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Abstract:

Probing dynamic processes occurring within the cell nucleus at the quantitative level has long been a challenge in mammalian biology. Advances in bio-imaging techniques over the past decade have enabled us to directly visualize nuclear processes in situ with unprecedented spatial and temporal resolution and single-molecule sensitivity. Here, using transcription as our primary focus, we survey recent imaging studies that specifically emphasize the quantitative understanding of nuclear dynamics in both time and space. These analyses not only inform on previously hidden physical parameters and mechanistic details, but also reveal a hierarchical organizational landscape for coordinating a wide range of transcriptional processes shared by mammalian systems of varying complexity, from single cells to whole embryos. © 2016 Plachta et al.

Registro:

Documento: Artículo
Título:Quantitative imaging of mammalian transcriptional dynamics: From single cells to whole embryos
Autor:Zhao, Z.W.; White, M.D.; Bissiere, S.; Levi, V.; Plachta, N.
Filiación:Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Conicet, C1428EHA, Argentina
Palabras clave:animal; cell nucleus; embryology; fluorescence microscopy; gene expression regulation; genetic epigenesis; genetics; mammal; single cell analysis; spatiotemporal analysis; transcription initiation; Animals; Cell Nucleus; Epigenesis, Genetic; Gene Expression Regulation; Mammals; Microscopy, Fluorescence; Single-Cell Analysis; Spatio-Temporal Analysis; Transcriptional Activation
Año:2016
Volumen:14
Número:1
DOI: http://dx.doi.org/10.1186/s12915-016-0331-9
Título revista:BMC Biology
Título revista abreviado:BMC Biol.
ISSN:17417007
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_17417007_v14_n1_p_Zhao

Referencias:

  • Misteli, T., Beyond the sequence: cellular organization of genome function (2007) Cell, 128 (4), pp. 787-800
  • Spector, D.L., Nuclear domains (2001) J Cell Sci, 114 (16), pp. 2891-2893
  • Phair, R.D., Misteli, T., High mobility of proteins in the mammalian cell nucleus (2000) Nature, 404 (6778), pp. 604-609
  • Kusumi, A., Tsunoyama, T.A., Hirosawa, K.M., Kasai, R.S., Fujiwara, T.K., Tracking single molecules at work in living cells (2014) Nat Chem Biol, 10 (7), pp. 524-532
  • Cognet, L., Leduc, C., Lounis, B., Advances in live-cell single-particle tracking and dynamic super-resolution imaging (2014) Curr Opin Chem Biol, 20, pp. 78-85
  • Zhao, Z., Probing the spatio-temporal organizations and dynamics of gene expression and DNA replication in the mammalian cell nucleus (2015) Doctoral dissertation, Harvard University, Graduate School of Arts, , http://nrs.harvard.edu/urn-3:HUL, Sciences. 2015 InstRepos:17463978
  • Tokunaga, M., Imamoto, N., Sakata-Sogawa, K., Highly inclined thin illumination enables clear single-molecule imaging in cells (2008) Nat Methods, 5 (2), pp. 159-161
  • Chen, B.-C., Legant, W.R., Wang, K., Shao, L., Milkie, D.E., Davidson, M.W., Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution (2014) Science, 346 (6208), p. 1257998
  • Gebhardt, J.C.M., Suter, D.M., Roy, R., Zhao, Z.W., Chapman, A.R., Basu, S., Single-molecule imaging of transcription factor binding to DNA in live mammalian cells (2013) Nat Methods, 10 (5), pp. 421-426
  • Ritter, J.G., Veith, R., Veenendaal, A., Siebrasse, J.P., Kubitscheck, U., Light sheet microscopy for single molecule tracking in living tissue (2010) PLoS One, 5 (7)
