Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers
Open accessAbstract
Selective activity of a specific set of enhancers defines tissue-specific gene transcription. The pioneer factor FOXA1 has been shown to induce functional enhancer competency through chromatin openings. We have previously found that FOXA1 is recruited to thousands of regions across the genome of a given cell type. Here, we monitored the chromatin structure at FOXA1 binding sites on a chromosome-wide scale using formaldehyde assisted isolation of regulatory elements (FAIRE). Surprisingly, we find that a significant fraction of FOXA1-bound sites have a relatively closed chromatin conformation linked to a shift of the epigenetic signature toward repressive histone marks. Importantly, these sites are not correlated with gene expression in a given cell type suggesting that FOXA1 is required, but not sufficient, for the functional activity of bound enhancers. Interestingly, we find that a significant proportion of the inactive FOXA1-bound regulatory sites in one cell type are actually functional in another cellular context. We found that at least half of the FOXA1 binding sites from a given cell type are shared with another cell lineage. Mechanisms that restrict the activity of shared FOXA1-bound enhancers likely play a significant role in defining the cell-type-specific functions of FOXA1.
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Low H3K4me1 loci are typically functionally inactive and not co-occupied.
“In support of this, our data show that these loci are typically functionally inactive and not co-occupied, in agreement with previous studies (Lupien et al. 2008;Eeckhoute et al. 2009).”
From Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver (2010) · cites this paper as Eeckhoute et al. 2009
The Results section (“Levels of FAIRE enrichment correlate with the transcriptional regulatory activity at FOXA1-bound enhancers”; page unavailable) reports that low-FAIRE FOXA1 sites are less likely to be functional and less often recruit ESR1. But the paper compares H3K4me2, not H3K4me1, and does not establish the claim for low-H3K4me1 loci generally. (LLM, conf=0.85)
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Chromatin modifications and their function
Kouzarides, T. (2007) · Cell · doi:10.1016/j.cell.2007.02.005 · Cited by 10,883 · cited 1× · see citing works
“…(H3K9ac), are associated with functionally competent genomic regions while meth- ylation of H3K9 (H3K9me) is related to repression (Bauer et al. 2002; Barski et al. 2007; Heintzman et al. 2007; Kouzarides 2007; Mikkelsen et al. 2007; Frietze et al. 2008; Komashko et al. 2008; Krum et al. 2008).”
High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845 · see citing works
A Gene-Expression Signature as a Predictor of Survival in Breast Cancer
van de Vijver, M. J., He, Y. D., Veer, L. V. ‘., Dai, H. A., Hart, A. A. M., Voskuil, D. W., Schreiber, G. J., Peterse, J. L., Roberts, C., Marton, M. J., et al. (2002) · New England Journal of Medicine · doi:10.1056/nejmoa021967 · Cited by 6,411 · see citing works
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223 · see citing works
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129 · see citing works
Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398 · cited 1× · see citing works
“These domains can be identified using formaldehyde-assisted isolation of regulatory elements (FAIRE) that allows for enrichment of nucleosome-depleted genomic regions when cross-linked chromatin is subjected to phenol-chloroform extraction (Nagy et al. 2003; Hogan et al. 2006).”
BackgroundGene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer
Wang, Y., Klijn, J. G. M., Zhang, Y., Sieuwerts, A. M., Look, M. P., Yang, F., Talantov, D., Timmermans, M. A. M., Gelder, M. E. M., Yu, J. X., et al. (2005) · The Lancet · doi:10.1016/s0140-6736(05)17947-1 · Cited by 2,848 · see citing works
The complex language of chromatin regulation during transcription
Berger, S. L. (2007) · Nature · doi:10.1038/nature05915 · Cited by 2,768 · see citing works
Chen, X., Han, X., Yuan, P., Fang, F., Huss, M., Vega, V. B., Wong, E., Orlov, Y. L., Zhang, W., Jiang, J., et al. (2008) · Cell · doi:10.1016/j.cell.2008.04.043 · Cited by 2,474 · see citing works
Cofactor Dynamics and Sufficiency in Estrogen Receptor–Regulated Transcription
Shang, Y., Hu, X., DiRenzo, J., Lazar, M. A., & Brown, M. A. (2000) · Cell · doi:10.1016/s0092-8674(00)00188-4 · Cited by 1,647 · see citing works
Self-citationMétivier, R., Penot, G., Hübner, M. R., Reid, G., Brand, H., Koš, M., & Gannon, F. (2003) · Cell · doi:10.1016/s0092-8674(03)00934-6 · Cited by 1,431 · see citing works
High-Resolution Mapping and Characterization of Open Chromatin across the Genome
