Abstract

Fluorescence Recovery After Photobleaching (FRAP) is an established method for validating chemical probes against the chromatin reading bromodomains, but so far requires constant human supervision. Here, we present Frapid, an automated open source code implementation of FRAP that fully handles cell identification through fuzzy logic analysis, drug dispensing with a custom-built fluid handler, image acquisition & analysis, and reporting. We successfully tested Frapid on 3 bromodomains as well as on spindlin1 (SPIN1), a methyl lysine binder, for the first time.

© 2016 Optical Society of America

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    [Crossref] [PubMed]
  23. R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
    [Crossref] [PubMed]
  24. O. Dushek, R. Das, and D. Coombs, “Analysis of membrane-localized binding kinetics with FRAP,” Eur. Biophys. J. 37(5), 627–638 (2008).
    [Crossref] [PubMed]
  25. N. W. Goehring, D. Chowdhury, A. A. Hyman, and S. W. Grill, “FRAP Analysis of Membrane-Associated Proteins: Lateral Diffusion and Membrane-Cytoplasmic Exchange,” Biophys. J. 99(8), 2443–2452 (2010).
    [Crossref] [PubMed]
  26. J. S. Goodwin and A. K. Kenworthy, “Photobleaching approaches to investigate diffusional mobility and trafficking of Ras in living cells,” Methods 37(2), 154–164 (2005).
    [Crossref] [PubMed]
  27. M. Kuzma-Kuzniarska, C. Yapp, T. W. Pearson-Jones, A. K. Jones, and P. A. Hulley, “Functional assessment of gap junctions in monolayer and three-dimensional cultures of human tendon cells using fluorescence recovery after photobleaching,” J. Biomed. Opt. 19(1), 015001 (2014).
    [Crossref] [PubMed]
  28. F. Gong, L.-Y. Chiu, B. Cox, F. Aymard, T. Clouaire, J. W. Leung, M. Cammarata, M. Perez, P. Agarwal, J. S. Brodbelt, G. Legube, and K. M. Miller, “Screen identifies bromodomain protein ZMYND8 in chromatin recognition of transcription-associated DNA damage that promotes homologous recombination,” Genes Dev. 29(2), 197–211 (2015).
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  29. L. C. Young, D. W. McDonald, and M. J. Hendzel, “Kdm4b Histone Demethylase Is a DNA Damage Response Protein and Confers a Survival Advantage following γ-Irradiation,” J. Biol. Chem. 288(29), 21376–21388 (2013).
    [Crossref] [PubMed]
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    [Crossref] [PubMed]

2015 (3)

H. Georg Breunig, A. Uchugonova, A. Batista, and K. König, “Software-aided automatic laser optoporation and transfection of cells,” Sci. Rep. 5, 11185 (2015).
[Crossref] [PubMed]

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
[Crossref] [PubMed]

F. Gong, L.-Y. Chiu, B. Cox, F. Aymard, T. Clouaire, J. W. Leung, M. Cammarata, M. Perez, P. Agarwal, J. S. Brodbelt, G. Legube, and K. M. Miller, “Screen identifies bromodomain protein ZMYND8 in chromatin recognition of transcription-associated DNA damage that promotes homologous recombination,” Genes Dev. 29(2), 197–211 (2015).
[Crossref] [PubMed]

2014 (3)

M. Kuzma-Kuzniarska, C. Yapp, T. W. Pearson-Jones, A. K. Jones, and P. A. Hulley, “Functional assessment of gap junctions in monolayer and three-dimensional cultures of human tendon cells using fluorescence recovery after photobleaching,” J. Biomed. Opt. 19(1), 015001 (2014).
[Crossref] [PubMed]

M. Philpott, C. M. Rogers, C. Yapp, C. Wells, J.-P. Lambert, C. Strain-Damerell, N. A. Burgess-Brown, A.-C. Gingras, S. Knapp, and S. Müller, “Assessing cellular efficacy of bromodomain inhibitors using fluorescence recovery after photobleaching,” Epigenetics Chromatin 7(1), 14 (2014).
[Crossref] [PubMed]

D. Gallenkamp, K. A. Gelato, B. Haendler, and H. Weinmann, “Bromodomains and their pharmacological inhibitors,” ChemMedChem 9(3), 438–464 (2014).
[Crossref] [PubMed]

2013 (4)

S. Picaud, D. Da Costa, A. Thanasopoulou, P. Filippakopoulos, P. V. Fish, M. Philpott, O. Fedorov, P. Brennan, M. E. Bunnage, D. R. Owen, J. E. Bradner, P. Taniere, B. O’Sullivan, S. Müller, J. Schwaller, T. Stankovic, and S. Knapp, “PFI-1, a highly selective protein interaction inhibitor, targeting BET Bromodomains,” Cancer Res. 73(11), 3336–3346 (2013).
[Crossref] [PubMed]

L. C. Young, D. W. McDonald, and M. J. Hendzel, “Kdm4b Histone Demethylase Is a DNA Damage Response Protein and Confers a Survival Advantage following γ-Irradiation,” J. Biol. Chem. 288(29), 21376–21388 (2013).
[Crossref] [PubMed]

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
[Crossref] [PubMed]

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
[Crossref] [PubMed]

2012 (1)

S. Müller and P. J. Brown, “Epigenetic chemical probes,” Clin. Pharmacol. Ther. 92(6), 689–693 (2012).
[Crossref] [PubMed]

2011 (2)

S. Muller, P. Filippakopoulos, and S. Knapp, “Bromodomains as therapeutic targets,” Expert Rev. Mol. Med. 13, e29 (2011).
[Crossref] [PubMed]

C. Conrad, A. Wünsche, T. H. Tan, J. Bulkescher, F. Sieckmann, F. Verissimo, A. Edelstein, T. Walter, U. Liebel, R. Pepperkok, and J. Ellenberg, “Micropilot: automation of fluorescence microscopy-based imaging for systems biology,” Nat. Methods 8(3), 246–249 (2011).
[Crossref] [PubMed]

2010 (4)

D. J. Cappelleri, A. Halasz, J. Y. Sul, T. K. Kim, J. Eberwine, and V. Kumar, “Towards A Fully Automated High-Throughput Phototransfection System,” JALA Charlottesv Va 15(4), 329–341 (2010).
[Crossref] [PubMed]

E. Nicodeme, K. L. Jeffrey, U. Schaefer, S. Beinke, S. Dewell, C. W. Chung, R. Chandwani, I. Marazzi, P. Wilson, H. Coste, J. White, J. Kirilovsky, C. M. Rice, J. M. Lora, R. K. Prinjha, K. Lee, and A. Tarakhovsky, “Suppression of inflammation by a synthetic histone mimic,” Nature 468(7327), 1119–1123 (2010).
[Crossref] [PubMed]