  • Cella Zanacchi, F., Lavagnino, Z., Perrone Donnorso, M., Bue, A., Furia, L., Faretta, M., Live-cell 3D super-resolution imaging in thick biological samples (2011) Nat Methods, 8 (12), pp. 1047-1049
  • Zhao, Z.W., Roy, R., Gebhardt, J.C.M., Suter, D.M., Chapman, A.R., Xie, X.S., Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy (2014) Proc Natl Acad Sci U S A, 111 (2), pp. 681-686
  • Gao, L., Shao, L., Higgins Christopher, D., Poulton John, S., Peifer, M., Davidson Michael, W., Noninvasive imaging beyond the diffraction limit of 3D dynamics in thickly fluorescent specimens (2012) Cell, 151 (6), pp. 1370-1385
  • Keppler, A., Gendreizig, S., Gronemeyer, T., Pick, H., Vogel, H., Johnsson, K., A general method for the covalent labeling of fusion proteins with small molecules in vivo (2003) Nat Biotech, 21 (1), pp. 86-89
  • Gautier, A., Juillerat, A., Heinis, C., Corrêa, I.R., Kindermann, M., Beaufils, F., An engineered protein tag for multiprotein labeling in living cells (2008) Chem Biol, 15 (2), pp. 128-136
  • Los, G.V., Encell, L.P., McDougall, M.G., Hartzell, D.D., Karassina, N., Zimprich, C., HaloTag: a novel protein labeling technology for cell imaging and protein analysis (2008) ACS Chem Biol, 3 (6), pp. 373-382
  • Bertrand, E., Chartrand, P., Schaefer, M., Shenoy, S.M., Singer, R.H., Long, R.M., Localization of ASH1 mRNA particles in living yeast (1998) Mol Cell, 2 (4), pp. 437-445
  • Chao, J.A., Patskovsky, Y., Almo, S.C., Singer, R.H., Structural basis for the coevolution of a viral RNA-protein complex (2008) Nat Struct Mol Biol, 15 (1), pp. 103-105
  • Nelles, D.A., Fang, M.Y., Connell, O.M.R., Xu, J.L., Markmiller, S.J., Doudna, J.A., Programmable RNA tracking in live cells with CRISPR/Cas9 (2016) Cell, 165 (2), pp. 488-496
  • Raj, A., Bogaard, P., Rifkin, S.A., Oudenaarden, A., Tyagi, S., Imaging individual mRNA molecules using multiple singly labeled probes (2008) Nat Methods, 5 (10), pp. 877-879
  • Ruan, Q., Cheng, M.A., Levi, M., Gratton, E., Mantulin, W.W., Spatial-temporal studies of membrane dynamics: scanning fluorescence correlation spectroscopy (SFCS) (2004) Biophys J, 87 (2), pp. 1260-1267
  • Dertinger, T., Pacheco, V., Hocht, I., Hartmann, R., Gregor, I., Enderlein, J., Two-focus fluorescence correlation spectroscopy: a new tool for accurate and absolute diffusion measurements (2007) ChemPhysChem, 8 (3), pp. 433-443
  • Burkhardt, M., Schwille, P., Electron multiplying CCD based detection for spatially resolved fluorescence correlation spectroscopy (2006) Opt Express, 14 (12), pp. 5013-5020
  • Bacia, K., Kim, S.A., Schwille, P., Fluorescence cross-correlation spectroscopy in living cells (2006) Nat Methods, 3 (2), pp. 83-89
  • Hebert, B., Costantino, S., Wiseman, P.W., Spatiotemporal image correlation spectroscopy (STICS) theory, verification, and application to protein velocity mapping in living CHO cells (2005) Biophys J, 88 (5), pp. 3601-3614
  • Digman, M.A., Brown, C.M., Sengupta, P., Wiseman, P.W., Horwitz, A.R., Gratton, E., Measuring fast dynamics in solutions and cells with a laser scanning microscope (2005) Biophys J, 89 (2), pp. 1317-1327
  • Hinde, E., Cardarelli, F., Digman, M.A., Gratton, E., In vivo pair correlation analysis of EGFP intranuclear diffusion reveals DNA-dependent molecular flow (2010) Proc Natl Acad Sci U S A, 107 (38), pp. 16560-16565
