SEARCH

SEARCH BY CITATION

References

  • Acar, M., Becskei, A. & van Oudenaarden, A. 2005. Enhancement of cellular memory by reducing stochastic transitions. Nature 435, 228232.
  • Aebersold, R. & Mann, M. 2003. Mass spectrometry-based proteomics. Nature 422, 198207.
  • Ahmad, K. & Henikoff, S. 2002. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell 9, 11911200.
  • Bai, L., Charvin, G., Siggia, E. D. & Cross, F. R. 2010. Nucleosome-depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle. Dev. Cell 18, 544555.
  • Balbo, A. & Bozzaro, S. 2006. Cloning of Dictyostelium eIF6 (p27BBP) and mapping its nucle(ol)ar localization subdomains. Eur. J. Cell Biol. 85, 10691078.
  • Bar-Even, A., Paulsson, J., Maheshri, N., Carmi, M., O’shea, E., Pilpel, Y. & Barkai, N. 2006. Noise in protein expression scales with natural protein abundance. Nat. Genet. 38, 636643.
  • Becskei, A., Seraphin, B. & Serrano, L. 2001. Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J. 20, 25282535.
  • Bertrand, E., Chartrand, P., Schaefer, M., Shenoy, S. M., Singer, R. H. & Long, R. M. 1998. Localization of ASH1 mRNA particles in living yeast. Mol. Cell 2, 437445.
  • Boireau, S., Maiuri, P., Basyuk, E., De La Mata, M., Knezevich, A., Pradet-Balade, B., Backer, V., Kornblihtt, A., Marcello, A. & Bertrand, E. 2007. The transcriptional cycle of HIV-1 in real-time and live cells. J. Cell Biol. 179, 291304.
  • Brickner, D. G., Cajigas, I., Fondufe-Mittendorf, Y., Ahmed, S., Lee, P. C., Widom, J. & Brickner, J. H. 2007. H2A.Z-mediated localization of genes at the nuclear periphery confers epigenetic memory of previous transcriptional state. PLoS Biol. 5, e81.
  • Brooks, R. F. 1981. Random transitions and cell cycle control. Prog. Clin. Biol. Res. 66 (Pt A), 593601.
  • Chambers, I., Silva, J., Colby, D., Nichols, J., Nijmeijer, B., Robertson, M., Vrana, J., Jones, K., Grotewold, L. & Smith, A. 2007. Nanog safeguards pluripotency and mediates germline development. Nature 450, 12301234.
  • Chang, H. H., Hemberg, M., Barahona, M., Ingber, D. E. & Huang, S. 2008. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature 453, 544547.
  • Charlesworth, M. C. & Parish, R. W. 1975. The isolation of nuclei and basic nucleoproteins from the cellular slime mold Dictyostelium discoideum. Eur. J. Biochem. 54, 307316.
  • Chubb, J. R., Bloomfield, G., Xu, Q., Kaller, M., Ivens, A., Skelton, J., Turner, B. M., Nellen, W., Shaulsky, G., Kay, R. R., Bickmore, W. A. & Singer, R. H. 2006a. Developmental timing in Dictyostelium is regulated by the Set1 histone methyltransferase. Dev. Biol. 292, 519532.
  • Chubb, J. R. & Liverpool, T. B. 2010. Bursts and pulses: insights from single cell studies into transcriptional mechanisms. Curr. Opin. Genet. Dev. 20, 478484.
  • Chubb, J. R., Trcek, T., Shenoy, S. M. & Singer, R. H. 2006b. Transcriptional pulsing of a developmental gene. Curr. Biol. 16, 10181025.
  • Clarke, M. & Gomer, R. H. 1995. PSF and CMF, autocrine factors that regulate gene expression during growth and early development of Dictyostelium. Experientia 51, 11241134.
  • Darzacq, X., Shav-Tal, Y., De Turris, V., Brody, Y., Shenoy, S. M., Phair, R. D. & Singer, R. H. 2007. In vivo dynamics of RNA polymerase II transcription. Nat. Struct. Mol. Biol. 14, 796806.
  • Davila Lopez, M. & Samuelsson, T. 2008. Early evolution of histone mRNA 3′ end processing. RNA 14, 110.