Boyle, A. P., Davis, S., Shulha, H. P., Meltzer, P., Margulies, E. H., Weng, Z., Furey, T. S., & Crawford, G. E. (2008) · Cell · doi:10.1016/j.cell.2007.12.014 · Cited by 1,415 · see citing works
Dynamic Regulation of Nucleosome Positioning in the Human Genome
Schones, D. E., Cui, K., Cuddapah, S., Roh, T., Barski, A., Wang, Z., Wei, G., & Zhao, K. (2008) · Cell · doi:10.1016/j.cell.2008.02.022 · Cited by 1,396 · see citing works
Carroll, J. S., Liu, X. S., Brodsky, A. S., Li, W., Meyer, C. A., Szary, A. J., Eeckhoute, J., Shao, W., Hestermann, E. V., Geistlinger, T. R., et al. (2005) · Cell · doi:10.1016/j.cell.2005.05.008 · Cited by 1,384 · see citing works
Self-citationGenome-wide analysis of estrogen receptor binding sites
Carroll, J. S., Meyer, C. A., Song, J. S., Li, W., Geistlinger, T., Eeckhoute, J., Brodsky, A. S., Keeton, E. K., Fertuck, K. C., Hall, G., et al. (2006) · Nature Genetics · doi:10.1038/ng1901 · Cited by 1,368 · see citing works
Self-citationAn Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells
Kim, J., Chu, J., Shen, X., Wang, J., & Orkin, S. H. (2008) · Cell · doi:10.1016/j.cell.2008.02.039 · Cited by 1,321 · see citing works
Control of Pancreas and Liver Gene Expression by HNF Transcription Factors
Odom, D. T., Zizlsperger, N., Gordon, D. B., Bell, G. W., Rinaldi, N. J., Murray, H. L., Volkert, T. L., Schreiber, J., Rolfe, A., Gifford, D. K., et al. (2004) · Science · doi:10.1126/science.1089769 · Cited by 1,312 · 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
In vivo enhancer analysis of human conserved non-coding sequences
Pennacchio, L. A., Ahituv, N., Moses, A. M., Prabhakar, S., Nobrega, M. A., Shoukry, M., Minovitsky, S., Dubchak, I., Holt, A., Lewis, K. D., et al. (2006) · Nature · doi:10.1038/nature05295 · Cited by 1,165 · see citing works
Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome
Kim, T. H., Abdullaev, Z., Smith, A. D., Ching, K. A., Loukinov, D. I., Green, R. D., Zhang, M. Q., Lobanenkov, V. V., & Ren, B. (2007) · Cell · doi:10.1016/j.cell.2006.12.048 · Cited by 1,022 · see citing works
FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription
Lupien, M., Eeckhoute, J., Meyer, C. A., Wang, Q., Zhang, Y., Li, W., Carroll, J. S., Liu, X. S., & Brown, M. (2008) · Cell · doi:10.1016/j.cell.2008.01.018 · Cited by 983 · see citing works
Self-citationRosenfeld, M. G., Lunyak, V. V., & Glass, C. K. (2006) · Genes & Development · doi:10.1101/gad.1424806 · Cited by 952 · see citing works
Giresi, P. G., Kim, J., McDaniell, R. M., Iyer, V. R., & Lieb, J. D. (2006) · Genome Research · doi:10.17615/8cez-3e87 · Cited by 949 · see citing works
XBP1 Controls Diverse Cell Type- and Condition-Specific Transcriptional Regulatory Networks
Acosta‐Alvear, D., Zhou, Y., Blais, A., Tsikitis, M., Lents, N. H., Arias, C., Lennon, C. J., Kluger, Y., & Dynlacht, B. D. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.06.011 · Cited by 853 · see citing works
Genome-wide analysis of Foxp3 target genes in developing and mature regulatory T cells
Zheng, Y., Josefowicz, S. Z., Kas, A., Chu, T.-T., Gavin, M. A., & Rudensky, A. Y. (2007) · Nature · doi:10.1038/nature05563 · Cited by 835 · see citing works
Wang, Q., Li, W., Liu, X. S., Carroll, J. S., Jänne, O. A., Keeton, E. K., Chinnaiyan, A. M., Pienta, K. J., & Brown, M. A. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.05.041 · Cited by 689 · see citing works
Self-citationHistone arginine methylation regulates pluripotency in the early mouse embryo
Torres‐Padilla, M., Parfitt, D.-E., Kouzarides, T., & Zernicka‐Goetz, M. (2007) · Nature · doi:10.1038/nature05458 · Cited by 592 · see citing works
Hepatic specification of the gut endoderm in vitro: cell signaling and transcriptional control.Preprint
Gualdi, R., Bossard, P., Zheng, M., Hamada, Y., Coleman, J. R., & Zaret, K. S. (1996) · Genes & Development · doi:10.1101/gad.10.13.1670 · Cited by 590 · see citing works
The initiation of liver development is dependent on Foxa transcription factors
Lee, C. S., Friedman, J. R., Fulmer, J. T., & Kaestner, K. H. (2005) · Nature · doi:10.1038/nature03649 · Cited by 581 · see citing works
The Foxa family of transcription factors in development and metabolism
Friedman, J. R., & Kaestner, K. (2006) · Cellular and Molecular Life Sciences (CMLS) · doi:10.1007/s00018-006-6095-6 · Cited by 541 · see citing works
Crawford, G. E., Holt, I. E., Whittle, J. R. R., Webb, B. D., Tai, D. S., Davis, S. R., Margulies, E. H., Chen, Y., Bernat, J. A., Ginsburg, D., et al. (2005) · Genome Research · doi:10.1101/gr.4074106 · Cited by 487 · see citing works
Whole-Genome Cartography of Estrogen Receptor α Binding Sites