  • Elson, E.L., Fluorescence correlation spectroscopy: past, present, future (2011) Biophys J, 101 (12), pp. 2855-2870
  • Macháň, R., Wohland, T., Recent applications of fluorescence correlation spectroscopy in live systems (2014) FEBS Lett, 588 (19), pp. 3571-3584
  • Angiolini, J., Plachta, N., Mocskos, E., Levi, V., Exploring the dynamics of cell processes through simulations of fluorescence microscopy experiments (2015) Biophys J, 108 (11), pp. 2613-2618
  • Dix, J.A., Hom, E.F.Y., Verkman, A.S., Fluorescence correlation spectroscopy simulations of photophysical phenomena and molecular interactions: a molecular dynamics/Monte Carlo approach (2006) J Phys Chem B, 110 (4), pp. 1896-1906
  • Kaur, G., Costa, M.W., Nefzger, C.M., Silva, J., Fierro-González, J.C., Polo, J.M., Probing transcription factor diffusion dynamics in the living mammalian embryo with photoactivatable fluorescence correlation spectroscopy (2013) Nat Commun, 4, p. 1637
  • Capoulade, J., Wachsmuth, M., Hufnagel, L., Knop, M., Quantitative fluorescence imaging of protein diffusion and interaction in living cells (2011) Nat Biotech, 29 (9), pp. 835-839
  • Wohland, T., Shi, X., Sankaran, J., Stelzer, E.H.K., Single plane illumination fluorescence correlation spectroscopy (SPIM-FCS) probes inhomogeneous three-dimensional environments (2010) Opt Express, 18 (10), pp. 10627-10641
  • Chen, Y., Muller, J.D., So, P.T., Gratton, E., The photon counting histogram in fluorescence fluctuation spectroscopy (1999) Biophys J, 77 (1), pp. 553-567
  • Digman, M.A., Dalal, R., Horwitz, A.F., Gratton, E., Mapping the number of molecules and brightness in the laser scanning microscope (2008) Biophys J, 94 (6), pp. 2320-2332
  • Axelrod, D., Koppel, D.E., Schlessinger, J., Elson, E., Webb, W.W., Mobility measurement by analysis of fluorescence photobleaching recovery kinetics (1976) Biophys J, 16 (9), pp. 1055-1069
  • Lippincott-Schwartz, J., Altan-Bonnet, N., Patterson, G.H., Photobleaching and photoactivation: following protein dynamics in living cells (2003) Nat Cell Biol, 5, pp. 7-14
  • Dunn, G.A., Dobbie, I.M., Monypenny, J., Holt, M.R., Zicha, D., Fluorescence localization after photobleaching (FLAP): a new method for studying protein dynamics in living cells (2002) J Microscopy, 205 (1), pp. 109-112
  • Sprague, B.L., Pego, R.L., Stavreva, D.A., McNally, J.G., Analysis of binding reactions by fluorescence recovery after photobleaching (2004) Biophys J, 86 (6), pp. 3473-3495
  • Wüstner, D., Solanko, L.M., Lund, F.W., Sage, D., Schroll, H.J., Lomholt, M.A., Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation (2012) BMC Bioinformatics, 13 (1), p. 296
  • Mueller, F., Wach, P., McNally, J.G., Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved quantitative fluorescence recovery after photobleaching (2008) Biophys J, 94 (8), pp. 3323-3339
  • Mueller, F., Morisaki, T., Mazza, D., McNally, J.G., Minimizing the impact of photoswitching of fluorescent proteins on FRAP analysis (2012) Biophys J, 102 (7), pp. 1656-1665
  • Erdel, F., Rippe, K., Quantifying transient binding of ISWI chromatin remodelers in living cells by pixel-wise photobleaching profile evolution analysis (2012) Proc Natl Acad Sci U S A, 109 (47), pp. E3221-E3230
  • Zhao, Z.W., Gebhardt, J.C.M., Suter, D.M., Xie, X.S., Reply to "Convergence of chromatin binding estimates in live cells" (2013) Nat Methods, 10 (8), p. 692