  • Dong, G. Q. & Mcmillen, D. R. 2008. Effects of protein maturation on the noise in gene expression. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 77, 021908.
  • Dubin, M., Fuchs, J., Graf, R., Schubert, I. & Nellen, W. 2010. Dynamics of a novel centromeric histone variant CenH3 reveals the evolutionary ancestral timing of centromere biogenesis. Nucleic Acids Res. 38, 75267537.
  • Eichinger, L., Pachebat, J. A., Glockner, G., Rajandream, M. A., Sucgang, R., Berriman, M., Song, J., Olsen, R., Szafranski, K., Xu, Q., Tunggal, B., Kummerfeld, S., Madera, M., Konfortov, B. A., Rivero, F., Bankier, A. T., Lehmann, R., Hamlin, N., Davies, R., Gaudet, P., Fey, P., Pilcher, K., Chen, G., Saunders, D., Sodergren, E., Davis, P., Kerhornou, A., Nie, X., Hall, N., Anjard, C., Hemphill, L., Bason, N., Farbrother, P., Desany, B., Just, E., Morio, T., Rost, R., Churcher, C., Cooper, J., Haydock, S., Van Driessche, N., Cronin, A., Goodhead, I., Muzny, D., Mourier, T., Pain, A., Lu, M., Harper, D., Lindsay, R., Hauser, H., James, K., Quiles, M., Madan Babu, M., Saito, T., Buchrieser, C., Wardroper, A., Felder, M., Thangavelu, M., Johnson, D., Knights, A., Loulseged, H., Mungall, K., Oliver, K., Price, C., Quail, M. A., Urushihara, H., Hernandez, J., Rabbinowitsch, E., Steffen, D., Sanders, M., Ma, J., Kohara, Y., Sharp, S., Simmonds, M., Spiegler, S., Tivey, A., Sugano, S., White, B., Walker, D., Woodward, J., Winckler, T., Tanaka, Y., Shaulsky, G., Schleicher, M., Weinstock, G., Rosenthal, A., Cox, E. C., Chisholm, R. L., Gibbs, R., Loomis, W. F., Platzer, M., Kay, R. R., Williams, J., Dear, P. H., Noegel, A. A., Barrell, B. & Kuspa, A. 2005. The genome of the social amoeba Dictyostelium discoideum. Nature 435, 4357.
  • Elowitz, M. B., Levine, A. J., Siggia, E. D. & Swain, P. S. 2002. Stochastic gene expression in a single cell. Science 297, 11831186.
  • Elsaesser, S. J., Goldberg, A. D. & Allis, C. D. 2010. New functions for an old variant: no substitute for histone H3.3. Curr. Opin. Genet. Dev. 20, 110117.
  • Emery, H. S. & Weiner, A. M. 1981. An irregular satellite sequence is found at the termini of the linear extrachromosomal rDNA in Dictyostelium discoideum. Cell 26, 411419.
  • Femino, A. M., Fay, F. S., Fogarty, K. & Singer, R. H. 1998. Visualization of single RNA transcripts in situ. Science 280, 585590.
  • Gandhi, S. J., Zenklusen, D., Lionnet, T. & Singer, R. H. 2011. Transcription of functionally related constitutive genes is not coordinated. Nat. Struct. Mol. Biol. 18, 2734.
  • Garcia, B. A., Hake, S. B., Diaz, R. L., Kauer, M., Morris, S. A., Recht, J., Shabanowitz, J., Mishra, N., Strahl, B. D., Allis, C. D. & Hunt, D. F. 2007. Organismal differences in post-translational modifications in histones H3 and H4. J. Biol. Chem. 282, 76417655.
  • Gillespie, P. J. & Blow, J. J. 2010. Clusters, factories and domains: the complex structure of S-phase comes into focus. Cell Cycle 9, 32183226.
  • Glockner, G. & Heidel, A. J. 2009. Centromere sequence and dynamics in Dictyostelium discoideum. Nucleic Acids Res. 37, 18091816.
  • Golding, I., Paulsson, J., Zawilski, S. M. & Cox, E. C. 2005. Real-time kinetics of gene activity in individual bacteria. Cell 123, 10251036.
  • Gregor, T., Tank, D. W., Wieschaus, E. F. & Bialek, W. 2007. Probing the limits to positional information. Cell 130, 153164.
