., Schroeder, M., Unnerstall, U., & Gaul, U. (2008) · Nature · doi:10.1038/nature06496 · Cited by 466 · see citing works
Hager, G. L., McNally, J. G., & Misteli, T. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.09.005 · Cited by 457 · see citing works
Self-citationUltradian hormone stimulation induces glucocorticoid receptor-mediated pulses of gene transcription
Stavreva, D. A., Wiench, M., John, S., Conway-Campbell, B. L., McKenna, M. A., Pooley, J. R., Johnson, T. A., Voss, T. C., Lightman, S. L., & Hager, G. L. (2009) · Nature Cell Biology · doi:10.1038/ncb1922 · Cited by 375 · see citing works
Self-citationGenome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays
Sabo, P. J., Kuehn, M. S., Thurman, R. E., Johnson, B., Johnson, E. M., Cao, H., Yu, M., Rosenzweig, E., Goldy, J., Haydock, A. K., et al. (2006) · Nature Methods · doi:10.1038/nmeth890 · Cited by 314 · see citing works
Self-citationInteraction of the Glucocorticoid Receptor with the Chromatin Landscape
John, S., Sabo, P. J., Johnson, T. A., Sung, M., Biddie, S. C., Lightman, S. L., Voss, T. C., Davis, S. R., Meltzer, P. S., Stamatoyannopoulos, J. A., et al. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.02.010 · Cited by 311 · see citing works
Self-citationRapid Periodic Binding and Displacement of the Glucocorticoid Receptor during Chromatin Remodeling
Nagaich, A. K., Walker, D. A., Wolford, R. G., & Hager, G. L. (2004) · Molecular Cell · doi:10.1016/s1097-2765(04)00178-9 · Cited by 239 · see citing works
Self-citationOestrogen-receptor-mediated transcription and the influence of co-factors and chromatin state
Green, K., & Carroll, J. (2007) · Nature Reviews. Cancer · doi:10.1038/nrc2211 · Cited by 235 · see citing works
Dynamic behavior of transcription factors on a natural promoter in living cells
Becker, M., Baumann, C. T., John, S., Walker, D. A., Vigneron, M., McNally, J. G., & Hager, G. L. (2002) · EMBO Reports · doi:10.1093/embo-reports/kvf244 · Cited by 211 · see citing works
Self-citationKraus, W. L., McInerney, E. M., & Katzenellenbogen, B. S. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.26.12314 · Cited by 208 · see citing works
Nucleosome Retention and the Stochastic Nature of Promoter Chromatin Remodeling for Transcription
Boeger, H., Griesenbeck, J., & Kornberg, R. D. (2008) · Cell · doi:10.1016/j.cell.2008.02.051 · Cited by 164 · see citing works
Stochastic gene expression: from single molecules to the proteome
Kaufmann-Malaga, B., & van Oudenaarden, A. (2007) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2007.02.007 · Cited by 159 · see citing works
A quantitative model of transcription factor–activated gene expression
Kim, H. D., & O'Shea, E. K. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1500 · Cited by 142 · see citing works
ATP-Dependent Mobilization of the Glucocorticoid Receptor during Chromatin Remodeling
Fletcher, T. M., Xiao, N., Mautino, G., Baumann, C. T., Wolford, R. G., Warren, B. S., & Hager, G. L. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.10.3255-3263.2002 · Cited by 138 · see citing works
Self-citationUnique ERα Cistromes Control Cell Type-Specific Gene Regulation
Krum, S. A., Miranda‐Carboni, G. A., Lupien, M., Eeckhoute, J., Carroll, J. S., & Brown, M. A. (2008) · Molecular Endocrinology · doi:10.1210/me.2008-0100 · Cited by 127 · see citing works
Explicit equilibrium modeling of transcription-factor binding and gene regulation
Granek, J. A., & Clarke, N. D. (2005) · Genome biology · doi:10.1186/gb-2005-6-10-r87 · Cited by 121 · see citing works
An ensemble model of competitive multi-factor binding of the genomePreprint