  • Li, G.-W., Xie, X.S., Central dogma at the single-molecule level in living cells (2011) Nature, 475 (7356), pp. 308-315
  • Giannone, G., Hosy, E., Levet, F., Constals, A., Schulze, K., Sobolevsky Alexander, I., Dynamic superresolution imaging of endogenous proteins on living cells at ultra-high density (2010) Biophys J, 99 (4), pp. 1303-1310
  • Manley, S., Gillette, J.M., Patterson, G.H., Shroff, H., Hess, H.F., Betzig, E., High-density mapping of single-molecule trajectories with photoactivated localization microscopy (2008) Nat Methods, 5 (2), pp. 155-157
  • Lubeck, E., Cai, L., Single-cell systems biology by super-resolution imaging and combinatorial labeling (2012) Nat Methods, 9 (7), pp. 743-748
  • Coleman, R.A., Liu, Z., Darzacq, X., Tjian, R., Singer, R.H., Lionnet, T., Imaging transcription: past, present, and future (2015) Cold Spring Harb Symp Quant Biol, 80, pp. 1-8
  • Coulon, A., Chow, C.C., Singer, R.H., Larson, D.R., Eukaryotic transcriptional dynamics: from single molecules to cell populations (2013) Nat Rev Genet, 14 (8), pp. 572-584
  • Darzacq, X., Yao, J., Larson, D.R., Causse, S.Z., Bosanac, L., Turris, V., Imaging transcription in living cells (2009) Annu Rev Biophys, 38 (1), pp. 173-196
  • Voss, T.C., Hager, G.L., Dynamic regulation of transcriptional states by chromatin and transcription factors (2014) Nat Rev Genet, 15 (2), pp. 69-81
  • Hager, G.L., McNally, J.G., Misteli, T., Transcription dynamics (2009) Mol Cell, 35 (6), pp. 741-753
  • McNally, J.G., Müller, W.G., Walker, D., Wolford, R., Hager, G.L., The glucocorticoid receptor: rapid exchange with regulatory sites in living cells (2000) Science, 287 (5456), pp. 1262-1265
  • MacQuarrie, K.L., Fong, A.P., Morse, R.H., Tapscott, S.J., Genome-wide transcription factor binding: beyond direct target regulation (2011) Trends Genet, 27 (4), pp. 141-148
  • Becker, M., Baumann, C., John, S., Walker, D.A., Vigneron, M., McNally, J.G., Dynamic behavior of transcription factors on a natural promoter in living cells (2002) EMBO Rep, 3 (12), pp. 1188-1194
  • Mikuni, S., Tamura, M., Kinjo, M., Analysis of intranuclear binding process of glucocorticoid receptor using fluorescence correlation spectroscopy (2007) FEBS Lett, 581 (3), pp. 389-393
  • Morisaki, T., Müller, W.G., Golob, N., Mazza, D., McNally, J.G., Single-molecule analysis of transcription factor binding at transcription sites in live cells (2014) Nat Commun, 5, p. 4456
  • Stasevich, T.J., Mueller, F., Michelman-Ribeiro, A., Rosales, T., Knutson, J.R., McNally, J.G., Cross-validating FRAP and FCS to quantify the impact of photobleaching on in vivo binding estimates (2010) Biophys J, 99 (9), pp. 3093-3101
  • Swinstead, E.E., Miranda, T.B., Paakinaho, V., Baek, S., Goldstein, I., Hawkins, M., Steroid receptors reprogram FoxA1 occupancy through dynamic chromatin transitions (2016) Cell, 165 (3), pp. 593-605
  • Nenseth, H.Z., Dezitter, X., Tesikova, M., Mueller, F., Klokk, T.I., Hager, G.L., Distinctly different dynamics and kinetics of two steroid receptors at the same response elements in living cells (2014) PLoS One, 9 (8)
  • Savatier, J., Jalaguier, S., Ferguson, M.L., Cavaillès, V., Royer, C.A., Estrogen receptor interactions and dynamics monitored in live cells by fluorescence cross-correlation spectroscopy (2010) Biochemistry, 49 (4), pp. 772-781
