Quantitative methods to analyze subnuclear protein organization in cell populations with varying degrees of protein expression

Journal of Biomedical Optics

Volumn 10, Issue 2, 2005, Pages

  Voss, Ty C ^a   Demarco, Ignacio A ^a   Booker, Cynthia F ^a   Day, Richard N ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

Author keywords

Bioimaging; Fluorescence microscopy; Glucocorticoid receptor interacting protein; Green fluorescent protein; Nuclear coactivator; Nuclear structure

Indexed keywords

CORRELATION METHODS; DNA; FLUORESCENCE; GENES; IMAGE ANALYSIS; MEDICAL IMAGING; PROTEINS; STATISTICAL METHODS;

BIOIMAGING; FLUORESCENCE MICROSCOPY; GLUCOCORTICOID RECEPTOR INTERACTING PROTEIN; GREEN FLUORESCENT PROTEIN; NUCLEAR COACTIVATOR; NUCLEAR STRUCTURE;

CELLS;

DNA BINDING PROTEIN; FLUORESCENT DYE; GREEN FLUORESCENT PROTEIN; HYBRID PROTEIN; LUMINESCENT AGENT; NCOR2 PROTEIN, MOUSE; NUCLEAR PROTEIN; NUCLEAR RECEPTOR COACTIVATOR 2; PHOTOPROTEIN; REPRESSOR PROTEIN; SILENCING MEDIATOR OF RETINOID AND THYROID HORMONE RECEPTOR; TRANSCRIPTION FACTOR; NUCLEAR RECEPTOR CO REPRESSOR 2; NUCLEAR RECEPTOR CO-REPRESSOR 2;

ANIMAL; ARTICLE; CELL LINE; COMPARATIVE STUDY; FLUORESCENCE MICROSCOPY; GENETIC TRANSFECTION; GENETICS; IMAGE PROCESSING; INTRANUCLEAR SPACE; METABOLISM; METHODOLOGY; MOUSE; TISSUE DISTRIBUTION;

ANIMALS; CELL LINE; DNA-BINDING PROTEINS; FLUORESCENT DYES; GREEN FLUORESCENT PROTEINS; IMAGE PROCESSING, COMPUTER-ASSISTED; INTRANUCLEAR SPACE; LUMINESCENT AGENTS; LUMINESCENT PROTEINS; MICE; MICROSCOPY, FLUORESCENCE; NUCLEAR PROTEINS; NUCLEAR RECEPTOR CO-REPRESSOR 2; NUCLEAR RECEPTOR COACTIVATOR 2; RECOMBINANT FUSION PROTEINS; REPRESSOR PROTEINS; TISSUE DISTRIBUTION; TRANSCRIPTION FACTORS; TRANSFECTION;

EID: 13844279979     PISSN: 10833668     EISSN: 15602281     Source Type: Journal    
DOI: 10.1117/1.1891085     Document Type: Article

References (44)