Lin, C., Vega, V. B., Thomsen, J. S., Zhang, T., Kong, S. L., Xie, M., Chiu, K. P., Lipovich, L., Barnett, D., Stossi, F., et al. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030087 · Cited by 459 · see citing works
Model-based analysis of tiling-arrays for ChIP-chip
Johnson, W. E., Li, W., Meyer, C. A., Gottardo, R., Carroll, J. S., Brown, M. A., & Liu, X. S. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0601180103 · Cited by 428 · see citing works
Self-citationBinding of the winged‐helix transcription factor HNF3 to a linker histone site on the nucleosome
Cirillo, L. A., McPherson, C. E., Bossard, P., Stevens, K., Cherian, S., Shim, E. Y., Clark, K., Burley, S. K., & Zaret, K. S. (1998) · The EMBO Journal · doi:10.1093/emboj/17.1.244 · Cited by 381 · see citing works
Laganière, J., Deblois, G., Lefèbvre, C., Bataille, A. R., Robert, F., & Giguère, V. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0505575102 · Cited by 367 · see citing works
Cell- and gene-specific regulation of primary target genes by the androgen receptorPreprint
Bolton, E. C., So, A. Y., Chaivorapol, C., Haqq, C. M., Li, H., & Yamamoto, K. R. (2007) · Genes & Development · doi:10.1101/gad.1564207 · Cited by 348 · see citing works
Methylation at arginine 17 of histone H3 is linked to gene activation
Bauer, U., Daujat, S., Nielsen, S. J., Nightingale, K. P., & Kouzarides, T. (2002) · EMBO Reports · doi:10.1093/embo-reports/kvf013 · Cited by 344 · see citing works
Positive Cross-Regulatory Loop Ties GATA-3 to Estrogen Receptor α Expression in Breast Cancer
Eeckhoute, J., Keeton, E. K., Lupien, M., Krum, S. A., Carroll, J. S., & Brown, M. A. (2007) · Cancer Research · doi:10.1158/0008-5472.can-07-0746 · Cited by 344 · see citing works
Self-citationHigh-throughput mapping of the chromatin structure of human promoters
Ozsolak, F., Song, J. S., Liu, X. S., & Fisher, D. E. (2007) · Nature Biotechnology · doi:10.1038/nbt1279 · Cited by 336 · 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
Bieda, M. C., Xu, X., Singer, M. A., Green, R., & Farnham, P. (2006) · Genome Research · doi:10.1101/gr.4887606 · Cited by 306 · see citing works
Eeckhoute, J., Carroll, J. S., Geistlinger, T., Torres‐Arzayus, M. I., & Brown, M. A. (2006) · Genes & Development · doi:10.1101/gad.1446006 · Cited by 303 · see citing works
Self-citationGao, N., Zhang, J., Rao, M. A., Case, T. C., Mirosevich, J., Wang, Y., Jin, R., Gupta, A., Rennie, P. S., & Matusik, R. J. (2003) · Molecular Endocrinology · doi:10.1210/me.2003-0020 · Cited by 279 · see citing works
Yang, A., Zhu, Z., Kapranov, P., McKeon, F., Church, G. M., Gingeras, T., & Struhl, K. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.10.018 · Cited by 277 · see citing works
Xi, H. S., Shulha, H. P., Lin, J. M., Vales, T. R., Fu, Y., Bodine, D. M., McKay, R. D. G., Chenoweth, J. G., Tesar, P. J., Furey, T. S., et al. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0030136 · Cited by 215 · see citing works
Zaret, K. (1999) · Developmental Biology · doi:10.1006/dbio.1999.9228 · Cited by 209 · see citing works
CARM1 Regulates Estrogen-Stimulated Breast Cancer Growth through Up-regulation of E2F1
Frietze, S. E., Lupien, M., Silver, P. A., & Brown, M. A. (2008) · Cancer Research · doi:10.1158/0008-5472.can-07-1983 · Cited by 205 · see citing works
Self-citationXu, X., Bieda, M. C., Jin, V. X., Rabinovich, A., Oberley, M. J., Green, R., & Farnham, P. (2007) · Genome Research · doi:10.1101/gr.6783507 · Cited by 202 · see citing works
Hua, S., Kallen, C. B., Dhar, R., Baquero, M. T., Mason, C. E., Russell, B. A., Shah, P. K., Liu, J., Khramtsov, A., Tretiakova, M., et al. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.25 · Cited by 187 · see citing works
Genome-Wide Identification of Estrogen Receptor α-Binding Sites in Mouse Liver
Gao, H., Fält, S., Sandelin, A., Gustafsson, J.-Α., & Dahlman‐Wright, K. (2007) · Molecular Endocrinology · doi:10.1210/me.2007-0121 · Cited by 154 · see citing works
Naeem, H., Cheng, D., Zhao, Q., Underhill, C., Tini, M., Bedford, M. T., & Torchia, J. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.00815-06 · Cited by 136 · see citing works
Predicting tissue-specific enhancers in the human genomePreprint
Pennacchio, L. A., Loots, G. G., Nóbrega, M. A., & Ovcharenko, I. (2007) · Genome Research · doi:10.1101/gr.5972507 · Cited by 131 · see citing works
E2F in vivo binding specificity: Comparison of consensus versus nonconsensus binding sitesPreprint
Rabinovich, A., Jin, V. X., Rabinovich, R., Xu, X., & Farnham, P. (2008) · Genome Research · doi:10.1101/gr.080622.108 · Cited by 129 · see citing works
Unique 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
Self-citationNagy, P. L., Cleary, M. L., Brown, P. O., & Lieb, J. D. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1131966100 · Cited by 116 · see citing works
