Selected Publications

Chromatin & Gene Expression Group

1. Kinyamu HK, Collins JB, Grissom SF, Hebbar PB, Archer TK, . Genome wide transcriptional profiling in breast cancer cells reveals distinct changes in hormone receptor target genes and chromatin modifying enzymes after proteasome inhibition. Molecular carcinogenesis 2008 47(11):845-885. [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18381591)
2. Wang Y, Yabuuchi A, McKinney-Freeman S, Ducharme DMK, Ray M, Chawengsaksophak K, Archer TK, Daley GQ. The intrinsic requirement of Cdx-Hox pathway during embryonic hematopoiesis in mouse. Proceedings of the National Academy of Sciences of the United States of America 2008 105(22):7756-7761. [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18511567)
3. Aoyagi S, Archer TK. Dynamics of coactivator recruitment and chromatin modifications during nuclear receptor mediated transcription. Molecular and cellular endocrinology 2008 280(1-2):1-5. [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17935877)
4. Hebbar PB, Archer TK. Altered histone H1 stoichiometry and an absence of nucleosome positioning on transfected DNA. The Journal of biological chemistry 2008 283(8):4595-4601. [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18156629)
5. Trotter KW, Archer TK. The BRG1 transcriptional coregulator. Nuclear receptor signaling 2008 6():E004. [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18301784)
6. Trotter KT, Fan H, Ivey ML, Kingston RE, Archer TK. The HSA domain of BRG1 mediates critical interactions required for glucocorticoid receptor-dependent transcriptional activation in vivo. Molecular and cellular biology 2008 28(4):1413-1426. [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18086889)
7. Jefferson WN, Archer TK. Intersection of nuclear receptors and the proteasome on the epigenetic landscape. Environmental and molecular mutagenesis 2008 49(1):83-95. [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18095329)
8. Aoyagi S, Archer TK. Nicotinamide uncouples hormone-dependent chromatin remodeling from transcription complex assembly. Molecular and cellular biology 2008 28(1):30-39. [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17954562)
9. Burkhart BA, Kennett SB, Archer TK. Osmotic stress-dependent repression is mediated by histone H3 phosphorylation and chromatin structure. The Journal of biological chemistry 2007 282(7):4400-4407. [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17158874)
10. Trotter KW, Archer TK. Nuclear receptors and chromatin remodeling machinery. Molecular and cellular endocrinology 2007 265-266:162-7. [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17240047)
11. Hebbar PB, Archer TK. Chromatin-dependent cooperativity between site-specific transcription factors in vivo. The Journal of biological chemistry 2007 282(11):8284-8291. [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17186943)
12. Aoyagi S, Archer TK. Dynamic histone acetylation/deacetylation with progesterone receptor-mediated transcription. Molecular endocrinology (Baltimore, Md.) 2007 21(4):843-856. [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17227884)
13. Kinyamu HK, Archer TK. Proteasome activity modulates chromatin modifications and RNA polymerase II phosphorylation to enhance glucocorticoid receptor mediated transcription. Mol Cell Biol. 2007 Apr 16; PMID: 17438138.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=pubmed_DocSum&db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=17438138)
14. Trotter KW, Archer TK. Nuclear receptors and chromatin remodeling machinery. Mol Cell Endocrinol. 2007 Feb;265-266:162-7. Epub 2007 Jan 19. PMID: 17240047.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=pubmed_DocSum&db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=17240047)
15. Aoyagi S, Archer TK. Dynamic histone acetylation/deacetylation with progesterone receptor-mediated transcription. Mol Endocrinol. 2007 Apr;21(4):843-56. Epub 2007 Jan 16. PMID: 17227884.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=pubmed_DocSum&db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=17227884)
16. Hebbar PB, Archer TK. Chromatin-dependent cooperativity between site-specific transcription factors in vivo. J Biol Chem. 2007 Mar 16;282(11):8284-91. Epub 2006 Dec 23. PMID: 17186943.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=pubmed_DocSum&db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=17186943)
17. Burkhart BA, Kennett SB, Archer TK. Osmotic stress-dependent repression is mediated by histone H3 phosphorylation and chromatin structure. J Biol Chem. 2007 Feb 16;282(7):4400-7. Epub 2006 Dec 11. PMID: 17158874.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=pubmed_DocSum&db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=17158874)
18. Wade PA, Archer TK. Epigenetics: environmental instructions for the genome. Environ Health Perspect. 2006 Mar;114(3):A140-1. PMID: 16507439.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=pubmed_DocSum&db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=16507439)