1. P. D. Andrews, I. S. Harper, and J. R. Swedlow, "To 5D and beyond: quantitative fluorescence microscopy in the postgenomic era", Traffic 3, 29-36 (2002). (Pubitemid 34567265)
2. J. R. Swedlow, I. Goldberg, E. Brauner, and P. K. Sorger, "Informatics and quantitative analysis in biological imaging", Science 300, 100-102 (2003). (Pubitemid 36423035)
3. R. Eils and C. Athale, "Computational imaging in cell biology", J. Cell Biol. 161, 477-481 (2003). (Pubitemid 36578572)
4. D. L. Spector, "Nuclear domains", J. Cell. Sci. 114, 2891-2893 (2001). (Pubitemid 32821528)
5. M. Carmo-Fonseca, "The contribution of nuclear compartmentalization to gene regulation", Cell 108, 513-521 (2002). (Pubitemid 34260876)
6. A. I. Lamond and W. C. Earnshaw, "Structure and function in the nucleus", Science 280, 547-553 (1998). (Pubitemid 28227750)
7. T. Misteli, "The concept of self-organization in cellular architecture", J. Cell Biol. 155, 181-185 (2001). (Pubitemid 34289292)
8. F. Schaufele, C. Y. Chang, W. Liu, J. D. Baxter, S. K. Nordeen, Y. Wan, R. N. Day, and D. P. McDonnell, "Temporally distinct and ligand-specific recruitment of nuclear receptor-interacting peptides and cofactors to subnuclear domains containing the estrogen receptor", Mol. Endocrinol. 14, 2024-2039 (2000). (Pubitemid 32055534)
9. H. Tazawa, W. Osman, Y. Shoji, E. Treuter, J. A. Gustafsson, and J. Zilliacus, "Regulation of subnuclear localization is associated with a mechanism for nuclear receptor corepression by RIP140", Mol. Cell. Biol. 23, 4187-4198 (2003). (Pubitemid 36675334)
10. R. N. Day, S. K. Nordeen, and Y. Wan, "Visualizing protein-protein interactions in the nucleus of the living cell", Mol. Endocrinol. 13, 517-526 (1999). (Pubitemid 30636419)
11. C. T. Baumann, H. Ma, R. Wolford, J. C. Reyes, P. Maruvada, C. Lim, P. M. Yen, M. R. Stallcup, and G. L. Hager, "The glucocorticoid receptor interacting protein 1 (GRIP1) localizes in discrete nuclear foci that associate with ND10 bodies and are enriched in components of the 26S proteasome", Mol. Endocrinol. 15, 485-500 (2001). (Pubitemid 32324434)
12. M. Soderstrom, A. Vo, T. Heinzel, R. M. Lavinsky, W. M. Yang, E. Seto, D. A. Peterson, M. G. Rosenfeld, and C. K. Glass, "Differential effects of nuclear receptor corepressor (N-CoR) expression levels on retinoic acid receptor-mediated repression support the existence of dynamically regulated corepressor complexes", Mol. Endocrinol. 11, 682-692 (1997). (Pubitemid 27225296)
13. M. Downes, P. Ordentlich, H. Y. Kao, J. G. Alvarez, and R. M. Evans, "Identification of a nuclear domain with deacetylase activity", Proc. Natl. Acad. Sci. U. S. A. 97, 10330-10335 (2000).
14. F. Schaufele, J. F. Enwright, X. Wang, C. Teoh, R. Srihari, R. Erickson, O. A. MacDougald, and R. N. Day, "CCAAT/enhancer binding protein alpha assembles essential cooperating factors in common subnuclear domains", Mol. Endocrinol. 15, 1665-1676 (2001). (Pubitemid 32939298)
15. T. C. Voss, I. A. Demarco, C. F. Booker, and R. N. Day, "A computer-assisted image analysis protocol that quantitatively measures subnuclear protein organization in cell populations", BioTechniques 36, 240-247 (2004). (Pubitemid 38174731)
16. A. Belmont, "Dynamics of chromatin, proteins, and bodies within the cell nucleus", Curr. Opin. Cell Biol. 15, 304-310 (2003). (Pubitemid 36638648)
17. H. Hong, K. Kohli, A. Trivedi, D. L. Johnson, and M. R. Stallcup, "GRIP1, a novel mouse protein that serves as a transcriptional coactivator in yeast for the hormone binding domains of steroid receptors", Proc. Natl. Acad. Sci. U. SA. 93, 4948-4952 (1996). (Pubitemid 26163504)
18. J. D. Chen and R. M. Evans, "A transcriptional co-repressor that interacts with nuclear hormone receptors [see comments]", Nature (London) 377, 454-457 (1995).
19. R. E. Campbell, O. Tour, A. E. Palmer, P. A. Steinbach, G. S. Baird, D. A. Zacharias, and R. Y. Tsien, "A monomeric red fluorescent protein", Proc. Natl. Acad. Sci. U. S. A. 99, 7877-7882 (2002). (Pubitemid 34650973)
20. G. R. MacGregor and C. T. Caskey, "Construction of plasmids that express E. coli beta-galactosidase in mammalian cells", Nucleic Acids Res. 17, 2365 (1989). (Pubitemid 19094025)
21. R. N. Day, A. Periasamy, and F. Schaufele, "Fluorescence resonance energy transfer microscopy of localized protein interactions in the living cell nucleus", Methods 25, 4-18 (2001). (Pubitemid 32905284)
22. R. N. Day, "Visualization of Pit-1 transcription factor interactions in the living cell nucleus by fluorescence resonance energy transfer microscopy", Mol. Endocrinol. 12, 1410-1419 (1998). (Pubitemid 128496201)