Wasson, T., & Hartemink, A. J. (2009) · Genome Research · doi:10.1101/gr.093450.109 · Cited by 107 · see citing works
Estrogen-receptor-α exchange and chromatin dynamics are ligand- and domain-dependent
Sharp, Z. D., Mancini, M. G., Hinojos, C. A., Dai, F., Berno, V., Szafran, A. T., Smith, K. P., Lele, T. T., Ingber, D. E., & Mancini, M. A. (2006) · Journal of Cell Science · doi:10.1242/jcs.03161 · Cited by 103 · see citing works
Walker, D. A., Htun, H., & Hager, G. L. (1999) · Methods · doi:10.1006/meth.1999.0874 · Cited by 98 · see citing works
Self-citationPhenomenological Theory of Gel Electrophoresis of Protein-Nucleic Acid Complexes
CANN, J. R. (1989) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)71455-5 · Cited by 93 · see citing works
Proteolytic turnover of the Gal4 transcription factor is not required for function in vivo
Nalley, K., Johnston, S. A., & Kodadek, T. (2006) · Nature · doi:10.1038/nature05067 · Cited by 82 · see citing works
Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome
van Werven, F. J., van Teeffelen, H. A. A. M., Holstege, F. C. P., & Timmers, H. T. M. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1674 · Cited by 81 · see citing works
Protein dynamics in the nuclear compartment
Hager, G. L., Elbi, C., & Becker, M. (2002) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(02)00278-2 · Cited by 72 · see citing works
Self-citationOstrowski, M. C., Huang, A.-L., Kessel, M., Wolford, R. G., & Hager, G. L. (1984) · The EMBO Journal · doi:10.1002/j.1460-2075.1984.tb02064.x · Cited by 70 · see citing works
Self-citationMulholland, N., Soeth, E., & Smith, C. L. (2003) · Oncogene · doi:10.1038/sj.onc.1206722 · Cited by 51 · see citing works
Combinatorial probabilistic chromatin interactions produce transcriptional heterogeneity
Voss, T. C., Schiltz, R. L., Sung, M., Johnson, T. A., John, S., & Hager, G. L. (2009) · Journal of Cell Science · doi:10.1242/jcs.035865 · Cited by 29 · see citing works
Self-citationAssays for Transcription Factors Access to Nucleosomal DNA
Li, Q., & Wränge, Ö. (1997) · Methods · doi:10.1006/meth.1997.0451 · Cited by 17 · see citing works
Burghaus, U. (2006) · Cited by 12 · see citing works
Rogowska, J. M., Vattuone, L., & Stephan, J. (2006) · Cited by 1 · see citing works
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- John S Thurman RE Sabo PJ Sung MH Biddie SC Johnson TA Hager GL Stamatoyannopoulos JA 2011 Chromatin accessibility dictates de novo regulatory factor binding Nat Genet 43 264 268 21258342 PMC6386452
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Transcription factors: from enhancer binding to developmental control
Spitz, F., & Furlong, E. E. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3207 · Cited by 2,227 · see citing works
Pioneer transcription factors: establishing competence for gene expression
Zaret, K. S., & Carroll, J. S. (2011) · Genes & Development · doi:10.1101/gad.176826.111 · Cited by 1,589 · see citing works
The selection and function of cell type-specific enhancers
Heinz, S., Romanoski, C. E., Benner, C., & Glass, C. K. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3949 · Cited by 1,010 · see citing works
Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution
Rhee, H. S., & Pugh, B. F. (2011) · Cell · doi:10.1016/j.cell.2011.11.013 · Cited by 760 · see citing works
Dynamic regulation of transcriptional states by chromatin and transcription factors
Voss, T. C., & Hager, G. L. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3623 · Cited by 504 · see citing works
Self-citationA Brief History of EpigeneticsPreprint
Felsenfeld, G. (2014) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a018200 · Cited by 420 · see citing works