  • Chen, J., Zhang, Z., Li, L., Chen, B.-C., Revyakin, A., Hajj, B., Single-molecule dynamics of enhanceosome assembly in embryonic stem cells (2014) Cell, 156 (6), pp. 1274-1285
  • Liu, Z., Legant, W.R., Chen, B.-C., Li, L., Grimm, J.B., Lavis, L.D., 3D imaging of Sox2 enhancer clusters in embryonic stem cells (2014) eLife, 3
  • White, M.D., Angiolini, J.F., Alvarez, Y.D., Kaur, G., Zhao, Z.W., Mocskos, E., Long-lived binding of Sox2 to DNA predicts cell fate in the four-cell mouse embryo (2016) Cell, 165 (1), pp. 75-87
  • Mazza, D., Abernathy, A., Golob, N., Morisaki, T., McNally, J.G., A benchmark for chromatin binding measurements in live cells (2012) Nucleic Acids Res, 40 (15)
  • Hinow, P., Rogers, C.E., Barbieri, C.E., Pietenpol, J.A., Kenworthy, A.K., DiBenedetto, E., The DNA binding activity of p53 displays reaction-diffusion kinetics (2006) Biophys J, 91 (1), pp. 330-342
  • Izeddin, I., Récamier, V., Bosanac, L., Cissé, I.I., Boudarene, L., Dugast-Darzacq, C., Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus (2014) eLife, 3
  • Sugo, N., Morimatsu, M., Arai, Y., Kousoku, Y., Ohkuni, A., Nomura, T., Single-molecule imaging reveals dynamics of CREB transcription factor bound to its target sequence (2015) Sci Rep, 5, p. 10662
  • Speil, J., Baumgart, E., Siebrasse, J.-P., Veith, R., Vinkemeier, U., Kubitscheck, U., Activated STAT1 transcription factors conduct distinct saltatory movements in the cell nucleus (2011) Biophys J, 101 (11), pp. 2592-2600
  • Brazda, P., Szekeres, T., Bravics, B., Tóth, K., Vámosi, G., Nagy, L., Live-cell fluorescence correlation spectroscopy dissects the role of coregulator exchange and chromatin binding in retinoic acid receptor mobility (2011) J Cell Sci, 124 (21), pp. 3631-3642
  • Michelman-Ribeiro, A., Mazza, D., Rosales, T., Stasevich, T.J., Boukari, H., Rishi, V., Direct measurement of association and dissociation rates of DNA binding in live cells by fluorescence correlation spectroscopy (2009) Biophys J, 97 (1), pp. 337-346
  • Kloster-Landsberg, M., Herbomel, G., Wang, I., Derouard, J., Vourc'h, C., Usson, Y., Cellular response to heat shock studied by multiconfocal fluorescence correlation spectroscopy (2012) Biophys J, 103 (6), pp. 1110-1119
  • Mazza, D., Mueller, F., Stasevich, T.J., McNally, J.G., Convergence of chromatin binding estimates in live cells (2013) Nat Methods, 10 (8), pp. 691-692
  • Elf, J., Li, G.-W., Xie, X.S., Probing transcription factor dynamics at the single-molecule level in a living cell (2007) Science, 316 (5828), pp. 1191-1194
  • Berg, O.G., Winter, R.B., Hippel, P.H., Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory (1981) Biochemistry, 20 (24), pp. 6929-6948
  • Normanno, D., Boudarene, L., Dugast-Darzacq, C., Chen, J., Richter, C., Proux, F., Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher (2015) Nat Commun, 6, p. 7357
  • Knight, S.C., Xie, L., Deng, W., Guglielmi, B., Witkowsky, L.B., Bosanac, L., Dynamics of CRISPR-Cas9 genome interrogation in living cells (2015) Science, 350 (6262), pp. 823-826
  • Plachta, N., Bollenbach, T., Pease, S., Fraser, S.E., Pantazis, P., Oct4 kinetics predict cell lineage patterning in the early mammalian embryo (2011) Nat Cell Biol, 13 (2), pp. 117-123
  • Bartman, C.R., Hsu, S.C., Hsiung, C.C.S., Raj, A., Blobel, G.A., Enhancer regulation of transcriptional bursting parameters revealed by forced chromatin looping (2016) Mol Cell, 62 (2), pp. 237-247