19. Bhattacharjee RN, Archer TK. Transcriptional silencing of the mouse mammary tumor virus promoter through chromatin remodeling is concomitant with histone H1 phosphorylation and histone H3 hyperphosphorylation at M phase. Virology. 2006 Mar 1;346(1):1-6. Epub 2006 Feb 3. PMID: 16458342.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?itool=pubmed_DocSum&db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=16458342)
20. Chen J, Kinyamu HK, Archer TK. Changes in Attitude, Changes in Latitude: Nuclear Receptors Remodeling Chromatin to Regulate Transcription. Mol. Endocrinol. 20: 1-13, 2006.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16002433&query_hl=2)
21. Kinyamu HK, Chen J, Archer TK. Linking the ubiquitin-proteasome pathway to chromatin remodeling/modification by nuclear receptors. J. Mol. Endocrinol. 34: 281-97, 2005.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15821097&query_hl=4)
22. Fan HY, Trotter KW, Archer TK, Kingston RE. Swapping function of two chromatin remodeling complexes. Mol. Cell 17: 805-15, 2005.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15780937&query_hl=6)
23. Aoyagi S, Trotter KW, Archer TK. ATP-dependent chromatin remodeling complexes and their role in nuclear receptor-dependent transcription in vivo. Vitam. Horm. 70: 281-307, 2005.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15727808&query_hl=8)
24. Burkhart BA, Hebbar PB, Trotter KW, Archer TK. Chromatin-dependent E1A activity modulates NF-kappaB RelA-mediated repression of glucocorticoid receptor-dependent transcription. J. Biol. Chem. 280: 6349-58, 2005.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15556937&query_hl=10)
25. Chen J, Archer TK. Regulating SWI/SNF subunit levels via protein-protein interactions and proteasomal degradation: BAF155 and BAF170 limit expression of BAF57. Mol. Cell. Biol. 25: 9016-27, 2005.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16199878)
26. Aoyagi S, Archer TK. Modulating molecular chaperone Hsp90 functions through reversible acetylation. Trends Cell. Biol. 15: 565-7, 2005.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16199163)
27. Butcher DT, Mancini-DiNardo DN, Archer TK, Rodenhiser DI. DNA binding sites for putative methylation boundaries in the unmethylated region of the BRCA1 promoter. Int. J. Cancer 111:669-78, 2004.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15252835&query_hl=2&itool=pubmed_docsum)
28. Trotter KW, Archer TK. Reconstitution of glucocorticoid receptor-dependent transcription in vivo. Mol. Cell Biol. 24: 3347-58, 2004.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15060156&query_hl=24)
29. Deterding LJ, Banks GC, Tomer KB, Archer TK. Understanding global changes in histone H1 phosphorylation using mass spectrometry. Methods 33: 53-8, 2004.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15039087&query_hl=22)
30. Kinyamu HK, Archer TK. Modifying chromatin to permit steroid hormone receptor-dependent transcription. Biochim. Biophys. Acta. 1677: 30-45, 2004.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15020043&query_hl=20)
31. Hsiao PW, Fryer CJ, Trotter KW, Wang W, Archer TK.: BAF60a mediates critical interactions between nuclear receptors and the BRG1 chromatin-remodeling complex for transactivation. Mol. Cell Biol. 23: 6210-20, 2003.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12917342&query_hl=18)
32. Kinyamu HK, Archer TK. Estrogen receptor-dependent proteasomal degradation of the glucocorticoid receptor is coupled to an increase in mdm2 protein expression. Mol. Cell Biol. 23: 5867-81, 2003.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12897156&query_hl=16)
33. Hebbar PB, Archer TK. Chromatin remodeling by nuclear receptors. Chromosoma 111: 495-504, 2003.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12743713&query_hl=14)
34. Hebbar PB, Archer TK. Nuclear factor 1 is required for both hormone-dependent chromatin remodeling and transcriptional activation of the mouse mammary tumor virus promoter. Mol. Cell. Biol. 23: 887-98, 2003.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12529394&query_hl=72)
35. Wilson MA, Deroo BJ, Ricci AR, Archer TK. The histone deacetylase inhibitor TSA blocks progesterone receptor-mediated transactivation of the MMTV promoter in vivo. J Biol. Chem. 277: 15171-81, 2002.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11821430&query_hl=66)
36. Deroo, B.J. and Archer, T.K.: Proteasome inhibitors reduce luciferase and Beta-galactosidase activity in tissue culture cells. J Biol. Chem. 277: 20120-20123, 2002.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11959849&query_hl=68)
37. Deroo, B.J., Rentsch, C., Sampath, S., Young, J., DeFranco, D.B. and Archer T.K.: Proteasomal inhibition enhances glucocorticoid receptor transactivation and alters its sub-nuclear trafficking. Mol Cell Biol. 22: 4113-4123, 2002.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12024025&query_hl=70)
38. Xing, W. and Archer, T.K.: Upstream stimulatory factors mediate estrogen receptor activity of the cathepsin promoter. Mol. Endo. 12:1310-1321, 1998.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9731700&query_hl=8)