The HPA – Immune Axis and the Immunomodulatory Actions of Glucocorticoids in the Brain
Bellavance, M.-A., & Rivest, S. (2014) · Frontiers in Immunology · doi:10.3389/fimmu.2014.00136 · Cited by 419 · see citing works
Advances in Targeting ‘Undruggable’ transcription Factors With Small Molecules
Henley, M. J., & Koehler, A. N. (2021) · Nature Reviews Drug Discovery · doi:10.1038/s41573-021-00199-0 · Cited by 409 · see citing works
Mechanisms of enhancer action: the known and the unknown
Panigrahi, A., & O’Malley, B. W. (2021) · Genome biology · doi:10.1186/s13059-021-02322-1 · Cited by 351 · see citing works
Steroid Receptors Reprogram FoxA1 Occupancy through Dynamic Chromatin Transitions
Swinstead, E. E., Miranda, T. B., Paakinaho, V., Baek, S., Goldstein, I., Hawkins, M., Karpova, T. S., Ball, D., Mazza, D., Lavis, L. D., et al. (2016) · Cell · doi:10.1016/j.cell.2016.02.067 · Cited by 312 · see citing works
Self-citationEukaryotic transcriptional dynamics: from single molecules to cell populations
Coulon, A., Chow, C. C., Singer, R. H., & Larson, D. R. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3484 · Cited by 309 · see citing works
Vandevyver, S., Dejager, L., Tuckermann, J., & Libert, C. (2013) · Endocrinology · doi:10.1210/en.2012-2045 · Cited by 296 · see citing works
de Kloet, E. R., Meijer, O. C., Nicola, A. F. D., Rijk, R. H. D., & Joëls, M. (2018) · Frontiers in Neuroendocrinology · doi:10.1016/j.yfrne.2018.02.003 · Cited by 279 · see citing works
Lickwar, C. R., Mueller, F., Hanlon, S. E., McNally, J. G., & Lieb, J. D. (2012) · Nature · doi:10.1038/nature10985 · Cited by 241 · see citing works
Madsen, M. S., Siersbæk, R., Boergesen, M., Nielsen, R., & Mandrup, S. (2014) · Molecular and Cellular Biology · doi:10.1128/mcb.01344-13 · Cited by 272 · see citing works
Single-molecule regulatory architectures captured by chromatin fiber sequencing
Stergachis, A. B., Debo, B. M., Haugen, E., Churchman, L. S., & Stamatoyannopoulos, J. A. (2020) · Science · doi:10.1126/science.aaz1646 · Cited by 257 · see citing works
Self-citationCLOCK:BMAL1 is a pioneer-like transcription factorPreprint
Menet, J. S., Pescatore, S., & Rosbash, M. (2014) · Genes & Development · doi:10.1101/gad.228536.113 · Cited by 252 · see citing works
Pioneer factors as master regulators of the epigenome and cell fate
Balsalobre, A., & Drouin, J. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00464-z · Cited by 251 · see citing works
Hartmann, K., Koenen, M., Schauer, S., Wittig-Blaich, S., Ahmad, M., Baschant, U., & Tuckermann, J. P. (2016) · Physiological Reviews · doi:10.1152/physrev.00011.2015 · Cited by 249 · see citing works
Yip, K. Y.-L., Cheng, C., Bhardwaj, N., Brown, J., Leng, J., Kundaje, A. B., Rozowsky, J. S., Birney, E., Bickel, P. J., Snyder, M. P., et al. (2012) · Genome biology · doi:10.1186/gb-2012-13-9-r48 · Cited by 244 · see citing works
Pioneer transcription factors shape the epigenetic landscape
Mayran, A., & Drouin, J. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.r117.001232 · Cited by 238 · see citing works
Boergesen, M., Pedersen, T. Å., Gross, B. S., van Heeringen, S. J., Hagenbeek, D., Bindesbøll, C., Caron, S., Lalloyer, F., Steffensen, K. R., Nebb, H. I., et al. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.06175-11 · Cited by 237 · see citing works
Transcription Factor Cooperativity in Early Adipogenic Hotspots and Super-Enhancers
Siersbæk, R., Rabiee, A., Nielsen, R., Sidoli, S., Traynor, S., Loft, A., Poulsen, L. L. C., Rogowska-Wrzesinska, A., Jensen, O. N., & Mandrup, S. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.04.042 · Cited by 234 · see citing works