  • Larson, D.R., Fritzsch, C., Sun, L., Meng, X., Lawrence, D.S., Singer, R.H., Direct observation of frequency modulated transcription in single cells using light activation (2013) eLife, 2
  • Molina, N., Suter, D.M., Cannavo, R., Zoller, B., Gotic, I., Naef, F., Stimulus-induced modulation of transcriptional bursting in a single mammalian gene (2013) Proc Natl Acad Sci U S A, 110 (51), pp. 20563-20568
  • Raj, A., Peskin, C.S., Tranchina, D., Vargas, D.Y., Tyagi, S., Stochastic mRNA synthesis in mammalian cells (2006) PLoS Biol, 4 (10)
  • Senecal, A., Munsky, B., Proux, F., Ly, N., Braye Floriane, E., Zimmer, C., Transcription factors modulate c-Fos transcriptional bursts (2014) Cell Rep, 8 (1), pp. 75-83
  • Singh, A., Razooky, B., Cox, C.D., Simpson, M.L., Weinberger, L.S., Transcriptional bursting from the HIV-1 promoter is a significant source of stochastic noise in HIV-1 gene expression (2010) Biophys J, 98 (8), pp. L32-L34
  • Suter, D.M., Molina, N., Gatfield, D., Schneider, K., Schibler, U., Naef, F., Mammalian genes are transcribed with widely different bursting kinetics (2011) Science, 332 (6028), pp. 472-474
  • Dar, R.D., Razooky, B.S., Singh, A., Trimeloni, T.V., McCollum, J.M., Cox, C.D., Transcriptional burst frequency and burst size are equally modulated across the human genome (2012) Proc Natl Acad Sci U S A, 109 (43), pp. 17454-17459
  • Singer, Z.S., Yong, J., Tischler, J., Hackett, J.A., Altinok, A., Surani, M.A., Dynamic heterogeneity and DNA methylation in embryonic stem cells (2014) Mol Cell, 55 (2), pp. 319-331
  • Bahar Halpern, K., Tanami, S., Landen, S., Chapal, M., Szlak, L., Hutzler, A., Bursty gene expression in the intact mammalian liver (2015) Mol Cell, 58 (1), pp. 147-156
  • Raj, A., Oudenaarden, A., Nature, nurture, or chance: stochastic gene expression and its consequences (2008) Cell, 135 (2), pp. 216-226
  • Eldar, A., Elowitz, M.B., Functional roles for noise in genetic circuits (2010) Nature, 467 (7312), pp. 167-173
  • Abranches, E., Guedes, A.M.V., Moravec, M., Maamar, H., Svoboda, P., Raj, A., Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency (2014) Development, 141 (14), pp. 2770-2779
  • Jackson, D.A., Hassan, A.B., Errington, R.J., Cook, P.R., Visualization of focal sites of transcription within human nuclei (1993) EMBO J, 12, pp. 1059-1065
  • Wansink, D.G., Schul, W., Kraan, I., Steensel, B., Driel, R., Jong, L., Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus (1993) J Cell Biol, 122 (2), pp. 283-293
  • Cho, W.-K., Jayanth, N., English, B.P., Inoue, T., Andrews, J.O., Conway, W., RNA polymerase II cluster dynamics predict mRNA output in living cells (2016) eLife, 5
  • Cisse, I.I., Izeddin, I., Causse, S.Z., Boudarene, L., Senecal, A., Muresan, L., Real-time dynamics of RNA polymerase II clustering in live human cells (2013) Science, 341 (6146), pp. 664-667
  • Chen, X., Wei, M., Zheng, M.M., Zhao, J., Hao, H., Chang, L., Study of RNA polymerase II clustering inside live-cell nuclei using Bayesian nanoscopy (2016) ACS Nano, 10 (2), pp. 2447-2454
  • Ghamari, A., Corput, M.P.C., Thongjuea, S., Cappellen, W.A., IJcken, W., Haren, J., In vivo live imaging of RNA polymerase II transcription factories in primary cells (2013) Genes Dev, 27 (7), pp. 767-777
  • Nelson, D.E., Ihekwaba, A.E.C., Elliott, M., Johnson, J.R., Gibney, C.A., Foreman, B.E., Oscillations in NF-ΚB signaling control the dynamics of gene expression (2004) Science, 306 (5696), pp. 704-708