Xu, J., Pope, S. D., Jazirehi, A. R., Attema, J. L., Papathanasiou, P., Watts, J. A., Zaret, K. S., Weissman, I. L., & Smale, S. T. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704579104 · Cited by 114 · see citing works
Cell Cycle–Specified Fluctuation of Nucleosome Occupancy at Gene Promoters
Hogan, G. J., Lee, C.-K., & Lieb, J. D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020158 · Cited by 109 · see citing works
Developmental control via GATA factor interplay at chromatin domains
Bresnick, E. H., Martowicz, M. L., Pal, S. K., & Johnson, K. D. (2005) · Journal of Cellular Physiology · doi:10.1002/jcp.20393 · Cited by 96 · see citing works
Steinfeld, I., Ron Shamir, A., & Kupiec, M. (2007) · Nature Genetics · doi:10.1038/ng1965 · Cited by 65 · see citing works
Komashko, V., Acevedo, L. G., Squazzo, S. L., Iyengar, S., Rabinovich, A., O’Geen, H., Green, R., & Farnham, P. (2008) · Genome Research · doi:10.1101/gr.074609.107 · Cited by 56 · see citing works
CCCTC-Binding Factor Confines the Distal Action of Estrogen Receptor
Chan, C. S., & Song, J. S. (2008) · Cancer Research · doi:10.1158/0008-5472.can-08-2632 · Cited by 38 · see citing works
GATA-1 Modulates the Chromatin Structure and Activity of the Chicken α-Globin 3′ Enhancer
Escamilla-Del-Arenal, M., & Targa, F. R. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.00943-07 · Cited by 23 · see citing works
Nagashima, T., Suzuki, T., Kondo, S., Kuroki, Y., Takahashi, K., Ide, K., Yumoto, N., Hasegawa, A., Toyoda, T., Kojima, T., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0001803 · Cited by 8 · see citing works
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Visscher, P. M., Brown, M. A., McCarthy, M. I., & Yang, J. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.11.029 · Cited by 2,425 · see citing works
Self-citationPioneer 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
FOXA1 is a key determinant of estrogen receptor function and endocrine response
Hurtado, A., Holmes, K. A., Ross-Innes, C. S., Schmidt, D., & Carroll, J. S. (2010) · Nature Genetics · doi:10.1038/ng.730 · Cited by 847 · see citing works
Chromatin accessibility: a window into the genome
Tsompana, M., & Buck, M. J. (2014) · Epigenetics & Chromatin · doi:10.1186/1756-8935-7-33 · Cited by 437 · see citing works
Arnal, J., Lenfant, F., Métivier, R., Flouriot, G., Henrion, D., Adlanmérini, M., Fontaine, C., Gourdy, P., Chambon, P., Katzenellenbogen, B. S., et al. (2017) · Physiological Reviews · doi:10.1152/physrev.00024.2016 · Cited by 428 · see citing works
Targeting Androgen Receptor in Estrogen Receptor-Negative Breast Cancer
Ni, M., Chen, Y., Lim, E., Wimberly, H., Bailey, S. T., Imai, Y., Rimm, D. L., Liu, X. S., & Brown, M. A. (2011) · Cancer Cell · doi:10.1016/j.ccr.2011.05.026 · Cited by 398 · see citing works
Self-citationSahu, B., Laakso, M., Ovaska, K., Mirtti, T. K., Lundin, J. E., Rannikko, A. S., Sankila, A., Turunen, J.-P., Lundin, M., Konsti, J., et al. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.328 · Cited by 386 · 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
Siersbæk, R., Nielsen, R., John, S., Sung, M., Baek, S., Loft, A., Hager, G. L., & Mandrup, S. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.65 · Cited by 350 · see citing works
Simon, J. M., Giresi, P. G., Davis, I. J., & Lieb, J. D. (2012) · Nature Protocols · doi:10.1038/nprot.2011.444 · Cited by 329 · see citing works
Toska, E., Osmanbeyoglu, H. U., Castel, P., Chan, C., Hendrickson, R. C., Elkabets, M., Dickler, M. N., Scaltriti, M., Leslie, C. S., Armstrong, S. A., et al. (2017) · Science · doi:10.1126/science.aah6893 · Cited by 262 · see citing works
Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancersPreprint
Sérandour, A. A., Avner, S., Percevault, F., Demay, F., Bizot, M., Lucchetti-Miganeh, C., Barloy-Hubler, F., Brown, M. A., Lupien, M., Métivier, R., et al. (2011) · Genome Research · doi:10.1101/gr.111534.110 · Cited by 228 · see citing works
Self-citationFOXA1: a transcription factor with parallel functions in development and cancer
Bernardo, G. M., & Keri, R. A. (2011) · Bioscience Reports · doi:10.1042/bsr20110046 · Cited by 225 · see citing works
Fu, J., Wolfs, M. G. M., Deelen, P., Westra, H.-J., Fehrmann, R. S. N., Meerman, G. J. T., Buurman, W. A., Rensen, S. S., Groen, H. J. M., Weersma, R. K., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002431 · Cited by 216 · see citing works
Predictive chromatin signatures in the mammalian genome
Hon, G. C., Hawkins, R. D., & Ren, B. (2009) · Human Molecular Genetics · doi:10.1093/hmg/ddp409 · Cited by 221 · see citing works
Lefterova, M. I., Steger, D. J., Zhuo, D. X., Qatanani, M., Mullican, S. E., Tuteja, G., Manduchi, E., Grant, G. R., & Lazar, M. A. (2010) · Molecular and Cellular Biology · doi:10.1128/mcb.01651-09 · Cited by 208 · see citing works