Warming Induces Significant Reprogramming of Beige, but Not Brown, Adipocyte Cellular Identity
Roh, H. C., Tsai, L. T.-Y., Shao, M., Tenen, D. E., Shen, Y., Kumari, M., Lyubetskaya, A., Jacobs, C. L., Dawes, B. A., Gupta, R. K., et al. (2018) · Cell Metabolism · doi:10.1016/j.cmet.2018.03.005 · Cited by 232 · see citing works
FoxA1 Specifies Unique Androgen and Glucocorticoid Receptor Binding Events in Prostate Cancer Cells
Sahu, B., Laakso, M., Pihlajamaa, P., Ovaska, K., Sinielnikov, I., Hautaniemi, S., & Jänne, O. A. (2012) · Cancer Research · doi:10.1158/0008-5472.can-12-2350 · Cited by 230 · see citing works
Grøntved, L., John, S., Baek, S., Liu, Y., Buckley, J. R., Vinson, C., Aguilera, G., & Hager, G. L. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.106 · Cited by 229 · see citing works
Self-citationDisentangling the Many Layers of Eukaryotic Transcriptional Regulation
Lelli, K. M., Slattery, M. G., & Mann, R. S. (2012) · Annual Review of Genetics · doi:10.1146/annurev-genet-110711-155437 · Cited by 218 · see citing works
He, H. H., Meyer, C. A., Hu, S. S., Chen, M.-W., Zang, C., Liu, Y., Rao, P. K., Fei, T., Xu, H., Long, H., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2762 · Cited by 218 · see citing works
Therapeutic Ligands Antagonize Estrogen Receptor Function by Impairing Its Mobility
Guan, J., Zhou, W. J., Hafner, M. A., Blake, R. A., Chalouni, C. M., Chen, I. P., Bruyn, T. D., Giltnane, J. M., Hartman, S. J., Heidersbach, A. J., et al. (2019) · Cell · doi:10.1016/j.cell.2019.06.026 · Cited by 216 · see citing works
Zhang, X., Bolt, M. J., Guertin, M. J., Chen, W., Zhang, S., Cherrington, B. D., Slade, D. J., Dreyton, C. J., Subramanian, V., Bicker, K. L., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1203280109 · Cited by 212 · see citing works
Evolution of transcription factor binding in metazoans — mechanisms and functional implications
Villar, D., Flicek, P., & Odom, D. T. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3481 · Cited by 206 · see citing works
Piper, J., Elze, M. C., Cauchy, P., Cockerill, P. N., Bonifer, C., & Ott, S. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt850 · Cited by 194 · see citing works
Visualizing transcription factor dynamics in living cells
Liu, Z. J., & Tjian, R. (2018) · The Journal of Cell Biology · doi:10.1083/jcb.201710038 · Cited by 182 · see citing works
Pioneer factor pax7 deploys a stable enhancer repertoire for specification of cell fate
Mayran, A., Khetchoumian, K., Hariri, F., Pastinen, T., Gauthier, Y., Balsalobre, A., & Drouin, J. (2018) · Nature Genetics · doi:10.1038/s41588-017-0035-2 · Cited by 171 · see citing works
Genetic determinants and epigenetic effects of pioneer-factor occupancy
Donaghey, J., Thakurela, S., Charlton, J., Chen, J., Smith, Z. D., Gu, H., Pop, R., Clement, K., Stamenova, E. K., Karnik, R., et al. (2018) · Nature Genetics · doi:10.1038/s41588-017-0034-3 · Cited by 169 · see citing works
Cheng, C., Alexander, R. P., Min, R., Leng, J., Yip, K. Y.-L., Rozowsky, J. S., Yan, K., Dong, X., Djebali, S., Ruan, Y., et al. (2012) · Genome Research · doi:10.1101/gr.136838.111 · Cited by 165 · see citing works
Single molecule analysis of transcription factor binding at transcription sites in live cells
Morisaki, T., Müller, W., Golob, N., Mazza, D., & McNally, J. (2014) · Nature Communications · doi:10.1038/ncomms5456 · Cited by 167 · see citing works
Information integration and energy expenditure in gene regulation
Estrada, J., Wong, F., DePace, A. H., & Gunawardena, J. (2016) · Cell · doi:10.1016/j.cell.2016.06.012 · Cited by 168 · see citing works