39. Hsiao, P-W., Deroo, B.J. and Archer, T.K.: Chromatin remodeling and tissue-selective responses of nuclear hormone receptors. Biochem. Cell Biol. 80: 343-351, 2002.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12123287&query_hl=2)
40. Deroo BJ, Archer TK. Differential activation of the IkBa and mouse mammary tumor virus promoters by progesterone and glucocorticoid receptors. J. Steroid Biochem. Mol. Biol. 81: 309-17, 2002.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12361720&query_hl=75)
41. Fryer CJ, Archer TK. Analyzing the contributions of chromatin structure in nuclear hormone receptor activated transcription in vivo. Methods In Molecular Biology: Steroid Receptor Methods (Lieberman B, Ed.) 176: 283-96, 2001.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11554329&query_hl=10)
42. Deroo, B.J. and Archer, T.K.: Glucocorticoid receptor-mediated chromatin remodeling in vivo. Oncogene 20:3039-3046, 2001.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11420719&query_hl=14)
43. Bhattacharjee, R,N., Banks, G.C., Trotter, K.W., Lee, H-L and Archer, T.K.: Histone H1 phosphorylation by Cdk2 selectively modulates MMTV transcription through chromatin remodeling. Mol. Cell. Biol. 21: 5417-25, 2001.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11463824&query_hl=44)
44. DiNardo DN, Butcher DT, Robinson DP, Archer TK, Rodenhiser DI. Functional analysis of CpG methylation in the BRCA1 promoter region. Oncogene 20: 5331-40, 2001.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11536045&query_hl=48)
45. Fryer, C.J. and Archer, T.K.: Analyzing the Contributions of Chromatin Structure in Nuclear Hormone Receptor Activated Transcription in Vivo. Methods In Molecular Biology: Steroid Receptor Methods (Lieberman B, Ed.) 176: 283-296, 2001.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11554329&query_hl=10)
46. Deroo BJ, Archer TK. Glucocorticoid receptor activation of the IkBa promoter within chromatin. Mol. Biol. Cell 12: 3365-74, 2001.
47. Fryer CJ, Kinyamu HK, Rogatsky I, Garabedian MJ, Archer TK. Selective activation of the glucocorticoid receptor by steroid antagonists in human breast cancer and osteosarcoma cells. J. Biol. Chem. 275: 17771-7, 2000.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10751396&query_hl=24)
48. Kinyamu HK, Fryer CJ, Horwitz KB, Archer TK. The MMTV promoter adopts distinct chromatin structures in human breast cancer cells with and without glucocorticoid receptor. J. Biol. Chem. 275: 20061-8, 2000.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10751396&query_hl=24)
49. Nie Z, Xue Y, Yang D, Zhou S, Deroo BJ, Archer TK, Weidong W. A specificity and targeting subunit of a human SWI/SNF-related chromatin-remodelling complex. Mol. Cell. Biol. 20: 8879-88, 2000.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11073988&query_hl=12)
50. Mancini DN, Singh SM, Archer TK, Rodenhiser D. Site-specific DNA methylation in the neurofibromatosis (NF1) promoter interferes with binding of CREB and SP1 transcription factors. Oncogene 18: 4108-19, 1999.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10435592&query_hl=11)
51. Archer TK, Ricci AR. Exonuclease III as a probe of chromatin structure in vivo. Methods Enzymol. 304:584-99, 1999.
52. Darnel AD, Archer TK, Yang K. Regulation of 11-beta-hydroxysteroid dehydrogenase type 2 by steroid hormones and epidermal growth factor in the Ishikawa human endometrial cell line. J. Steroid Biochem. Mol Biol. 70:203-10, 1999.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10622409&query_hl=20)
53. Fryer CJ, Nordeen SK, Archer TK. Antiprogestins mediate differential effects on glucocorticoid receptor remodeling of chromatin structure. J. Biol. Chem. 273:1175-83, 1998.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9422784&query_hl=31)
54. Watson CE, Archer TK. Chromatin and steroid-receptor-mediated transcription. in: Molecular Biology of Steroid and Nuclear Hormone Receptors. (Freedman, L.P. ed), Ch. 8, Pg. 209-35, Birkhser, Boston, 1998.
55. Lee H-L, Archer TK. Prolonged glucocorticoid exposure dephosphorylates histone H1 and inactivates the MMTV promoter. EMBO J. 17:1454-66, 1998.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9482742&query_hl=1)
56. Mancini DN, Rodenhiser DI, Ainsworth PJ, O'Malley FP, Singh SM, Xing W, Archer TK. CpG methylation within the 5' regulatory region of the BRCA1 gene is tumor specific and includes a putative CREB binding site. Oncogene 16:1161-69, 1998.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9528858&query_hl=3)
57. Fryer CJ, Archer TK. Chromatin remodelling of the glucocorticoid receptor requires the BRG1 complex. Nature 393:81-91, 1998.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9590696&query_hl=5)
58. Xing W, Archer TK. Upstream stimulatory factors mediate estrogen receptor activity of the cathepsin promoter. Mol. Endocrinol. 12:1310-21, 1998.  [Abstract] (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9731700&query_hl=8)

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