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
[Crossref] [PubMed]

N. W. Goehring, D. Chowdhury, A. A. Hyman, and S. W. Grill, “FRAP Analysis of Membrane-Associated Proteins: Lateral Diffusion and Membrane-Cytoplasmic Exchange,” Biophys. J. 99(8), 2443–2452 (2010).
[Crossref] [PubMed]

2008 (2)

O. Dushek, R. Das, and D. Coombs, “Analysis of membrane-localized binding kinetics with FRAP,” Eur. Biophys. J. 37(5), 627–638 (2008).
[Crossref] [PubMed]

J. B. Warner, A. A. Philippakis, S. A. Jaeger, F. S. He, J. Lin, and M. L. Bulyk, “Systematic identification of mammalian regulatory motifs’ target genes and functions,” Nat. Methods 5(4), 347–353 (2008).
[PubMed]

2006 (1)

2005 (1)

J. S. Goodwin and A. K. Kenworthy, “Photobleaching approaches to investigate diffusional mobility and trafficking of Ras in living cells,” Methods 37(2), 154–164 (2005).
[Crossref] [PubMed]

2003 (1)

R. G. Phair and T. Misteli, “Measurement of Dynamic Protein Binding to Chromatin In Vivo,” Using Photobleaching Microscopy. 375, 393–414 (2003).

2001 (1)

T. Misteli, “Protein dynamics: implications for nuclear architecture and gene expression,” Science 291(5505), 843–847 (2001).
[Crossref] [PubMed]

2000 (1)

M. H. H. Jones, N. Hamana, and M. Shimane, “Identification and characterization of BPTF, a novel Bromodomain transcription factor,” Genomics 63(1), 35–39 (2000).
[Crossref] [PubMed]

1993 (1)

B. Kosko and S. Isaka, “Fuzzy logic,” Sci. Am. 269(1), 1845–1908 (1993).
[Crossref]

1990 (1)

C. Aslanidis and P. J. de Jong, “Ligation-independent cloning of PCR products (LIC-PCR),” Nucleic Acids Res. 18(20), 6069–6074 (1990).
[Crossref] [PubMed]

1965 (1)

L. A. Zadeh, “Fuzzy sets *,” Inf. Control 8(3), 338–353 (1965).
[Crossref]

Agarwal, P.

F. Gong, L.-Y. Chiu, B. Cox, F. Aymard, T. Clouaire, J. W. Leung, M. Cammarata, M. Perez, P. Agarwal, J. S. Brodbelt, G. Legube, and K. M. Miller, “Screen identifies bromodomain protein ZMYND8 in chromatin recognition of transcription-associated DNA damage that promotes homologous recombination,” Genes Dev. 29(2), 197–211 (2015).
[Crossref] [PubMed]

Aik, W.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
[Crossref] [PubMed]

Arrowsmith, C. H.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
[Crossref] [PubMed]

Aslanidis, C.

C. Aslanidis and P. J. de Jong, “Ligation-independent cloning of PCR products (LIC-PCR),” Nucleic Acids Res. 18(20), 6069–6074 (1990).
[Crossref] [PubMed]

Aymard, F.

F. Gong, L.-Y. Chiu, B. Cox, F. Aymard, T. Clouaire, J. W. Leung, M. Cammarata, M. Perez, P. Agarwal, J. S. Brodbelt, G. Legube, and K. M. Miller, “Screen identifies bromodomain protein ZMYND8 in chromatin recognition of transcription-associated DNA damage that promotes homologous recombination,” Genes Dev. 29(2), 197–211 (2015).
[Crossref] [PubMed]

Bader, G. D.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
[Crossref] [PubMed]

Bagg, E. A.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
[Crossref] [PubMed]

Barsyte-Lovejoy, D.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
[Crossref] [PubMed]

Batista, A.

H. Georg Breunig, A. Uchugonova, A. Batista, and K. König, “Software-aided automatic laser optoporation and transfection of cells,” Sci. Rep. 5, 11185 (2015).
[Crossref] [PubMed]

Bedford, M. T.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
[Crossref] [PubMed]

Beinke, S.

E. Nicodeme, K. L. Jeffrey, U. Schaefer, S. Beinke, S. Dewell, C. W. Chung, R. Chandwani, I. Marazzi, P. Wilson, H. Coste, J. White, J. Kirilovsky, C. M. Rice, J. M. Lora, R. K. Prinjha, K. Lee, and A. Tarakhovsky, “Suppression of inflammation by a synthetic histone mimic,” Nature 468(7327), 1119–1123 (2010).
[Crossref] [PubMed]

Boutros, P. C.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
[Crossref] [PubMed]

Bradner, J. E.

S. Picaud, D. Da Costa, A. Thanasopoulou, P. Filippakopoulos, P. V. Fish, M. Philpott, O. Fedorov, P. Brennan, M. E. Bunnage, D. R. Owen, J. E. Bradner, P. Taniere, B. O’Sullivan, S. Müller, J. Schwaller, T. Stankovic, and S. Knapp, “PFI-1, a highly selective protein interaction inhibitor, targeting BET Bromodomains,” Cancer Res. 73(11), 3336–3346 (2013).
[Crossref] [PubMed]

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N. W. Goehring, D. Chowdhury, A. A. Hyman, and S. W. Grill, “FRAP Analysis of Membrane-Associated Proteins: Lateral Diffusion and Membrane-Cytoplasmic Exchange,” Biophys. J. 99(8), 2443–2452 (2010).
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Gong, F.

F. Gong, L.-Y. Chiu, B. Cox, F. Aymard, T. Clouaire, J. W. Leung, M. Cammarata, M. Perez, P. Agarwal, J. S. Brodbelt, G. Legube, and K. M. Miller, “Screen identifies bromodomain protein ZMYND8 in chromatin recognition of transcription-associated DNA damage that promotes homologous recombination,” Genes Dev. 29(2), 197–211 (2015).
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Gonzalez-Perez, A.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
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Goodwin, J. S.

J. S. Goodwin and A. K. Kenworthy, “Photobleaching approaches to investigate diffusional mobility and trafficking of Ras in living cells,” Methods 37(2), 154–164 (2005).
[Crossref] [PubMed]

Greenblatt, J. F.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
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Grill, S. W.

N. W. Goehring, D. Chowdhury, A. A. Hyman, and S. W. Grill, “FRAP Analysis of Membrane-Associated Proteins: Lateral Diffusion and Membrane-Cytoplasmic Exchange,” Biophys. J. 99(8), 2443–2452 (2010).
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Guo, H.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
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P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
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Halasz, A.