  • Tay, S., Hughey, J.J., Lee, T.K., Lipniacki, T., Quake, S.R., Covert, M.W., Single-cell NF-ΚB dynamics reveal digital activation and analogue information processing (2010) Nature, 466 (7303), pp. 267-271
  • Ashall, L., Horton, C.A., Nelson, D.E., Paszek, P., Harper, C.V., Sillitoe, K., Pulsatile stimulation determines timing and specificity of NF-ΚB-dependent transcription (2009) Science, 324 (5924), pp. 242-246
  • Turner, D.A., Paszek, P., Woodcock, D.J., Nelson, D.E., Horton, C.A., Wang, Y., Physiological levels of TNFα stimulation induce stochastic dynamics of NF-ΚB responses in single living cells (2010) J Cell Sci, 123 (16), pp. 2834-2843
  • Sero, J.E., Sailem, H.Z., Ardy, R.C., Almuttaqi, H., Zhang, T., Bakal, C., Cell shape and the microenvironment regulate nuclear translocation of NF-ΚB in breast epithelial and tumor cells (2015) Mol Syst Biol, 11 (3), p. 790
  • Moss, B.L., Elhammali, A., Fowlkes, T., Gross, S., Vinjamoori, A., Contag, C.H., Interrogation of inhibitor of nuclear factor ΚB α/nuclear factor ΚB (IΚBα/NF-ΚB) negative feedback loop dynamics: from single cells to live animals in vivo (2012) J Biol Chem, 287 (37), pp. 31359-31370
  • Yissachar, N., Sharar Fischler, T., Cohen Ariel, A., Reich-Zeliger, S., Russ, D., Shifrut, E., Dynamic response diversity of NFAT isoforms in individual living cells (2013) Mol Cell, 49 (2), pp. 322-330
  • Nguyen, H.Q., Bosco, G., Gene positioning effects on expression in eukaryotes (2015) Annu Rev Genet, 49 (1), pp. 627-646
  • Hübner, M.R., Eckersley-Maslin, M.A., Spector, D.L., Chromatin organization and transcriptional regulation (2013) Curr Opin Genet Dev, 23 (2), pp. 89-95
  • Cremer, T., Cremer, M., Chromosome territories (2010) Cold Spring Harb Perspect Biol, 2 (3)
  • Verschure, P.J., Kraan, I., Manders, E.M.M., Driel, R., Spatial relationship between transcription sites and chromosome territories (1999) J Cell Biol, 147 (1), pp. 13-24
  • Kurz, A., Lampel, S., Nickolenko, J.E., Bradl, J., Benner, A., Zirbel, R.M., Active and inactive genes localize preferentially in the periphery of chromosome territories (1996) J Cell Biol, 135 (5), pp. 1195-1205
  • Clemson, C.M., Hall, L.L., Byron, M., McNeil, J., Lawrence, J.B., The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences (2006) Proc Natl Acad Sci U S A, 103 (20), pp. 7688-7693
  • Reddy, K.L., Zullo, J.M., Bertolino, E., Singh, H., Transcriptional repression mediated by repositioning of genes to the nuclear lamina (2008) Nature, 452 (7184), pp. 243-247
  • Chen, C.-K., Blanco, M., Jackson, C., Aznauryan, E., Ollikainen, N., Surka, C., Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing (2016) Science, 354 (6311), pp. 468-472
  • Lahav, G., Rosenfeld, N., Sigal, A., Geva-Zatorsky, N., Levine, A.J., Elowitz, M.B., Dynamics of the p53-Mdm2 feedback loop in individual cells (2004) Nat Genet, 36 (2), pp. 147-150
  • Hamstra, D.A., Bhojani, M.S., Griffin, L.B., Laxman, B., Ross, B.D., Rehemtulla, A., Real-time evaluation of p53 oscillatory behavior in vivo using bioluminescent imaging (2006) Cancer Res, 66 (15), pp. 7482-7489
  • Loewer, A., Batchelor, E., Gaglia, G., Lahav, G., Basal dynamics of p53 reveal transcriptionally attenuated pulses in cycling cells (2010) Cell, 142 (1), pp. 89-100
  • Purvis, J.E., Karhohs, K.W., Mock, C., Batchelor, E., Loewer, A., Lahav, G., p53 dynamics control cell fate (2012) Science, 336 (6087), pp. 1440-1444