DNase Footprint Signatures Are Dictated by Factor Dynamics and DNA Sequence
Sung, M., Guertin, M. J., Baek, S., & Hager, G. L. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.08.016 · Cited by 158 · see citing works
Self-citationMolecular Co-occupancy Identifies Transcription Factor Binding Cooperativity In Vivo
Sönmezer, C., Kleinendorst, R., Imanci, D., Barzaghi, G., Villacorta, L., Schübeler, D., Benes, V., Molina, N., & Krebs, A. R. (2021) · Molecular Cell · doi:10.1016/j.molcel.2020.11.015 · Cited by 162 · see citing works
Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions
Morris, S. A., Baek, S., Sung, M., John, S., Wiench, M., Johnson, T. A., Schiltz, R. L., & Hager, G. L. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2718 · Cited by 156 · see citing works
Self-citationLim, H., Uhlenhaut, N. H., Rauch, A., Weiner, J., Hübner, S., Hübner, N., Won, K., Lazar, M. A., Tuckermann, J. P., & Steger, D. J. (2015) · Genome Research · doi:10.1101/gr.188581.114 · Cited by 156 · see citing works
Generating specificity in genome regulation through transcription factor sensitivity to chromatin
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D’Amato, N. C., Gordon, M. A., Babbs, B. L., Spoelstra, N. S., Butterfield, K., Torkko, K. C., Phan, V. T., Barton, V. N., Rogers, T. J., Sartorius, C. A., et al. (2016) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-16-0167 · Cited by 154 · see citing works
Mifsud, K. R., & Reul, J. M. H. M. (2018) · Stress · doi:10.1080/10253890.2018.1456526 · Cited by 154 · see citing works
Reddy, T. E., Gertz, J., Crawford, G. E., Garabedian, M. J., & Myers, R. M. (2012) · Molecular and Cellular Biology · doi:10.1128/mcb.00062-12 · Cited by 149 · see citing works
Gaarenstroom, T., & Hill, C. S. (2014) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2014.01.009 · Cited by 146 · see citing works
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DNA binding triggers tetramerization of the glucocorticoid receptor in live cells
Presman, D. M., Ganguly, S., Schiltz, R. L., Johnson, T. A., Karpova, T., & Hager, G. L. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1606774113 · Cited by 142 · see citing works
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Suter, D. M. (2020) · Trends in Cell Biology · doi:10.1016/j.tcb.2020.03.003 · Cited by 143 · see citing works
Wu, D., Sunkel, B. D., Chen, Z., Liu, X., Ye, Z., Li, Q., Grenade, C., Ke, J., Zhang, C., Chen, H., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1382 · Cited by 138 · see citing works
Grøntved, L., Waterfall, J. J., Kim, D. W., Baek, S., Sung, M., Zhao, L., Park, J. W., Nielsen, R., Walker, R. L., Zhu, Y. J., et al. (2015) · Nature Communications · doi:10.1038/ncomms8048 · Cited by 137 · see citing works
Self-citationPresman, D. M., Ogara, M. F., Stortz, M., Álvarez, L. D., Pooley, J. R., Schiltz, R. L., Grøntved, L., Johnson, T. A., Mittelstadt, P. R., Ashwell, J. D., et al. (2014) · PLoS Biology · doi:10.1371/journal.pbio.1001813 · Cited by 138 · see citing works
Self-citationA phosphorylated transcription factor regulates sterol biosynthesis in Fusarium graminearum
Liu, Z., Jian, Y., Chen, Y., Kistler, H. C., He, P., Ma, Z., & Yin, Y. (2019) · Nature Communications · doi:10.1038/s41467-019-09145-6 · Cited by 137 · see citing works
Minderjahn, J., Schmidt, A., Fuchs, A., Schill, R., Raithel, J., Babina, M., Schmidl, C., Gebhard, C., Schmidhofer, S., Mendes, K., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-13960-2 · Cited by 136 · see citing works
Nuclear microenvironments modulate transcription from low-affinity enhancers