D. J. Cappelleri, A. Halasz, J. Y. Sul, T. K. Kim, J. Eberwine, and V. Kumar, “Towards A Fully Automated High-Throughput Phototransfection System,” JALA Charlottesv Va 15(4), 329–341 (2010).
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Hamana, N.

M. H. H. Jones, N. Hamana, and M. Shimane, “Identification and characterization of BPTF, a novel Bromodomain transcription factor,” Genomics 63(1), 35–39 (2000).
[Crossref] [PubMed]

He, F. S.

J. B. Warner, A. A. Philippakis, S. A. Jaeger, F. S. He, J. Lin, and M. L. Bulyk, “Systematic identification of mammalian regulatory motifs’ target genes and functions,” Nat. Methods 5(4), 347–353 (2008).
[PubMed]

Heightman, T. D.

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
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Hendzel, M. J.

L. C. Young, D. W. McDonald, and M. J. Hendzel, “Kdm4b Histone Demethylase Is a DNA Damage Response Protein and Confers a Survival Advantage following γ-Irradiation,” J. Biol. Chem. 288(29), 21376–21388 (2013).
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Herold, J. M.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
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Hickman, T. T.

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
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Hopkinson, R. J.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
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Huang, X.-P.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
[Crossref] [PubMed]

Hulley, P. A.

M. Kuzma-Kuzniarska, C. Yapp, T. W. Pearson-Jones, A. K. Jones, and P. A. Hulley, “Functional assessment of gap junctions in monolayer and three-dimensional cultures of human tendon cells using fluorescence recovery after photobleaching,” J. Biomed. Opt. 19(1), 015001 (2014).
[Crossref] [PubMed]

Hyman, A. A.

N. W. Goehring, D. Chowdhury, A. A. Hyman, and S. W. Grill, “FRAP Analysis of Membrane-Associated Proteins: Lateral Diffusion and Membrane-Cytoplasmic Exchange,” Biophys. J. 99(8), 2443–2452 (2010).
[Crossref] [PubMed]

Isaka, S.

B. Kosko and S. Isaka, “Fuzzy logic,” Sci. Am. 269(1), 1845–1908 (1993).
[Crossref]

Jaeger, S. A.

J. B. Warner, A. A. Philippakis, S. A. Jaeger, F. S. He, J. Lin, and M. L. Bulyk, “Systematic identification of mammalian regulatory motifs’ target genes and functions,” Nat. Methods 5(4), 347–353 (2008).
[PubMed]

James, L. I.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
[Crossref] [PubMed]

Janzen, W. P.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
[Crossref] [PubMed]

Jeffrey, K. L.

E. Nicodeme, K. L. Jeffrey, U. Schaefer, S. Beinke, S. Dewell, C. W. Chung, R. Chandwani, I. Marazzi, P. Wilson, H. Coste, J. White, J. Kirilovsky, C. M. Rice, J. M. Lora, R. K. Prinjha, K. Lee, and A. Tarakhovsky, “Suppression of inflammation by a synthetic histone mimic,” Nature 468(7327), 1119–1123 (2010).
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Jin, J.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
[Crossref] [PubMed]

Jones, A. K.

M. Kuzma-Kuzniarska, C. Yapp, T. W. Pearson-Jones, A. K. Jones, and P. A. Hulley, “Functional assessment of gap junctions in monolayer and three-dimensional cultures of human tendon cells using fluorescence recovery after photobleaching,” J. Biomed. Opt. 19(1), 015001 (2014).
[Crossref] [PubMed]

Jones, M. H. H.

M. H. H. Jones, N. Hamana, and M. Shimane, “Identification and characterization of BPTF, a novel Bromodomain transcription factor,” Genomics 63(1), 35–39 (2000).
[Crossref] [PubMed]

Kawamura, A.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
[Crossref] [PubMed]

Keates, T.

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
[Crossref] [PubMed]

Kenworthy, A. K.

J. S. Goodwin and A. K. Kenworthy, “Photobleaching approaches to investigate diffusional mobility and trafficking of Ras in living cells,” Methods 37(2), 154–164 (2005).
[Crossref] [PubMed]

Kim, T. K.

D. J. Cappelleri, A. Halasz, J. Y. Sul, T. K. Kim, J. Eberwine, and V. Kumar, “Towards A Fully Automated High-Throughput Phototransfection System,” JALA Charlottesv Va 15(4), 329–341 (2010).
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King, O. N. F.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
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Kireev, D. B.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
[Crossref] [PubMed]

Kirilovsky, J.

E. Nicodeme, K. L. Jeffrey, U. Schaefer, S. Beinke, S. Dewell, C. W. Chung, R. Chandwani, I. Marazzi, P. Wilson, H. Coste, J. White, J. Kirilovsky, C. M. Rice, J. M. Lora, R. K. Prinjha, K. Lee, and A. Tarakhovsky, “Suppression of inflammation by a synthetic histone mimic,” Nature 468(7327), 1119–1123 (2010).
[Crossref] [PubMed]

Klose, R. J.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
[Crossref] [PubMed]

Knapp, S.

M. Philpott, C. M. Rogers, C. Yapp, C. Wells, J.-P. Lambert, C. Strain-Damerell, N. A. Burgess-Brown, A.-C. Gingras, S. Knapp, and S. Müller, “Assessing cellular efficacy of bromodomain inhibitors using fluorescence recovery after photobleaching,” Epigenetics Chromatin 7(1), 14 (2014).
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S. Picaud, D. Da Costa, A. Thanasopoulou, P. Filippakopoulos, P. V. Fish, M. Philpott, O. Fedorov, P. Brennan, M. E. Bunnage, D. R. Owen, J. E. Bradner, P. Taniere, B. O’Sullivan, S. Müller, J. Schwaller, T. Stankovic, and S. Knapp, “PFI-1, a highly selective protein interaction inhibitor, targeting BET Bromodomains,” Cancer Res. 73(11), 3336–3346 (2013).
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S. Muller, P. Filippakopoulos, and S. Knapp, “Bromodomains as therapeutic targets,” Expert Rev. Mol. Med. 13, e29 (2011).
[Crossref] [PubMed]

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
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König, K.

H. Georg Breunig, A. Uchugonova, A. Batista, and K. König, “Software-aided automatic laser optoporation and transfection of cells,” Sci. Rep. 5, 11185 (2015).
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Korboukh, V. K.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
[Crossref] [PubMed]

Kosko, B.

B. Kosko and S. Isaka, “Fuzzy logic,” Sci. Am. 269(1), 1845–1908 (1993).
[Crossref]

Krichevsky, L.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
[Crossref] [PubMed]

Kristensen, J. B. L.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
[Crossref] [PubMed]

Krojer, T.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
[Crossref] [PubMed]

Kumar, V.