Kong, S. L., Li, G., Loh, S. L., Sung, W.-K. K., & Liu, E. T. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.59 · Cited by 202 · see citing works
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Kaestner, K. H. (2010) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2010.06.005 · Cited by 198 · see citing works
PBX1 Genomic Pioneer Function Drives ERα Signaling Underlying Progression in Breast Cancer
Magnani, L., Ballantyne, E. B., Zhang, X., & Lupien, M. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002368 · Cited by 193 · see citing works
Self-citationDynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers
Sérandour, A. A., Avner, S., Oger, F., Bizot, M., Percevault, F., Lucchetti-Miganeh, C., Palierne, G., Gheeraert, C., Barloy-Hubler, F., Péron, C. L., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks595 · Cited by 186 · see citing works
Self-citationMagnani, L., Stoeck, A., Zhang, X., Lánczky, A., Mirabella, A., Wang, T., Győrffy, B., & Lupien, M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1219992110 · Cited by 181 · see citing works
Self-citationLupien, M., Meyer, C. A., Bailey, S. T., Eeckhoute, J., Cook, J., Westerling, T., Zhang, X., Carroll, J. S., Rhodes, D. R., Liu, X., et al. (2010) · Genes & Development · doi:10.1101/gad.1944810 · Cited by 165 · see citing works
Self-citationPioneer factors: directing transcriptional regulators within the chromatin environment
Magnani, L., Eeckhoute, J., & Lupien, M. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.07.002 · Cited by 161 · see citing works
Self-citationSelective amputation of the pharynx identifies a FoxA-dependent regeneration program in planaria
Adler, C. E., Seidel, C. W., McKinney, S., & Alvarado, A. S. (2014) · eLife · doi:10.7554/elife.02238 · Cited by 157 · see citing works
AP‐2γ regulates oestrogen receptor‐mediated long‐range chromatin interaction and gene transcription
Tan, S. K., Lin, Z. H., Chang, C. W., Varang, V., Chng, K. R., Pan, Y. F., Yong, E., Sung, W.-K. K., & Cheung, E. C. W. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.151 · Cited by 156 · see citing works
Pham, T.-H., Benner, C., Lichtinger, M., Schwarzfischer, L., Hu, Y., Andreesen, R., Chen, W., & Rehli, M. (2012) · Blood · doi:10.1182/blood-2012-01-402453 · Cited by 143 · see citing works
Determinants of Receptor- and Tissue-Specific Actions in Androgen Signaling
Pihlajamaa, P., Sahu, B., & Jänne, O. A. (2015) · Endocrine Reviews · doi:10.1210/er.2015-1034 · Cited by 141 · see citing works
FOXA1 is an independent prognostic marker for ER-positive breast cancer
Mehta, R. J., Jain, R., Leung, S. C. Y., Choo, J. R., Nielsen, T. O., Huntsman, D. D., Nakshatri, H., & Badve, S. (2011) · Breast Cancer Research and Treatment · doi:10.1007/s10549-011-1482-6 · Cited by 127 · see citing works
Chromatin signatures of active enhancers
Spicuglia, S., & Vanhille, L. (2012) · Nucleus · doi:10.4161/nucl.19232 · Cited by 116 · see citing works
Hoffman, B. G., Robertson, G., Zavaglia, B., Beach, M., Cullum, R., Lee, S., Soukhatcheva, G., Li, L., Wederell, E. D., Thiessen, N., et al. (2010) · Genome Research · doi:10.1101/gr.104356.109 · Cited by 115 · see citing works
“Secondary co-occupying transcription factors ensure nucleosome displacement Previously, it was shown that differential recruitment of ESR1 and AR in breast and prostate cancer cell lines, respectively, correlates with the accessibility and functionality of FOXA1 sites (Eeckhoute et al. 2009).”
BackgroundResultBoudot, A. J., Kerdivel, G., Habauzit, D., Eeckhoute, J., Dily, F. L., Flouriot, G., Samson, M., & Pakdel, F. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020898 · Cited by 113 · see citing works
Self-citationMechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1
Pham, T.-H., Minderjahn, J., Schmidl, C., Hoffmeister, H., Schmidhofer, S., Chen, W., Längst, G., Benner, C., & Rehli, M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt355 · Cited by 102 · see citing works
Aberrant Estrogen Regulation of PEMT Results in Choline Deficiency-associated Liver Dysfunction
Resseguie, M., da Costa, K.-A., Galanko, J. A., Patel, M., Davis, I. J., & Zeisel, S. H. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.106922 · Cited by 106 · see citing works
Methyltransferase G9A regulates T cell differentiation during murine intestinal inflammation
Antignano, F., Burrows, K., Hughes, M. R., Han, J. M., Kron, K. J., Penrod, N. M., Oudhoff, M. J., Wang, S. K. H., Min, P. H., Gold, M. J., et al. (2014) · Journal of Clinical Investigation · doi:10.1172/jci69592 · Cited by 102 · see citing works
Self-citationAndrogen receptor genomic regulation.