Tsai, A., Muthusamy, A. K., Alves, M. R. P., Lavis, L. D., Singer, R. H., Stern, D. L., & Crocker, J. (2017) · eLife · doi:10.7554/elife.28975 · Cited by 135 · see citing works
Transcriptional control of energy metabolism by nuclear receptors
Scholtes, C., & Giguère, V. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00486-7 · Cited by 129 · see citing works
Cryptic glucocorticoid receptor-binding sites pervade genomic NF-κB response elements
Hudson, W. H., de Vera, I. M. S., Nwachukwu, J. C., Weikum, E. R., Herbst, A., Yang, Q., Bain, D. L., Nettles, K. W., Kojetin, D. J., & Ortlund, E. A. (2018) · Nature Communications · doi:10.1038/s41467-018-03780-1 · Cited by 131 · see citing works
Miranda, T. B., Voss, T. C., Sung, M.-H., Baek, S., John, S., Hawkins, M., Grøntved, L., Schiltz, R. L., & Hager, G. L. (2013) · Cancer Research · doi:10.1158/0008-5472.can-13-0742 · Cited by 130 · see citing works
Self-citationSebastian, S., Faralli, H., Yao, Z., Rakopoulos, P., Palii, C. G., Cao, Y., Singh, K., Liu, Q.-C., Chu, A., Aziz, A., et al. (2013) · Genes & Development · doi:10.1101/gad.215400.113 · Cited by 122 · see citing works
Transcription factor assisted loading and enhancer dynamics dictate the hepatic fasting response
Goldstein, I., Baek, S., Presman, D. M., Paakinaho, V., Swinstead, E. E., & Hager, G. L. (2017) · Genome Research · doi:10.1101/gr.212175.116 · Cited by 121 · see citing works
Self-citationDynamic regulation of transcription factors by nucleosome remodeling
Li, M., Hada, A., Sen, P., Olufemi, L., Hall, M. A., Smith, B. Y., Forth, S. T., McKnight, J. N., Patel, A. K., Bowman, G. D., et al. (2015) · eLife · doi:10.7554/elife.06249 · Cited by 112 · see citing works
Uncovering cis-regulatory sequence requirements for context-specific transcription factor bindingPreprint
Yáñez-Cuna, J. O., Dinh, H. Q., Kvon, E. Z., Shlyueva, D., & Stark, A. (2012) · Genome Research · doi:10.1101/gr.132811.111 · Cited by 113 · see citing works
Transcriptional and Chromatin Regulation during Fasting – The Genomic Era
Goldstein, I., & Hager, G. L. (2015) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2015.09.005 · Cited by 110 · see citing works
Self-citationTwo methods for full-length RNA sequencing for low quantities of cells and single cells
Pan, X., Durrett, R., Zhu, H., Tanaka, Y., Li, Y., Zi, X., Marjani, S. L., Euskirchen, G. M., Ma, C., LaMotte, R. H., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1217322109 · Cited by 110 · see citing works
Molecular Spies in Action: Genetically Encoded Fluorescent Biosensors Light up Cellular Signals
Gest, A. M. M., Sahan, A. Z., Zhong, Y., Lin, W., Mehta, S., & Zhang, J. (2024) · Chemical Reviews · doi:10.1021/acs.chemrev.4c00293 · Cited by 110 · see citing works
Hindley, C. J., Ali, F. R., McDowell, G. S., Cheng, K., Jones, A., Guillemot, F., & Philpott, A. (2012) · Development · doi:10.1242/dev.077552 · Cited by 99 · see citing works
Activation of the Notch Signaling Pathway In Vivo Elicits Changes in CSL Nuclear Dynamics
Gomez-Lamarca, M. J., Sanjuan, J. F., Stojnic, R., Rehman, S. A., Mureşan, L., Jones, M. L., Pillidge, Z., Cerda‐Moya, G., Yuan, Z., Baloul, S., et al. (2018) · Developmental Cell · doi:10.1016/j.devcel.2018.01.020 · Cited by 99 · see citing works
Epigenetics, chromatin and genome organization: recent advances from the ENCODE project
Siggens, L., & Ekwall, K. (2014) · Journal of Internal Medicine · doi:10.1111/joim.12231 · Cited by 98 · see citing works
Goldstein, I., Paakinaho, V., Baek, S., Sung, M.-H., & Hager, G. L. (2017) · Nature Communications · doi:10.1038/s41467-017-02055-5 · Cited by 97 · see citing works
Self-citationQuantifying transcription factor kinetics: At work or at play?