D. J. Cappelleri, A. Halasz, J. Y. Sul, T. K. Kim, J. Eberwine, and V. Kumar, “Towards A Fully Automated High-Throughput Phototransfection System,” JALA Charlottesv Va 15(4), 329–341 (2010).
[Crossref] [PubMed]

Kung, A. L.

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
[Crossref] [PubMed]

Kuzma-Kuzniarska, M.

M. Kuzma-Kuzniarska, C. Yapp, T. W. Pearson-Jones, A. K. Jones, and P. A. Hulley, “Functional assessment of gap junctions in monolayer and three-dimensional cultures of human tendon cells using fluorescence recovery after photobleaching,” J. Biomed. Opt. 19(1), 015001 (2014).
[Crossref] [PubMed]

La Thangue, N.

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
[Crossref] [PubMed]

Lambert, J.-P.

M. Philpott, C. M. Rogers, C. Yapp, C. Wells, J.-P. Lambert, C. Strain-Damerell, N. A. Burgess-Brown, A.-C. Gingras, S. Knapp, and S. Müller, “Assessing cellular efficacy of bromodomain inhibitors using fluorescence recovery after photobleaching,” Epigenetics Chromatin 7(1), 14 (2014).
[Crossref] [PubMed]

Lee, K.

E. Nicodeme, K. L. Jeffrey, U. Schaefer, S. Beinke, S. Dewell, C. W. Chung, R. Chandwani, I. Marazzi, P. Wilson, H. Coste, J. White, J. Kirilovsky, C. M. Rice, J. M. Lora, R. K. Prinjha, K. Lee, and A. Tarakhovsky, “Suppression of inflammation by a synthetic histone mimic,” Nature 468(7327), 1119–1123 (2010).
[Crossref] [PubMed]

Legube, G.

F. Gong, L.-Y. Chiu, B. Cox, F. Aymard, T. Clouaire, J. W. Leung, M. Cammarata, M. Perez, P. Agarwal, J. S. Brodbelt, G. Legube, and K. M. Miller, “Screen identifies bromodomain protein ZMYND8 in chromatin recognition of transcription-associated DNA damage that promotes homologous recombination,” Genes Dev. 29(2), 197–211 (2015).
[Crossref] [PubMed]

Lejeune, C.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
[Crossref] [PubMed]

Leung, J. W.

F. Gong, L.-Y. Chiu, B. Cox, F. Aymard, T. Clouaire, J. W. Leung, M. Cammarata, M. Perez, P. Agarwal, J. S. Brodbelt, G. Legube, and K. M. Miller, “Screen identifies bromodomain protein ZMYND8 in chromatin recognition of transcription-associated DNA damage that promotes homologous recombination,” Genes Dev. 29(2), 197–211 (2015).
[Crossref] [PubMed]

Li, X. S.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
[Crossref] [PubMed]

Liebel, U.

C. Conrad, A. Wünsche, T. H. Tan, J. Bulkescher, F. Sieckmann, F. Verissimo, A. Edelstein, T. Walter, U. Liebel, R. Pepperkok, and J. Ellenberg, “Micropilot: automation of fluorescence microscopy-based imaging for systems biology,” Nat. Methods 8(3), 246–249 (2011).
[Crossref] [PubMed]

Lin, J.

J. B. Warner, A. A. Philippakis, S. A. Jaeger, F. S. He, J. Lin, and M. L. Bulyk, “Systematic identification of mammalian regulatory motifs’ target genes and functions,” Nat. Methods 5(4), 347–353 (2008).
[PubMed]

Linding, R.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
[Crossref] [PubMed]

Lopez-Bigas, N.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
[Crossref] [PubMed]

Lora, J. M.

E. Nicodeme, K. L. Jeffrey, U. Schaefer, S. Beinke, S. Dewell, C. W. Chung, R. Chandwani, I. Marazzi, P. Wilson, H. Coste, J. White, J. Kirilovsky, C. M. Rice, J. M. Lora, R. K. Prinjha, K. Lee, and A. Tarakhovsky, “Suppression of inflammation by a synthetic histone mimic,” Nature 468(7327), 1119–1123 (2010).
[Crossref] [PubMed]

MacNevin, C. J.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
[Crossref] [PubMed]

Marazzi, I.

E. Nicodeme, K. L. Jeffrey, U. Schaefer, S. Beinke, S. Dewell, C. W. Chung, R. Chandwani, I. Marazzi, P. Wilson, H. Coste, J. White, J. Kirilovsky, C. M. Rice, J. M. Lora, R. K. Prinjha, K. Lee, and A. Tarakhovsky, “Suppression of inflammation by a synthetic histone mimic,” Nature 468(7327), 1119–1123 (2010).
[Crossref] [PubMed]

Marcon, E.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
[Crossref] [PubMed]

Marks, D. S.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
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McDonald, D. W.

L. C. Young, D. W. McDonald, and M. J. Hendzel, “Kdm4b Histone Demethylase Is a DNA Damage Response Protein and Confers a Survival Advantage following γ-Irradiation,” J. Biol. Chem. 288(29), 21376–21388 (2013).
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McDonough, M. A.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
[Crossref] [PubMed]

McKeown, M. R.

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
[Crossref] [PubMed]

Miller, K. M.

F. Gong, L.-Y. Chiu, B. Cox, F. Aymard, T. Clouaire, J. W. Leung, M. Cammarata, M. Perez, P. Agarwal, J. S. Brodbelt, G. Legube, and K. M. Miller, “Screen identifies bromodomain protein ZMYND8 in chromatin recognition of transcription-associated DNA damage that promotes homologous recombination,” Genes Dev. 29(2), 197–211 (2015).
[Crossref] [PubMed]

Misteli, T.

R. G. Phair and T. Misteli, “Measurement of Dynamic Protein Binding to Chromatin In Vivo,” Using Photobleaching Microscopy. 375, 393–414 (2003).

T. Misteli, “Protein dynamics: implications for nuclear architecture and gene expression,” Science 291(5505), 843–847 (2001).
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Mondal, P. P.

Morse, E. M.

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
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Muller, S.

S. Muller, P. Filippakopoulos, and S. Knapp, “Bromodomains as therapeutic targets,” Expert Rev. Mol. Med. 13, e29 (2011).
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Müller, S.