Jin, H., Kim, J., & Yu, J. (2013) · Europe PMC (PubMed Central) · doi:10.3978/j.issn.2223-4683.2013.09.01 · Cited by 95 · see citing works
Svotelis, A., Bianco, S., Madore, J., Huppé, G., Nordell-Markovits, A., Mes‐Masson, A., & Gévry, N. Y. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.284 · Cited by 93 · see citing works
Zhang, C., Wang, L., Wu, D., Chen, H., Chen, Z., Thomas‐Ahner, J. M., Zynger, D. L., Eeckhoute, J., Yu, J., Luo, J., et al. (2011) · Cancer Research · doi:10.1158/0008-5472.can-11-1882 · Cited by 93 · see citing works
Self-citationThe Chromatin Fingerprint of Gene Enhancer Elements
Zentner, G. E., & Scacheri, P. C. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.r111.296491 · Cited by 89 · see citing works
Zhang, Z., Yang, C., Gao, W., Chen, T., Qian, T., Hu, J. X., & Tan, Y. (2015) · Cancer Letters · doi:10.1016/j.canlet.2015.03.008 · Cited by 89 · see citing works
Amplitude modulation of androgen signaling by c-MYCPreprint
Ni, M., Chen, Y., Fei, T., Li, D., Lim, E., Liu, X. S., & Brown, M. A. (2013) · Genes & Development · doi:10.1101/gad.209569.112 · Cited by 88 · see citing works
Self-citationMolecular basis for gene-specific transactivation by nuclear receptors
Aagaard, M. M., Siersbæk, R., & Mandrup, S. (2010) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2010.12.018 · Cited by 86 · see citing works
FoxA1 is a Key Mediator of Hormonal Response in Breast and Prostate Cancer
Robinson, J. L. L., & Carroll, J. S. (2012) · Frontiers in Endocrinology · doi:10.3389/fendo.2012.00068 · Cited by 85 · see citing works
Cistromics of hormone-dependent cancer
Lupien, M., & Brown, M. A. (2009) · Endocrine Related Cancer · doi:10.1677/erc-09-0038 · Cited by 83 · see citing works
Self-citationCurrent perspectives on FOXA1 regulation of androgen receptor signaling and prostate cancer
Yang, Y. A., & Yu, J. (2015) · Genes & Diseases · doi:10.1016/j.gendis.2015.01.003 · Cited by 79 · see citing works
Sulahian, R., Casey, F., Shen, J., Qian, Z., Shin, H., Ogino, S., Weir, B. A., Vázquez, F., Liu, X. S., Hahn, W. C., et al. (2013) · Oncogene · doi:10.1038/onc.2013.517 · Cited by 74 · see citing works
Self-citationEpigenetic pioneering by SWI/SNF family remodelers
Ahmad, K., Brahma, S., & Henikoff, S. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.10.045 · Cited by 74 · see citing works
Coactivator Function Defines the Active Estrogen Receptor Alpha Cistrome
Lupien, M., Eeckhoute, J., Meyer, C. A., Krum, S. A., Rhodes, D. R., Liu, X., & Brown, M. A. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.00020-09 · Cited by 74 · see citing works
Self-citationBerchowitz, L. E., Hanlon, S. L., Lieb, J. D., & Copenhaver, G. P. (2009) · Genome Research · doi:10.1101/gr.096297.109 · Cited by 72 · see citing works
Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer
Zhou, S., Hawley, J. R., Soares, F., Grillo, G., Teng, M., Tonekaboni, S. A. M., Hua, J. T., Kron, K. J., Mazrooei, P., Ahmed, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14318-9 · Cited by 69 · see citing works
Self-citationChromatin and epigenetic determinants of estrogen receptor alpha (ESR1) signaling
Magnani, L., & Lupien, M. (2013) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2013.04.026 · Cited by 66 · see citing works
Self-citationThe Forkhead Transcription Factor FOXK2 Promotes AP-1-Mediated Transcriptional Regulation
Ji, Z., Donaldson, I. J., Liu, J., Hayes, A., Zeef, L. A. H., & Sharrocks, A. D. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.05504-11 · Cited by 64 · see citing works
Minireview: Pioneer Transcription Factors in Cell Fate Specification
Drouin, J. (2014) · Molecular Endocrinology · doi:10.1210/me.2014-1084 · Cited by 51 · see citing works
Cross-regulation between FOXA1 and ErbB2 Signaling in Estrogen Receptor-Negative Breast Cancer
Naderi, A., Meyer, M., & Dowhan, D. H. (2012) · Neoplasia · doi:10.1593/neo.12294 · Cited by 51 · see citing works
Holmes, K. A., Hurtado, A., Brown, G. D., Launchbury, R., Ross-Innes, C. S., Hadfield, J., Odom, D. T., & Carroll, J. S. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1018863108 · Cited by 50 · see citing works
Kerschner, J. L., Gosalia, N., Leir, S., & Harris, A. (2014) · Epigenetics · doi:10.4161/epi.27696 · Cited by 52 · see citing works
Organ-specific gene expression: the bHLH protein Sage provides tissue specificity toDrosophilaFoxA
Fox, R. M., Vaishnavi, A., Maruyama, R., & Andrew, D. J. (2013) · Development · doi:10.1242/dev.092924 · Cited by 46 · see citing works
Eeckhoute, J., Oger, F., Staels, B., & Lefèbvre, P. (2012) · PPAR Research · doi:10.1155/2012/164140 · Cited by 45 · see citing works
Self-citationWarrick, J. I., Hu, W., Yamashita, H., Walter, V., Shuman, L., Craig, J. M., Gellert, L. L., Castro, M. A. A., Robertson, A. G., Kuo, F., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34251-3 · Cited by 44 · see citing works
Traboulsi, T., Ezzy, M. E., Dumeaux, V., Audemard, E. O., & Mader, S. (2018) · Oncogene · doi:10.1038/s41388-018-0468-9 · Cited by 44 · see citing works
Cytosine modifications modulate the chromatin architecture of transcriptional enhancersPreprint
Mahé, E. A., Madigou, T., Sérandour, A. A., Bizot, M., Avner, S., Chalmel, F., Palierne, G., Métivier, R., & Salbert, G. (2017) · Genome Research · doi:10.1101/gr.211466.116 · Cited by 42 · see citing works
Emerging patterns of epigenomic variation
Milosavljevic, A. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.03.001 · Cited by 39 · see citing works
Noncoding deletions reveal a gene that is critical for intestinal function
Oz-Levi, D., Olender, T., Bar-Joseph, I., Zhu, Y., Marek‐Yagel, D., Barozzi, I., Osterwalder, M., Alkelai, A., Ruzzo, E. K., Han, Y., et al. (2019) · Nature · doi:10.1038/s41586-019-1312-2 · Cited by 38 · see citing works
A Detailed Protocol for Formaldehyde‐Assisted Isolation of Regulatory Elements (FAIRE)
Simon, J. M., Giresi, P. G., Davis, I. J., & Lieb, J. D. (2013) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb2126s102 · Cited by 37 · see citing works
Analysis of Chromatin Dynamics during Glucocorticoid Receptor Activation
Burd, C. J., Ward, J. M., Crusselle‐Davis, V. J., Kissling, G. E., Phadke, D. P., Shah, R., & Archer, T. (2012) · Molecular and Cellular Biology · doi:10.1128/mcb.06206-11 · Cited by 36 · see citing works
FOXA1 hypermethylation: link between parity and ER-negative breast cancer in African American women?