Mueller, F., Stasevich, T. J., Mazza, D., & McNally, J. G. (2013) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409238.2013.833891 · Cited by 96 · see citing works
Swift, J., & Coruzzi, G. M. (2016) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2016.08.007 · Cited by 91 · see citing works
Stavreva, D. A., Coulon, A., Baek, S., Sung, M., John, S., Stixová, L., Tesikova, M., Hakim, O., Miranda, T. B., Hawkins, M. E., et al. (2015) · Genome Research · doi:10.1101/gr.184168.114 · Cited by 93 · see citing works
Self-citationCurrent concepts in glucocorticoid resistance
Yang, N., Ray, D. W., & Matthews, L. C. (2012) · Steroids · doi:10.1016/j.steroids.2012.05.007 · Cited by 92 · see citing works
Need, E. F., Selth, L. A., Harris, T. J., Birrell, S. N., Tilley, W. D., & Buchanan, G. (2012) · Molecular Endocrinology · doi:10.1210/me.2011-1314 · Cited by 87 · see citing works
Positional specificity of different transcription factor classes within enhancers
Grossman, S. R., Engreitz, J., Ray, J. P., Nguyen, T. H., Hacohen, N., & Lander, E. S. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1804663115 · Cited by 88 · see citing works
Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation
Packer, J. S., & Trapnell, C. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.06.001 · Cited by 84 · see citing works
Modulating transcription factor activity: Interfering with protein-protein interaction networks
François, M., Donovan, P., & Fontaine, F. R. (2018) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2018.07.019 · Cited by 80 · see citing works
Mechanisms by which transcription factors gain access to target sequence elements in chromatin
Guertin, M. J., & Lis, J. (2012) · Current Opinion in Genetics and Development · doi:10.1016/j.gde.2012.11.008 · Cited by 84 · see citing works
Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria
García, H. G., Sánchez, Á., Boedicker, J. Q., Osborne, M. L., Gelles, J., Kondev, J., & Phillips, R. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.06.004 · Cited by 81 · see citing works
Tewari, A. K., Yardımcı, G. G., Shibata, Y., Sheffield, N. C., Song, L., Taylor, B. S., Georgiev, S. G., Coetzee, G. A., Ohler, U., Furey, T. S., et al. (2012) · Genome biology · doi:10.1186/gb-2012-13-10-r88 · Cited by 76 · see citing works
Johnson, T. A., Chereji, R. V., Stavreva, D. A., Morris, S. A., Hager, G. L., & Clark, D. J. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1044 · Cited by 76 · see citing works
Self-citationHuang, Q., Ma, C., Chen, L., Luo, D., Chen, R., & Liang, F. (2018) · Frontiers in Endocrinology · doi:10.3389/fendo.2018.00370 · Cited by 78 · see citing works
van Weert, L. T. C. M., Buurstede, J. C., Mahfouz, A. E., Braakhuis, P. S. M., Polman, J. A. E., Sips, H. C. M., Roozendaal, B., Balog, J., de Kloet, E. R., Datson, N. A., et al. (2017) · Endocrinology · doi:10.1210/en.2016-1422 · Cited by 77 · see citing works
Enhancers and chromatin structures: regulatory hubs in gene expression and diseases
Hu, Z., & Tee, W. (2017) · Bioscience Reports · doi:10.1042/bsr20160183 · Cited by 78 · see citing works
Zhu, B., Gates, L. A., Stashi, E., Dasgupta, S., Gonzales, N., Dean, A., Dacso, C. C., York, B., & O’Malley, B. W. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.10.024 · Cited by 75 · see citing works
Dominance of the strongest: Inflammatory cytokines versus glucocorticoids
Dejager, L., Vandevyver, S., Πέττα, Ι., & Libert, C. (2013) · Cytokine & Growth Factor Reviews · doi:10.1016/j.cytogfr.2013.12.006 · Cited by 75 · see citing works
Frequency Modulation of Transcriptional Bursting Enables Sensitive and Rapid Gene Regulation
Li, C., Cesbron, F., Oehler, M., Brunner, M., & Höfer, T. (2018) · Cell Systems · doi:10.1016/j.cels.2018.01.012 · Cited by 75 · see citing works
Deciphering Steroid Receptor Crosstalk in Hormone-Driven Cancers
Truong, T. H., & Lange, C. A. (2018) · Endocrinology · doi:10.1210/en.2018-00831 · Cited by 73 · see citing works
Endocrine disruptors of sex hormone activities
Varticovski, L., Stavreva, D. A., McGowan, A., Raziuddin, R., & Hager, G. L. (2021) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2021.111415 · Cited by 75 · see citing works
Self-citationGerber, A. N., Newton, R. C., & Sasse, S. K. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.100687 · Cited by 72 · see citing works
Genome-wide footprinting: ready for prime time?