M. Philpott, C. M. Rogers, C. Yapp, C. Wells, J.-P. Lambert, C. Strain-Damerell, N. A. Burgess-Brown, A.-C. Gingras, S. Knapp, and S. Müller, “Assessing cellular efficacy of bromodomain inhibitors using fluorescence recovery after photobleaching,” Epigenetics Chromatin 7(1), 14 (2014).
[Crossref] [PubMed]

S. Picaud, D. Da Costa, A. Thanasopoulou, P. Filippakopoulos, P. V. Fish, M. Philpott, O. Fedorov, P. Brennan, M. E. Bunnage, D. R. Owen, J. E. Bradner, P. Taniere, B. O’Sullivan, S. Müller, J. Schwaller, T. Stankovic, and S. Knapp, “PFI-1, a highly selective protein interaction inhibitor, targeting BET Bromodomains,” Cancer Res. 73(11), 3336–3346 (2013).
[Crossref] [PubMed]

S. Müller and P. J. Brown, “Epigenetic chemical probes,” Clin. Pharmacol. Ther. 92(6), 689–693 (2012).
[Crossref] [PubMed]

Muller-Knapp, S.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
[Crossref] [PubMed]

Munro, S.

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
[Crossref] [PubMed]

Mustonen, V.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
[Crossref] [PubMed]

Ng, S. S.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
[Crossref] [PubMed]

Nicodeme, E.

E. Nicodeme, K. L. Jeffrey, U. Schaefer, S. Beinke, S. Dewell, C. W. Chung, R. Chandwani, I. Marazzi, P. Wilson, H. Coste, J. White, J. Kirilovsky, C. M. Rice, J. M. Lora, R. K. Prinjha, K. Lee, and A. Tarakhovsky, “Suppression of inflammation by a synthetic histone mimic,” Nature 468(7327), 1119–1123 (2010).
[Crossref] [PubMed]

Norris, J. L.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
[Crossref] [PubMed]

O’Sullivan, B.

S. Picaud, D. Da Costa, A. Thanasopoulou, P. Filippakopoulos, P. V. Fish, M. Philpott, O. Fedorov, P. Brennan, M. E. Bunnage, D. R. Owen, J. E. Bradner, P. Taniere, B. O’Sullivan, S. Müller, J. Schwaller, T. Stankovic, and S. Knapp, “PFI-1, a highly selective protein interaction inhibitor, targeting BET Bromodomains,” Cancer Res. 73(11), 3336–3346 (2013).
[Crossref] [PubMed]

Olsen, L.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
[Crossref] [PubMed]

Oppermann, U.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
[Crossref] [PubMed]

Ouellette, B. F. F.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
[Crossref] [PubMed]

Owen, D. R.

S. Picaud, D. Da Costa, A. Thanasopoulou, P. Filippakopoulos, P. V. Fish, M. Philpott, O. Fedorov, P. Brennan, M. E. Bunnage, D. R. Owen, J. E. Bradner, P. Taniere, B. O’Sullivan, S. Müller, J. Schwaller, T. Stankovic, and S. Knapp, “PFI-1, a highly selective protein interaction inhibitor, targeting BET Bromodomains,” Cancer Res. 73(11), 3336–3346 (2013).
[Crossref] [PubMed]

Pearson, J.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
[Crossref] [PubMed]

Pearson-Jones, T. W.

M. Kuzma-Kuzniarska, C. Yapp, T. W. Pearson-Jones, A. K. Jones, and P. A. Hulley, “Functional assessment of gap junctions in monolayer and three-dimensional cultures of human tendon cells using fluorescence recovery after photobleaching,” J. Biomed. Opt. 19(1), 015001 (2014).
[Crossref] [PubMed]

Pepperkok, R.

C. Conrad, A. Wünsche, T. H. Tan, J. Bulkescher, F. Sieckmann, F. Verissimo, A. Edelstein, T. Walter, U. Liebel, R. Pepperkok, and J. Ellenberg, “Micropilot: automation of fluorescence microscopy-based imaging for systems biology,” Nat. Methods 8(3), 246–249 (2011).
[Crossref] [PubMed]

Perez, M.

F. Gong, L.-Y. Chiu, B. Cox, F. Aymard, T. Clouaire, J. W. Leung, M. Cammarata, M. Perez, P. Agarwal, J. S. Brodbelt, G. Legube, and K. M. Miller, “Screen identifies bromodomain protein ZMYND8 in chromatin recognition of transcription-associated DNA damage that promotes homologous recombination,” Genes Dev. 29(2), 197–211 (2015).
[Crossref] [PubMed]

Phair, R. G.

R. G. Phair and T. Misteli, “Measurement of Dynamic Protein Binding to Chromatin In Vivo,” Using Photobleaching Microscopy. 375, 393–414 (2003).

Philippakis, A. A.

J. B. Warner, A. A. Philippakis, S. A. Jaeger, F. S. He, J. Lin, and M. L. Bulyk, “Systematic identification of mammalian regulatory motifs’ target genes and functions,” Nat. Methods 5(4), 347–353 (2008).
[PubMed]

Philpott, M.

M. Philpott, C. M. Rogers, C. Yapp, C. Wells, J.-P. Lambert, C. Strain-Damerell, N. A. Burgess-Brown, A.-C. Gingras, S. Knapp, and S. Müller, “Assessing cellular efficacy of bromodomain inhibitors using fluorescence recovery after photobleaching,” Epigenetics Chromatin 7(1), 14 (2014).
[Crossref] [PubMed]

S. Picaud, D. Da Costa, A. Thanasopoulou, P. Filippakopoulos, P. V. Fish, M. Philpott, O. Fedorov, P. Brennan, M. E. Bunnage, D. R. Owen, J. E. Bradner, P. Taniere, B. O’Sullivan, S. Müller, J. Schwaller, T. Stankovic, and S. Knapp, “PFI-1, a highly selective protein interaction inhibitor, targeting BET Bromodomains,” Cancer Res. 73(11), 3336–3346 (2013).
[Crossref] [PubMed]

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
[Crossref] [PubMed]

Picaud, S.

S. Picaud, D. Da Costa, A. Thanasopoulou, P. Filippakopoulos, P. V. Fish, M. Philpott, O. Fedorov, P. Brennan, M. E. Bunnage, D. R. Owen, J. E. Bradner, P. Taniere, B. O’Sullivan, S. Müller, J. Schwaller, T. Stankovic, and S. Knapp, “PFI-1, a highly selective protein interaction inhibitor, targeting BET Bromodomains,” Cancer Res. 73(11), 3336–3346 (2013).
[Crossref] [PubMed]

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
[Crossref] [PubMed]

Prinjha, R. K.

E. Nicodeme, K. L. Jeffrey, U. Schaefer, S. Beinke, S. Dewell, C. W. Chung, R. Chandwani, I. Marazzi, P. Wilson, H. Coste, J. White, J. Kirilovsky, C. M. Rice, J. M. Lora, R. K. Prinjha, K. Lee, and A. Tarakhovsky, “Suppression of inflammation by a synthetic histone mimic,” Nature 468(7327), 1119–1123 (2010).
[Crossref] [PubMed]

Qi, J.