  • Batchelor, E., Loewer, A., Mock, C., Lahav, G., Stimulus-dependent dynamics of p53 in single cells (2011) Mol Syst Biol, 7 (1), p. 488
  • Lee, R.E.C., Walker, S.R., Savery, K., Frank, D.A., Gaudet, S., Fold change of nuclear NF-ΚB determines TNF-induced transcription in single cells (2014) Mol Cell, 53 (6), pp. 867-879
  • Gaglia, G., Guan, Y., Shah, J.V., Lahav, G., Activation and control of p53 tetramerization in individual living cells (2013) Proc Natl Acad Sci U S A, 110 (38), pp. 15497-15501
  • Hinde, E., Yokomori, K., Gaus, K., Hahn, K.M., Gratton, E., Fluctuation-based imaging of nuclear Rac1 activation by protein oligomerisation (2014) Sci Rep, 4, p. 4219
  • Hinde, E., Cardarelli, F., Gratton, E., Spatiotemporal regulation of Heterochromatin Protein 1- alpha oligomerization and dynamics in live cells (2015) Sci Rep, 5, p. 12001
  • Hinde, E., Pandzic, E., Yang, Z., Ng, I.H.W., Jans, D.A., Bogoyevitch, M.A., Quantifying the dynamics of the oligomeric transcription factor STAT3 by pair correlation of molecular brightness (2016) Nat Commun, 7, p. 11047
  • Stasevich, T.J., Hayashi-Takanaka, Y., Sato, Y., Maehara, K., Ohkawa, Y., Sakata-Sogawa, K., Regulation of RNA polymerase II activation by histone acetylation in single living cells (2014) Nature, 516 (7530), pp. 272-275
  • Bintu, L., Yong, J., Antebi, Y.E., McCue, K., Kazuki, Y., Uno, N., Dynamics of epigenetic regulation at the single-cell level (2016) Science, 351 (6274), pp. 720-724
  • Chen, K.H., Boettiger, A.N., Moffitt, J.R., Wang, S., Zhuang, X., Spatially resolved, highly multiplexed RNA profiling in single cells (2015) Science, 348 (6233)
  • Coskun, A.F., Cai, L., Dense transcript profiling in single cells by image correlation decoding (2016) Nat Methods, 13, pp. 657-660
  • Jungmann, R., Avendano, M.S., Woehrstein, J.B., Dai, M., Shih, W.M., Yin, P., Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT (2014) Nat Methods, 11 (3), pp. 313-318
  • Almassalha, L.M., Bauer, G.M., Chandler, J.E., Gladstein, S., Cherkezyan, L., Stypula-Cyrus, Y., Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy (2016) Proc Natl Acad Sci U S A, 113 (42), pp. E6372-E6381
  • Lu, F.-K., Basu, S., Igras, V., Hoang, M.P., Ji, M., Fu, D., Label-free DNA imaging in vivo with stimulated Raman scattering microscopy (2015) Proc Natl Acad Sci U S A, 112 (37), pp. 11624-11629

Citas:

---------- APA ----------
Zhao, Z.W., White, M.D., Bissiere, S., Levi, V. & Plachta, N. (2016) . Quantitative imaging of mammalian transcriptional dynamics: From single cells to whole embryos. BMC Biology, 14(1).
http://dx.doi.org/10.1186/s12915-016-0331-9
---------- CHICAGO ----------
Zhao, Z.W., White, M.D., Bissiere, S., Levi, V., Plachta, N. "Quantitative imaging of mammalian transcriptional dynamics: From single cells to whole embryos" . BMC Biology 14, no. 1 (2016).
http://dx.doi.org/10.1186/s12915-016-0331-9
---------- MLA ----------
Zhao, Z.W., White, M.D., Bissiere, S., Levi, V., Plachta, N. "Quantitative imaging of mammalian transcriptional dynamics: From single cells to whole embryos" . BMC Biology, vol. 14, no. 1, 2016.
http://dx.doi.org/10.1186/s12915-016-0331-9
---------- VANCOUVER ----------
Zhao, Z.W., White, M.D., Bissiere, S., Levi, V., Plachta, N. Quantitative imaging of mammalian transcriptional dynamics: From single cells to whole embryos. BMC Biol. 2016;14(1).
http://dx.doi.org/10.1186/s12915-016-0331-9