23. R. Y. Tsien, "The green fluorescent protein", Annu. Rev. Biochem. 67, 509-544 (1998). (Pubitemid 28411137)
24. P. Van Roessel and A. H. Brand, "Imaging into the future: visualizing gene expression and protein interactions with fluorescent proteins", Nat. Cell Biol. 4, E15-20 (2002). (Pubitemid 34071973)
25. A. K. Hadjantonakis and A. Nagy, "The color of mice: in the light of GFP-variant reporters", Histochem. Cell Biol. 115, 49-58 (2001). (Pubitemid 32202053)
26. G. Feng, R. H. Mellor, M. Bernstein, C. Keller-Peck, Q. T. Nguyen, M. Wallace, J. M. Nerbonne, J. W. Lichtman, and J. R. Sanes, "Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP", Neuron 28, 41-51 (2000).
27. M. K. Walsh and J. W. Lichtman, "In vivo time-lapse imaging of synaptic takeover associated with naturally occurring synapse elimination", Neuron 37, 67-73 (2003). (Pubitemid 36106434)
28. M. Dundr, J. G. McNally, J. Cohen, and T. Misteli, "Quantitation of GFP-fusion proteins in single living cells", J. Struct. Biol. 140, 92-99 (2002). (Pubitemid 36139850)
29. C. S. Chiu, E. Kartalov, M. Unger, S. Quake, and H. A. Lester, "Single-molecule measurements calibrate green fluorescent protein surface densities on transparent beads for use with 'knock-in' animals and other expression systems", J. Neurosci. Methods 105, 55-63 (2001). (Pubitemid 32109225)
30. C. M. Pickart and R. E. Cohen, "Proteasomes and their kin: proteases in the machine age", Nat. Rev. Mol. Cell Biol. 5, 177-187 (2004). (Pubitemid 38325799)
31. A. I. Lamond and D. L. Spector, "Nuclear speckles: a model for nuclear organelles", Nat. Rev. Mol. Cell Biol. 4, 605-612 (2003). (Pubitemid 36934962)
32. J. T. Elliott, A. Tona, and A. L. Plant, "Comparison of reagents for shape analysis of fixed cells by automated fluorescence microscopy", Cytometry 52 A, 90-100 (2003). (Pubitemid 37521507)
33. D. Webb, M. A. Hamilton, G. J. Harkin, S. Lawrence, A. K. Camper, and Z. Lewandowski, "Assessing technician effects when extracting quantities from microscope images", J. Microbiol. Methods 53, 97-106 (2003). (Pubitemid 36255531)
34. B. E. Black, M. J. Vitto, D. Gioeli, A. Spencer, N. Afshar, M. R. Conaway, M. J. Weber, and B. M. Paschal, "Transient, liganddependent arrest of the androgen receptor in subnuclear foci alters phosphorylation and coactivator interactions", Mol. Endocrinol. 18, 834-850 (2004). (Pubitemid 38429476)
35. D. L. Stenoien, M. G. Mancini, K. Patel, E. A. Allegretto, C. L. Smith, and M. A. Mancini, "Subnuclear trafficking of estrogen receptor-alpha and steroid receptor coactivator-1", Mol. Endocrinol. 14, 518-534 (2000). (Pubitemid 32260520)
36. O. J. Rivera, C. S. Song, V. E. Centonze, J. D. Lechleiter, B. Chatterjee, and A. K. Roy, "Role of the promyelocytic leukemia body in the dynamic interaction between the androgen receptor and steroid receptor coactivator-1 in living cells", Mol. Endocrinol. 17, 128-140 (2003). (Pubitemid 36132664)
37. V. Perissi, A. Aggarwal, C. K. Glass, D. W. Rose, and M. G. Rosenfeld, "A corepressor/coactivator exchange complex required for transcriptional activation by nuclear receptors and other regulated transcription factors", Cell 116, 511-526 (2004). (Pubitemid 38264429)
38. J. P. Taylor, F. Tanaka, J. Robitschek, C. M. Sandoval, A. Taye, S. Markovic-Plese, and K. H. Fischbeck, "Aggresomes protect cells by enhancing the degradation of toxic polyglutamine-containing protein", Hum. Mol. Genet. 12, 749-757 (2003). (Pubitemid 36416961)
39. V. Tarlac and E. Storey, "Role of proteolysis in polyglutamine disorders", J. Neurosci. Res. 74, 406-416 (2003). (Pubitemid 37362817)
40. T. C. Voss, I. A. De Mareo, C. F. Booker, R. N. Day, "Corepressor subnuclear organization is regulated by estrogen receptor via a mechanism that requires the DNA-binding domain", Mol. Cell. Endocrinol., 231(1-2), 33-47 (2005). (Pubitemid 40248815)
41. J. E. Sleeman, P. Ajuh, and A. I. Lamond, "snRNP protein expression enhances the formation of Cajal bodies containing p80-coilin and SMN", J. Cell. Sci. 114, 4407-4419 (2001). (Pubitemid 34082861)
42. A. G. Matera, "Nuclear bodies: multifaceted subdomains of the interchromatin space", Trends Cell Biol. 9, 302-309 (1999).
43. S. Khochbin and H. Y. Kao, "Histone deacetylase complexes: functional entities or molecular reservoirs", FEBS Lett. 494, 141-144 (2001). (Pubitemid 32322671)
44. M. D. Hebert and A. G. Matera, "Self-association of coilin reveals a common theme in nuclear body localization", Mol. Biol. Cell 11, 4159-4171 (2000).