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
[Crossref] [PubMed]

Raphael, B. J.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
[Crossref] [PubMed]

Ratcliffe, P. J.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
[Crossref] [PubMed]

Reimand, J.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
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Rice, C. M.

E. Nicodeme, K. L. Jeffrey, U. Schaefer, S. Beinke, S. Dewell, C. W. Chung, R. Chandwani, I. Marazzi, P. Wilson, H. Coste, J. White, J. Kirilovsky, C. M. Rice, J. M. Lora, R. K. Prinjha, K. Lee, and A. Tarakhovsky, “Suppression of inflammation by a synthetic histone mimic,” Nature 468(7327), 1119–1123 (2010).
[Crossref] [PubMed]

Rogers, C. M.

M. Philpott, C. M. Rogers, C. Yapp, C. Wells, J.-P. Lambert, C. Strain-Damerell, N. A. Burgess-Brown, A.-C. Gingras, S. Knapp, and S. Müller, “Assessing cellular efficacy of bromodomain inhibitors using fluorescence recovery after photobleaching,” Epigenetics Chromatin 7(1), 14 (2014).
[Crossref] [PubMed]

Rose, N. R.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
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Rydzik, A. M.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
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Sagum, C. A.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
[Crossref] [PubMed]

Sander, C.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
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Schaefer, U.

E. Nicodeme, K. L. Jeffrey, U. Schaefer, S. Beinke, S. Dewell, C. W. Chung, R. Chandwani, I. Marazzi, P. Wilson, H. Coste, J. White, J. Kirilovsky, C. M. Rice, J. M. Lora, R. K. Prinjha, K. Lee, and A. Tarakhovsky, “Suppression of inflammation by a synthetic histone mimic,” Nature 468(7327), 1119–1123 (2010).
[Crossref] [PubMed]

Schofield, C. J.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
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Schwaller, J.

S. Picaud, D. Da Costa, A. Thanasopoulou, P. Filippakopoulos, P. V. Fish, M. Philpott, O. Fedorov, P. Brennan, M. E. Bunnage, D. R. Owen, J. E. Bradner, P. Taniere, B. O’Sullivan, S. Müller, J. Schwaller, T. Stankovic, and S. Knapp, “PFI-1, a highly selective protein interaction inhibitor, targeting BET Bromodomains,” Cancer Res. 73(11), 3336–3346 (2013).
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Schwartz, B.

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
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Shen, Y.

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
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Shibata, T.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
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Shimane, M.

M. H. H. Jones, N. Hamana, and M. Shimane, “Identification and characterization of BPTF, a novel Bromodomain transcription factor,” Genomics 63(1), 35–39 (2000).
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Sieckmann, F.

C. Conrad, A. Wünsche, T. H. Tan, J. Bulkescher, F. Sieckmann, F. Verissimo, A. Edelstein, T. Walter, U. Liebel, R. Pepperkok, and J. Ellenberg, “Micropilot: automation of fluorescence microscopy-based imaging for systems biology,” Nat. Methods 8(3), 246–249 (2011).
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Smith, W. B.

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
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Stankovic, T.

S. Picaud, D. Da Costa, A. Thanasopoulou, P. Filippakopoulos, P. V. Fish, M. Philpott, O. Fedorov, P. Brennan, M. E. Bunnage, D. R. Owen, J. E. Bradner, P. Taniere, B. O’Sullivan, S. Müller, J. Schwaller, T. Stankovic, and S. Knapp, “PFI-1, a highly selective protein interaction inhibitor, targeting BET Bromodomains,” Cancer Res. 73(11), 3336–3346 (2013).
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Stein, L. D.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
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Strain-Damerell, C.

M. Philpott, C. M. Rogers, C. Yapp, C. Wells, J.-P. Lambert, C. Strain-Damerell, N. A. Burgess-Brown, A.-C. Gingras, S. Knapp, and S. Müller, “Assessing cellular efficacy of bromodomain inhibitors using fluorescence recovery after photobleaching,” Epigenetics Chromatin 7(1), 14 (2014).
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Stuart, J. M.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
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Sul, J. Y.

D. J. Cappelleri, A. Halasz, J. Y. Sul, T. K. Kim, J. Eberwine, and V. Kumar, “Towards A Fully Automated High-Throughput Phototransfection System,” JALA Charlottesv Va 15(4), 329–341 (2010).
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Tan, T. H.

C. Conrad, A. Wünsche, T. H. Tan, J. Bulkescher, F. Sieckmann, F. Verissimo, A. Edelstein, T. Walter, U. Liebel, R. Pepperkok, and J. Ellenberg, “Micropilot: automation of fluorescence microscopy-based imaging for systems biology,” Nat. Methods 8(3), 246–249 (2011).
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Taniere, P.

S. Picaud, D. Da Costa, A. Thanasopoulou, P. Filippakopoulos, P. V. Fish, M. Philpott, O. Fedorov, P. Brennan, M. E. Bunnage, D. R. Owen, J. E. Bradner, P. Taniere, B. O’Sullivan, S. Müller, J. Schwaller, T. Stankovic, and S. Knapp, “PFI-1, a highly selective protein interaction inhibitor, targeting BET Bromodomains,” Cancer Res. 73(11), 3336–3346 (2013).
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Tarakhovsky, A.

E. Nicodeme, K. L. Jeffrey, U. Schaefer, S. Beinke, S. Dewell, C. W. Chung, R. Chandwani, I. Marazzi, P. Wilson, H. Coste, J. White, J. Kirilovsky, C. M. Rice, J. M. Lora, R. K. Prinjha, K. Lee, and A. Tarakhovsky, “Suppression of inflammation by a synthetic histone mimic,” Nature 468(7327), 1119–1123 (2010).
[Crossref] [PubMed]

Tempel, W.

L. I. James, D. Barsyte-Lovejoy, N. Zhong, L. Krichevsky, V. K. Korboukh, J. M. Herold, C. J. MacNevin, J. L. Norris, C. A. Sagum, W. Tempel, E. Marcon, H. Guo, C. Gao, X.-P. Huang, S. Duan, A. Emili, J. F. Greenblatt, D. B. Kireev, J. Jin, W. P. Janzen, P. J. Brown, M. T. Bedford, C. H. Arrowsmith, and S. V. Frye, “Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain,” Nat. Chem. Biol. 9(3), 184–191 (2013).
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Thanasopoulou, A.