Sung, M., Baek, S., & Hager, G. L. (2016) · Nature Methods · doi:10.1038/nmeth.3766 · Cited by 69 · see citing works
Self-citationVahrenkamp, J. M., Yang, C.-H., Rodriguez, A. C., Almomen, A. A., Berrett, K. C., Trujillo, A., Guillen, K. P., Welm, B. E., Jarboe, E. A., Janat-Amsbury, M. M., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.02.076 · Cited by 72 · see citing works
Molecular Architecture of Transcription Factor Hotspots in Early Adipogenesis
Siersbæk, R., Baek, S., Rabiee, A., Nielsen, R., Traynor, S., Clark, N., Sandelin, A., Jensen, O. N., Sung, M., Hager, G. L., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.04.043 · Cited by 65 · see citing works
Self-citationChromatin scanning by dynamic binding of pioneer factors
Zaret, K. S., Lerner, J., & Iwafuchi-Doi, M. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.024 · Cited by 68 · see citing works
Gene Regulation in and out of Equilibrium
Wong, F. J., & Gunawardena, J. (2020) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-121219-081542 · Cited by 65 · see citing works
Miranda, T. B., Morris, S. A., & Hager, G. L. (2013) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2013.03.002 · Cited by 66 · see citing works
Self-citationPark, J., Estrada, J., Johnson, G. L., Vincent, B. J., Ricci-Tam, C., Bragdon, M. D. J., Shulgina, Y., Cha, A., Wunderlich, Z., Gunawardena, J., et al. (2018) · bioRxiv · doi:10.7554/elife.41266 · Cited by 68 · see citing works
Wiley, J. W., Higgins, G. A., & Athey, B. D. (2015) · Neurogastroenterology & Motility · doi:10.1111/nmo.12706 · Cited by 65 · see citing works
- Authors
- Voss, T. C., Schiltz, R. L., Sung, M.-H., Yen, P. M., Stamatoyannopoulos, J. A., Biddie, S. C., Johnson, T. A., Miranda, T. B., John, S., & Hager, G. L.
- Affiliations
- National Institutes of Health (US)
- National University of Singapore (SG)
- University of Washington (US)
- Corresponding author
- Hager, Gordon L.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2011-08
- Volume
- 146
- Issue
- 4
- Pages
- 544-554
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3210475
- OpenAlex
- W1963958393
- Cited by
- 307
- References
- 42
- Citations by year
- 2026: 5 · 2025: 10 · 2024: 11 · 2023: 11 · 2022: 16 · 2021: 20 · 2020: 17 · 2019: 23 · 2018: 33 · 2017: 23 · 2016: 29 · 2015: 23 · 2014: 25 · 2013: 26 · 2012: 29
- FWCI
- 11.18
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health
- National Cancer Institute (ZIABC005450)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- glucocorticoid receptor, glucocorticoid response element, transcription factor-DNA binding, chromatin accessibility, chromatin remodeling, receptor isoforms, photobleaching, transcriptional regulation
- MeSH terms
- Adenosine Triphosphate, Animals, Mammary Tumor Virus, Mouse, Models, Biological, Monte Carlo Method, Nucleosomes, Receptors, Estrogen, Receptors, Glucocorticoid, Regulatory Sequences, Nucleic Acid, Transcription Factors, Response Elements, Chromatin Assembly and Disassembly, Cell Line, Tumor, Mice
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