Espinal, A. C., Buas, M. F., Wang, D., Cheng, D. T.-Y., Sucheston‐Campbell, L. E., Hu, Q., Yan, L., Ondracek, R. P., Cortes, E., Tang, L., et al. (2017) · Breast Cancer Research and Treatment · doi:10.1007/s10549-017-4418-y · Cited by 36 · see citing works
Lennartsson, A., Arner, E., Fagiolini, M., Saxena, A., Andersson, R., Takahashi, H., Noro, Y., Sng, J., Sandelin, A., Hensch, T. K., et al. (2015) · Epigenetics & Chromatin · doi:10.1186/s13072-015-0043-3 · Cited by 35 · see citing works
Boudot, A. J., Kerdivel, G., Lecomte, S., Flouriot, G., Desille, M., Godey, F., Lévêque, J., Tas, P., Dréan, Y. L., & Pakdel, F. (2014) · BMC Cancer · doi:10.1186/1471-2407-14-407 · Cited by 34 · see citing works
Histone signature of metanephric mesenchyme cell lines
McLaughlin, N., Yao, X., Li, Y., Saifudeen, Z. R., & El-Dahr, S. S. (2013) · Epigenetics · doi:10.4161/epi.25753 · Cited by 30 · see citing works
A Distinct Chromatin State Drives Therapeutic Resistance in Invasive Lobular Breast Cancer
Nardone, A., Qiu, X., Spisák, S., Nagy, Z., Feiglin, A., Feit, A. S., Feit, G. C., Xie, Y., Font‐Tello, A., Guarducci, C., et al. (2022) · Cancer Research · doi:10.1158/0008-5472.can-21-3186 · Cited by 27 · see citing works
Lo, R., Celius, T., Karmaus, A. L., Dere, E., MacPherson, L., Harper, P. A., Zacharewski, T. R., & Matthews, J. B. (2011) · Toxicology and Applied Pharmacology · doi:10.1016/j.taap.2011.08.016 · Cited by 26 · see citing works
Defining specificity of transcription factor regulatory activities
Eeckhoute, J., Métivier, R., & Salbert, G. (2009) · Journal of Cell Science · doi:10.1242/jcs.054916 · Cited by 26 · see citing works
Self-citationGenome-wide interplay of nuclear receptors with the epigenome
Martens, J. H. A., Rao, N., & Stunnenberg, H. G. (2010) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2010.10.005 · Cited by 26 · see citing works
Maruyama, R., Grevengoed, E., Stempniewicz, P., & Andrew, D. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020901 · Cited by 23 · see citing works
Pascual-Carreras, E., Herrera-Úbeda, C., Rosselló, M., Coronel-Córdoba, P., García‐Fernàndez, J., Saló, E., & Adell, T. (2021) · Scientific Reports · doi:10.1038/s41598-020-80627-0 · Cited by 23 · see citing works
Characterization of Chromatin Structure-associated Histone Modifications in Breast Cancer Cells
Hong, C. P., Choe, M. K., & Roh, T. (2012) · Genomics & Informatics · doi:10.5808/gi.2012.10.3.145 · Cited by 20 · see citing works
Transcription Factor Interactions in Genomic Nuclear Receptor Function
George, C. L., Lightman, S. L., & Biddie, S. C. (2011) · Epigenomics · doi:10.2217/epi.11.66 · Cited by 21 · see citing works
Chen, T., He, S., Zhang, Z., Gao, W., Li, Y., & Tan, Y. (2014) · Experimental Cell Research · doi:10.1016/j.yexcr.2014.04.020 · Cited by 20 · see citing works
Chromatin Landscape and Endocrine Response in Breast Cancer
Magnani, L., Brunelle, M., Gévry, N. Y., & Lupien, M. (2012) · Epigenomics · doi:10.2217/epi.12.64 · Cited by 16 · see citing works
Self-citationInterrogating genomic and epigenomic data to understand prostate cancer
Kim, J., & Yu, J. (2012) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2011.12.003 · Cited by 16 · see citing works
Mapping Open Chromatin with Formaldehyde-Assisted Isolation of Regulatory Elements
Nammo, T., Rodríguez‐Seguí, S. A., & Ferrer, J. P. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-316-5_21 · Cited by 14 · see citing works
Differential Glucocorticoid Receptor-mediated Transcription Mechanisms
Aoyagi, S., & Archer, T. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.195040 · Cited by 13 · see citing works
Ovesen, J. L., Fan, Y., Zhang, X., Chen, J., Medvedovic, M., Xia, Y., & Puga, A. (2014) · PLoS ONE · doi:10.1371/journal.pone.0097849 · Cited by 13 · see citing works
Lai, Y.-R., Lu, Y., Lien, H.-W., Huang, C., & Hwang, S. L. (2016) · Biochemical Journal · doi:10.1042/bcj20160392 · Cited by 13 · see citing works
Crosstalk and DC-SCRIPT: Expanding nuclear receptor modulation
Ansems, M., Hontelez, S., Karthaus, N., Span, P. N., & Adema, G. J. (2010) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2010.05.001 · Cited by 12 · see citing works
Cistrome plasticity and mechanisms of cistrome reprogramming