S. Picaud, D. Da Costa, A. Thanasopoulou, P. Filippakopoulos, P. V. Fish, M. Philpott, O. Fedorov, P. Brennan, M. E. Bunnage, D. R. Owen, J. E. Bradner, P. Taniere, B. O’Sullivan, S. Müller, J. Schwaller, T. Stankovic, and S. Knapp, “PFI-1, a highly selective protein interaction inhibitor, targeting BET Bromodomains,” Cancer Res. 73(11), 3336–3346 (2013).
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Thinnes, C. C.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
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Tumber, A.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
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H. Georg Breunig, A. Uchugonova, A. Batista, and K. König, “Software-aided automatic laser optoporation and transfection of cells,” Sci. Rep. 5, 11185 (2015).
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Valencia, A.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
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Vazquez, M.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
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Verissimo, F.

C. Conrad, A. Wünsche, T. H. Tan, J. Bulkescher, F. Sieckmann, F. Verissimo, A. Edelstein, T. Walter, U. Liebel, R. Pepperkok, and J. Ellenberg, “Micropilot: automation of fluorescence microscopy-based imaging for systems biology,” Nat. Methods 8(3), 246–249 (2011).
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Vicidomini, G.

Walport, L. J.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
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Walter, T.

C. Conrad, A. Wünsche, T. H. Tan, J. Bulkescher, F. Sieckmann, F. Verissimo, A. Edelstein, T. Walter, U. Liebel, R. Pepperkok, and J. Ellenberg, “Micropilot: automation of fluorescence microscopy-based imaging for systems biology,” Nat. Methods 8(3), 246–249 (2011).
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Wang, Y.

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
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Warner, J. B.

J. B. Warner, A. A. Philippakis, S. A. Jaeger, F. S. He, J. Lin, and M. L. Bulyk, “Systematic identification of mammalian regulatory motifs’ target genes and functions,” Nat. Methods 5(4), 347–353 (2008).
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Weinmann, H.

D. Gallenkamp, K. A. Gelato, B. Haendler, and H. Weinmann, “Bromodomains and their pharmacological inhibitors,” ChemMedChem 9(3), 438–464 (2014).
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Wells, C.

M. Philpott, C. M. Rogers, C. Yapp, C. Wells, J.-P. Lambert, C. Strain-Damerell, N. A. Burgess-Brown, A.-C. Gingras, S. Knapp, and S. Müller, “Assessing cellular efficacy of bromodomain inhibitors using fluorescence recovery after photobleaching,” Epigenetics Chromatin 7(1), 14 (2014).
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West, N.

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
[Crossref] [PubMed]

White, J.

E. Nicodeme, K. L. Jeffrey, U. Schaefer, S. Beinke, S. Dewell, C. W. Chung, R. Chandwani, I. Marazzi, P. Wilson, H. Coste, J. White, J. Kirilovsky, C. M. Rice, J. M. Lora, R. K. Prinjha, K. Lee, and A. Tarakhovsky, “Suppression of inflammation by a synthetic histone mimic,” Nature 468(7327), 1119–1123 (2010).
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Wiest, O.

P. Filippakopoulos, J. Qi, S. Picaud, Y. Shen, W. B. Smith, O. Fedorov, E. M. Morse, T. Keates, T. T. Hickman, I. Felletar, M. Philpott, S. Munro, M. R. McKeown, Y. Wang, A. L. Christie, N. West, M. J. Cameron, B. Schwartz, T. D. Heightman, N. La Thangue, C. A. French, O. Wiest, A. L. Kung, S. Knapp, and J. E. Bradner, “Selective inhibition of BET bromodomains,” Nature 468(7327), 1067–1073 (2010).
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Wilson, P.

E. Nicodeme, K. L. Jeffrey, U. Schaefer, S. Beinke, S. Dewell, C. W. Chung, R. Chandwani, I. Marazzi, P. Wilson, H. Coste, J. White, J. Kirilovsky, C. M. Rice, J. M. Lora, R. K. Prinjha, K. Lee, and A. Tarakhovsky, “Suppression of inflammation by a synthetic histone mimic,” Nature 468(7327), 1119–1123 (2010).
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Wu, G.

P. Creixell, J. Reimand, S. Haider, G. Wu, T. Shibata, M. Vazquez, V. Mustonen, A. Gonzalez-Perez, J. Pearson, C. Sander, B. J. Raphael, D. S. Marks, B. F. F. Ouellette, A. Valencia, G. D. Bader, P. C. Boutros, J. M. Stuart, R. Linding, N. Lopez-Bigas, L. D. Stein, and Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium, “Pathway and network analysis of cancer genomes,” Nat. Methods 12(7), 615–621 (2015).
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Wünsche, A.

C. Conrad, A. Wünsche, T. H. Tan, J. Bulkescher, F. Sieckmann, F. Verissimo, A. Edelstein, T. Walter, U. Liebel, R. Pepperkok, and J. Ellenberg, “Micropilot: automation of fluorescence microscopy-based imaging for systems biology,” Nat. Methods 8(3), 246–249 (2011).
[Crossref] [PubMed]

Yapp, C.

M. Philpott, C. M. Rogers, C. Yapp, C. Wells, J.-P. Lambert, C. Strain-Damerell, N. A. Burgess-Brown, A.-C. Gingras, S. Knapp, and S. Müller, “Assessing cellular efficacy of bromodomain inhibitors using fluorescence recovery after photobleaching,” Epigenetics Chromatin 7(1), 14 (2014).
[Crossref] [PubMed]

M. Kuzma-Kuzniarska, C. Yapp, T. W. Pearson-Jones, A. K. Jones, and P. A. Hulley, “Functional assessment of gap junctions in monolayer and three-dimensional cultures of human tendon cells using fluorescence recovery after photobleaching,” J. Biomed. Opt. 19(1), 015001 (2014).
[Crossref] [PubMed]

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
[Crossref] [PubMed]

Yeoh, K. K.

R. J. Hopkinson, A. Tumber, C. Yapp, R. Chowdhury, W. Aik, K. H. Che, X. S. Li, J. B. L. Kristensen, O. N. F. King, M. C. Chan, K. K. Yeoh, H. Choi, L. J. Walport, C. C. Thinnes, J. T. Bush, C. Lejeune, A. M. Rydzik, N. R. Rose, E. A. Bagg, M. A. McDonough, T. Krojer, W. W. Yue, S. S. Ng, L. Olsen, P. E. Brennan, U. Oppermann, S. Muller-Knapp, R. J. Klose, P. J. Ratcliffe, C. J. Schofield, and A. Kawamura, “5-Carboxy-8-hydroxyquinoline is a broad spectrum 2-oxoglutarate oxygenase inhibitor which causes iron translocation,” Chem. Sci. (Camb.) 4(8), 3110–3117 (2013).
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Young, L. C.

