Analysis of chromatin dynamics during glucocorticoid receptor activation

Molecular and Cellular Biology

Volumn 32, Issue 10, 2012, Pages 1805-1817

  Burd, Craig J ^a   Ward, James M ^a   Crusselle Davis, Valerie J ^a   Kissling, Grace E ^a   Phadke, Dhiral ^b   Shah, Ruchir R ^b   Archer, Trevor K ^a  

^a NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^b SRA International   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; BRG1 PROTEIN; GLUCOCORTICOID RECEPTOR; LIGAND;

ARTICLE; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN STRUCTURE; FORMALDEHYDE ASSISTED ISOLATED OF REGULATORY ELEMENT; MOLECULAR DYNAMICS; PRIORITY JOURNAL; REGULATORY SEQUENCE; SEQUENCE DATABASE;

BINDING SITES; CELL LINE, TUMOR; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; FORMALDEHYDE; HUMANS; LIGANDS; PROTEIN BINDING; RECEPTORS, GLUCOCORTICOID; RESPONSE ELEMENTS;

EID: 84861371572     PISSN: 02707306     EISSN: 10985549     Source Type: Journal    
DOI: 10.1128/MCB.06206-11     Document Type: Article

References (46)

1. Acevedo ML, Kraus WL. 2004. Transcriptional activation by nuclear receptors. Essays Biochem. 40:73-88.
2. Archer TK, Lefebvre P, Wolford RG, Hager GL. 1992. Transcription factor loading on the MMTV promoter: a bimodal mechanism for promoter activation. Science 255:1573-1576.
3. Archer TK, Zaniewski E, Moyer ML, Nordeen SK. 1994. The differential capacity of glucocorticoids and progestins to alter chromatin structure and induce gene expression in human breast cancer cells. Mol. Endocrinol. 8:1154-1162.
4. Belikov S, Astrand C, Wrange O. 2009. FoxA1 binding directs chromatin structure and the functional response of a glucocorticoid receptorregulated promoter. Mol. Cell. Biol. 29:5413-5425.
5. Burch JB, Weintraub H. 1983. Temporal order of chromatin structural changes associated with activation of the major chicken vitellogenin gene. Cell 33:65-76.
6. Burd CJ, Kinyamu HK, Miller FW, Archer TK. 2008. UV radiation regulates Mi-2 through protein translation and stability. J. Biol. Chem. 283:34976-34982.
7. Carey MF, Peterson CL, Smale ST. 2009. Chromatin immunoprecipitation (ChIP). Cold Spring Harb. Protoc. 2009:pdb.prot5279.
8. Cirillo LA, et al. 2002. Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. Mol. Cell 9:279-289.
9. Dechassa ML, et al. 2010. SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes. Mol. Cell 38:590-602.
10. Dilworth FJ, Chambon P. 2001. Nuclear receptors coordinate the activities of chromatin remodeling complexes and coactivators to facilitate initiation of transcription. Oncogene 20:3047-3054.
11. Eeckhoute J, et al. 2009. Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers. Genome Res. 19:372-380.
12. Evans RM. 2005. The nuclear receptor superfamily: a Rosetta stone for physiology. Mol. Endocrinol. 19:1429-1438.
13. Fryer CJ, Archer TK. 1998. Chromatin remodelling by the glucocorticoid receptor requires the BRG1 complex. Nature 393:88-91.
14. Gevry N, et al. 2009. Histone H2A. Z is essential for estrogen receptor signaling. Genes Dev. 23:1522-1533.
15. Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. 2007. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 17:877-885.
16. Giresi PG, Lieb JD. 2009. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods 48:233-239.
17. Hager GL, et al. 1993. Influence of chromatin structure on the binding of transcription factors to DNA. Cold Spring Harb Symp. Quant Biol. 58:63-71.
18. Hebbar PB, Archer TK. 2007. Chromatin-dependent cooperativity between site-specific transcription factors in vivo. J. Biol. Chem. 282:8284-8291.
19. Heinz S, et al. 2010. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38:576-589.
20. John S, et al. 2008. Interaction of the glucocorticoid receptor with the chromatin landscape. Mol. Cell 29:611-624.
21. John S, et al. 2011. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat. Genet. 43:264-268.