García-Bassets, I., & Wang, D. (2012) · Cell Cycle · doi:10.4161/cc.21281 · Cited by 11 · see citing works
Arora, S., Yang, J., Akiyama, T., James, D. Q., Morrissey, A., Blanda, T. R., Badjatia, N., Lai, W., Ko, M. S. H., Pugh, B. F., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.06.561228 · Cited by 8 · see citing works
Xia, K., Huang, W., Zhao, X., Huang, X., Chen, Y., Li, Y., & Tan, Y. (2022) · PubMed Central · Cited by 7 · see citing works
Kneppers, J., Bergman, A. M., & Zwart, W. T. (2022) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-11836-4_15 · Cited by 6 · see citing works
The role of FOXA subfamily factors in embryonic development and carcinogenesis of the pancreas
Zinovyeva, M. V., Kuzmich, A. I., MONASTYRSKAYA, G. S., & Sverdlov, E. D. (2016) · Molecular Genetics Microbiology and Virology · doi:10.3103/s0891416816030113 · Cited by 6 · see citing works
Zinovyeva, M. V., Kuzmich, A. I., MONASTYRSKAYA, G. S., & Sverdlov, E. D. (2016) · Molecular Genetics Microbiology and Virology (Russian) · doi:10.18821/0208-0613-2016-34-3-98-103 · Cited by 5 · see citing works
Simon, J. M., Giresi, P. G., Davis, I. J., & Lieb, J. D. (2014) · Nature Protocols · doi:10.1038/nprot.2014.062 · Cited by 4 · see citing works
Chromatin Variants Reveal the Genetic Determinants of Oncogenesis in Breast CancerPreprint
Bahl, S., Carroll, J. S., & Lupien, M. (2022) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a041322 · Cited by 4 · see citing works
Self-citationGilfillan, S., Wang, S., Katika, M. R., Norum, J. H., Bergholtz, H., Fiorito, E., Nordhagen, S., Sharma, Y., Singh, S. K., Somisety, V. S., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.22.308569 · Cited by 1 · see citing works
Tipping the Balance: Factors That Influence the ER Signaling Network in Breast Cancer
Jasper, J. S. (2014) · DukeSpace (Duke University)
Magnani, L., Louloupi, A., & Zwart, W. T. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-801899-6.00023-1
Discerning the role of FOXA1 in mammary gland development and breast cancer
Bernardo, G. M. (2011) · OhioLink ETD Center (Ohio Library and Information Network)
Identifying FoxA1 interacting partners : insight into androgen regulated prostatic genes.
Sun, Q. (2010) · Europe PMC (PubMed Central)
FOXA1 is an independent prognostic marker for ER-positive breast cancer
Tudy, P. S. (2012)
A novel DNA sequence motif in human and mouse genomes
Zhang, S., Du, F., & Ji, H. (2015) · Scientific Reports · doi:10.1038/srep10444
Twenty-First Century Glucocorticoid Receptor Molecular Biology
Wang, C., Oldenkamp, R., Oellers, R., & Logie, C. (2018) · InTech eBooks · doi:10.5772/intechopen.72016
- Authors
- Eeckhoute, J., Lupien, M., Meyer, C. A., Verzi, M. P., Shivdasani, R. A., Liu, X. S., & Brown, M.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Brigham and Women's Hospital (US)
- Harvard University (US)
- ORCID
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2009-01-07
- Volume
- 19
- Issue
- 3
- Pages
- 372-380
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC2661808
- OpenAlex
- W2147789776
- Cited by
- 106
- References
- 63
- Citations by year
- 2026: 1 · 2023: 3 · 2022: 5 · 2021: 3 · 2020: 2 · 2019: 2 · 2018: 2 · 2017: 4 · 2016: 4 · 2015: 6 · 2014: 10 · 2013: 9 · 2012: 16
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- HAL (submittedVersion)
- Funders
- Dana-Farber Cancer Institute
- Dana-Farber/Harvard Cancer Center
- Centre National de la Recherche Scientifique
- National Human Genome Research Institute (R01HG004069)
- National Cancer Institute (P01CA8011105)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK074967)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- FOXA1, enhancers, chromatin remodeling, cell type specificity, FAIRE, chromatin accessibility, histone modifications, pioneer factors
- MeSH terms
- Binding Sites, Chromosome Mapping, Enhancer Elements, Genetic, Humans, Organ Specificity, Protein Binding, Tumor Cells, Cultured, Transcriptional Activation, Conserved Sequence, Cell Lineage, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, Chromatin Assembly and Disassembly, Hepatocyte Nuclear Factor 3-alpha
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