L. C. Young, D. W. McDonald, and M. J. Hendzel, “Kdm4b Histone Demethylase Is a DNA Damage Response Protein and Confers a Survival Advantage following γ-Irradiation,” J. Biol. Chem. 288(29), 21376–21388 (2013).
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Figures (10)

Fig. 1
Fig. 1 (a) Schematic flowchart of the automated FRAP system, Frapid. Visual Basic (VB) and MATLAB communicate file directories and cell coordinates between each other. VB is the main controller and handles hardware control (fluid pump, stage movement, image acquisition file saving, etc. On the other hand, MATLAB receives file information from VB and imports images. Then, MATLAB performs image analysis routines, identify cells based on fuzzy logic, analyze FRAP recovery curves, and export to Microsoft Excel for emailing. MATLAB returns control to VB once it has completed the script. (b-c) Each low resolution tile scan image is segmented based on GFP fluorescence to identify individual objects. The area, average intensity, eccentricity, and roundness are extracted from each nucleus and run through MATLAB’s fuzzy logic toolbox to obtain an overall score between 0 and 1. (d-e) Fuzzy logic is highly advantageous over traditional Boolean logic in achieving a higher yield of cells. Due to the relaxed rules of fuzzy logic, a cell (shown as (d)) that is still reasonably near the ideal range of size and intensity, for example, can still be considered for FRAP without outright rejection. (f) Depending on the score, the cell is prioritized and ranked for FRAP, with ‘1’ being scored for the most ideal cell.

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Fig. 2
Fig. 2 Exploded view of fluid handler showing ring mount, main bracket, rack, tube holder, bracket, pinion gear and stepper motor. Technical details and instructions can be obtained from http://www.thesgc.org/frapid.

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Fig. 3
Fig. 3 The custom-built fluid handler, which replaces the microscope condenser during Frapid. The fluid handler is attached to the microscope arm via the ring mount. A rack and pinion gear converts rotational motion from the stepper motor to linear movement. The rack is also attached to a tube holder that guides the tubing from the retracted position (during lateral stage movement) to the extended position (when aspiring and dispensing fluid into well). Electrical components for controlling the stepper motor can be found at http://www.thesgc.org/frapid.

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Fig. 4
Fig. 4 Data presented in spreadsheet format with average and standard deviation half times for each well. Results displayed in an Excel spreadsheet detailing the a)- verdict, b) – cell number, c)- recovery halftime, d)- R2 value for goodness of curve fit, e)- the plateau from curve fitting, f)- normalized recovery plot showing data points (blue) and curve fit (red), g) – image of cell during pre-bleach, h) – image of cell immediately after bleach, i) – segmentation mask of cell, j) – automated pre-calculation for determining the population standard deviation, label l. Specifically, this is the square of the difference between the individual cell’s recovery half time and the population average recovery half time, k) – average recovery half time of cells with verdict ‘1’, l) – standard deviation of individual half time values of cells with verdict ‘1’, m) – the position of the well represented by a two digit number that designates the column and row numbers respectively. Cells 7 and 8 were rejected due to their R2 value and/or plateau of curve fit. Users can manually change the verdict of any cell, causing the average and standard deviation to update automatically.

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Fig. 5
Fig. 5 Comparison of half recovery times on the same cells selected by Frapid and manual FRAP. Samples included either CECR2 WT, CECR2 WT with inhibitor, or the catalytically inactivating mutant (N140A). Frapid identified the same cells as in manual FRAP producing half recovery times that were similar, suggesting that empirically determined fuzzy parameters were optimal. Error bars are standard error of mean.

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Fig. 6
Fig. 6 (a) Montage comparing fluorescence recovery for BRD4 in cells transfected with either BRD4 WT, N140F / N443F mutant, or BRD4 WT + PFI-1. White circle represents bleach region. (b) Bar chart of average recovery times for each condition tested. ** and * denote p<0.0005 and p<0.005 respectively as determined by Wilcoxon Rank-sum test. Error bars are standard deviation and each group represents 20 cells. (c) Average recovery curves of more than 20 cells for each condition. Scale bar represents 5µm.

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Fig. 7
Fig. 7 CECR2. a) – Montage of U2OS cells expressing green fluorescent protein fused to wild-type CECR2, wild-type CECR2 treated with NVS-1, or N140A mutant. White circle represents bleach region. b) - bar chart comparing half recovery time between wildtype, N140A mutant, or wildtype treated with NVS-1. * represents p<0.005 determined by Wilcoxon Rank-Sum test. Error bars are standard deviation and each group represents 20 cells. c) – Fluorescence recovery curves over time comparing wildtype, N140A mutant, or wildtype treated with NVS-1 or the inactive version, NVS-1C. Each curve is represented by 20 cells. Scale bar represents 5µm.

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Fig. 8
Fig. 8 BRPF1. a) – Montage of U2OS cells expressing green fluorescent protein fused to wild-type BRPF1, N708F mutant, or wild-type BRPF1 treated with OF-1. White circle represents bleach region. b) - bar chart comparing half recovery time between wildtype, N708F mutant, or wildtype treated with OF-1. * represents p<0.005 determined by Wilcoxon Rank-Sum test. Error bars are standard deviation and each group represents 20 cells. c) – Fluorescence recovery curves over time comparing wildtype, N708F mutant, or wildtype treated with OF-1. Each curve is represented by 20 cells. Scale bar represents 5µm.

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Fig. 9
Fig. 9 Validation of Frapid by comparing FRAP half recovery times obtained manually and automatically. Frapid was tested on BRD4, CECR2, and BRPF1 WT and corresponding amino acid substituted mutants. Error bars are 95% confidence intervals from 20 cells. Half recovery times between manual FRAP and Frapid are comparable and sufficiently similar to identify potent compounds. Error bars are standard error of mean.

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Fig. 10
Fig. 10 SPIN1. a) – Montage of U2OS cells expressing green fluorescent protein fused to wild-type SPIN1, wild-type SPIN1 treated with IOX1, or F141A mutant. White circle represents bleach region. b) - bar chart comparing half recovery time between F141A mutant, wildtype, or wildtype treated with IOX1. * represents p<0.005 determined by Wilcoxon Rank-Sum test. Error bars are standard deviation and each group represents 20 cells. c) – Fluorescence recovery curves over time comparing wildtype, F141A mutant, or wildtype treated with IOX1. Each curve is represented by 20 cells. Scale bar represents 5µm.

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Tables (3)

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Table 1 Acquisition parameters for Tilescan

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Table 2 Acquisition parameters for Imagescan

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Table 3 Acquisition parameters for FRAP

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Equations (3)

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F (t) norm = F (t) ROI −F (t) BG F (t) total −F (t) BG × F (p) total −F (p) BG F (p) ROI −F (p) BG
y=y0+A1(1−exp(−x/t1))+A2(1−exp(−x/t2))
y 1/2 =y0+ A1+A2 2

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