22. Kininis M, Kraus WL. 2008. A global view of transcriptional regulation by nuclear receptors: gene expression, factor localization, and DNA sequence analysis. Nucl. Recept. Signal. 6:e005.
23. Lander ES, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
24. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25.
25. Lee HL, Archer TK. 1994. Nucleosome-mediated disruption of transcription factor-chromatin initiation complexes at the mouse mammary tumor virus long terminal repeat in vivo. Mol. Cell. Biol. 14:32-41.
26. Lee KC, Lee Kraus W. 2001. Nuclear receptors, coactivators and chromatin: new approaches, new insights. Trends Endocrinol. Metab. 12:191-197.
27. McDonnell DP, Wardell SE. 2010. The molecular mechanisms underlying the pharmacological actions of ER modulators: implications for new drug discovery in breast cancer. Curr. Opin. Pharmacol. 10:620-628.
28. Muchardt C, Yaniv M. 1993. A human homologue of Saccharomyces cerevisiae SNF2/SWI2 and Drosophila brm genes potentiates transcriptional activation by the glucocorticoid receptor. EMBO J. 12:4279-4290.
29. Owen-Hughes T, Utley RT, Cote J, Peterson CL, Workman JL. 1996. Persistent site-specific remodeling of a nucleosome array by transient action of the SWI/SNF complex. Science 273:513-516.
30. Peterson CL, Tamkun JW. 1995. The SWI-SNF complex: a chromatin remodeling machine? Trends Biochem. Sci. 20:143-146.
31. R Development Core Team. 2011. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
32. Reddy TE, et al. 2009. Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. Genome Res. 19:2163-2171.
33. Reik A, Schutz G, Stewart AF. 1991. Glucocorticoids are required for establishment and maintenance of an alteration in chromatin structure: induction leads to a reversible disruption of nucleosomes over an enhancer. EMBO J. 10:2569-2576.
34. Sharp ZD, et al. 2006. Estrogen-receptor-alpha exchange and chromatin dynamics are ligand- and domain-dependent. J. Cell Sci. 119:4101-4116.
35. Stafford JM, Wilkinson JC, Beechem JM, Granner DK. 2001. Accessory factors facilitate the binding of glucocorticoid receptor to the phosphoenolpyruvate carboxykinase gene promoter. J. Biol. Chem. 276:39885-39891.
36. Trotter KW, Archer TK. 2008. The BRG1 transcriptional coregulator. Nucl. Recept Signal. 6:e004.
37. Trotter KW, Archer TK. 2004. Reconstitution of glucocorticoid receptordependent transcription in vivo. Mol. Cell. Biol. 24:3347-3358.
38. Trotter KW, Fan HY, Ivey ML, Kingston RE, Archer TK. 2008. The HSA domain of BRG1 mediates critical interactions required for glucocorticoid receptor-dependent transcriptional activation in vivo. Mol. Cell. Biol. 28: 1413-1426.
39. Truss M, Bartsch J, Mows C, Chavez S, Beato M. 1996. Chromatin structure of the MMTV promoter and its changes during hormonal induction. Cell. Mol. Neurobiol. 16:85-101.
40. Tsai CC, Fondell JD. 2004. Nuclear receptor recruitment of histonemodifying enzymes to target gene promoters. Vitam. Horm. 68:93-122.
41. Voss TC, et al. 2011. Dynamic exchange at regulatory elements during chromatin remodeling underlies assisted loading mechanism. Cell 146: 544-554.
42. Wolf IM, Heitzer MD, Grubisha M, DeFranco DB. 2008. Coactivators and nuclear receptor transactivation. J. Cell Biochem. 104:1580-1586.
43. Xi H, et al. 2007. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet. 3:e136.
44. Yoshinaga SK, Peterson CL, Herskowitz I, Yamamoto KR. 1992. Roles of SWI1, SWI2, and SWI3 proteins for transcriptional enhancement by steroid receptors. Science 258:1598-1604.
45. Zaret KS, Yamamoto KR. 1984. Reversible and persistent changes in chromatin structure accompany activation of a glucocorticoid-dependent enhancer element. Cell 38:29-38.
46. Zhou VW, Goren A, Bernstein BE. 2011. Charting histone modifications and the functional organization of mammalian genomes. Nat. Rev. Genet. 12:7-18.