  • Huang, S. 2009. Reprogramming cell fates: reconciling rarity with robustness. Bioessays 31, 546560.
  • Hudson, J. J., Hsu, D. W., Guo, K., Zhukovskaya, N., Liu, P. H., Williams, J. G., Pears, C. J. & Lakin, N. D. 2005. DNA-PKcs-dependent signaling of DNA damage in Dictyostelium discoideum. Curr. Biol. 15, 18801885.
  • Huh, D. & Paulsson, J. 2011. Non-genetic heterogeneity from stochastic partitioning at cell division. Nat. Genet. 43, 95100.
  • Janicki, S. M., Tsukamoto, T., Salghetti, S. E., Tansey, W. P., Sachidanandam, R., Prasanth, K. V., Ried, T., Shav-Tal, Y., Bertrand, E., Singer, R. H. & Spector, D. L. 2004. From silencing to gene expression: real-time analysis in single cells. Cell 116, 683698.
  • Kaller, M., Euteneuer, U. & Nellen, W. 2006a. Differential effects of heterochromatin protein 1 isoforms on mitotic chromosome distribution and growth in Dictyostelium discoideum. Eukaryot. Cell 5, 530543.
  • Kaller, M., Nellen, W. & Chubb, J. R. 2006b. Epigenetics in Dictyostelium. Methods Mol. Biol. 346, 491505.
  • Kalmar, T., Lim, C., Hayward, P., Munoz-Descalzo, S., Nichols, J., Garcia-Ojalvo, J. & Martinez Arias, A. 2009. Regulated fluctuations in nanog expression mediate cell fate decisions in embryonic stem cells. PLoS Biol. 7, e1000149.
  • Katoh, M., Curk, T., Xu, Q., Zupan, B., Kuspa, A. & Shaulsky, G. 2006. Developmentally regulated DNA methylation in Dictyostelium discoideum. Eukaryot. Cell 5, 1825.
  • Katz, D. J., Edwards, T. M., Reinke, V. & Kelly, W. G. 2009. A C. elegans LSD1 demethylase contributes to germline immortality by reprogramming epigenetic memory. Cell 137, 308320.
  • Kim, T. & Buratowski, S. 2009. Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5′ transcribed regions. Cell 137, 259272.
  • Ko, M. S., Nakauchi, H. & Takahashi, N. 1990. The dose dependence of glucocorticoid-inducible gene expression results from changes in the number of transcriptionally active templates. EMBO J. 9, 28352842.
  • Kouzarides, T. 2007. Chromatin modifications and their function. Cell 128, 693705.
  • Kuhlmann, M., Borisova, B. E., Kaller, M., Larsson, P., Stach, D., Na, J., Eichinger, L., Lyko, F., Ambros, V., Soderbom, F., Hammann, C. & Nellen, W. 2005. Silencing of retrotransposons in Dictyostelium by DNA methylation and RNAi. Nucleic Acids Res. 33, 64056417.
  • Kundu, S., Horn, P. J. & Peterson, C. L. 2007. SWI/SNF is required for transcriptional memory at the yeast GAL gene cluster. Genes Dev. 21, 9971004.
  • Laine, J. P., Singh, B. N., Krishnamurthy, S. & Hampsey, M. 2009. A physiological role for gene loops in yeast. Genes Dev. 23, 26042609.
  • Lander, A. D. 2007. Morpheus unbound: reimagining the morphogen gradient. Cell 128, 245256.
  • Larson, D. R., Singer, R. H. & Zenklusen, D. 2009. A single molecule view of gene expression. Trends Cell Biol. 19, 630637.
  • Li, H., Ilin, S., Wang, W., Duncan, E. M., Wysocka, J., Allis, C. D. & Patel, D. J. 2006. Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature 442, 9195.
  • Lionnet, T., Czaplinski, K., Darzacq, X., Shav-Tal, Y., Wells, A. L., Chao, J. A., Park, H. Y., De Turris, V., Lopez-Jones, M. & Singer, R. H. 2011. A transgenic mouse for in vivo detection of endogenous labeled mRNA. Nat. Methods 8, 165170.
  • Losick, R. & Desplan, C. 2008. Stochasticity and cell fate. Science 320, 6568.
  • Malleshaiah, M. K., Shahrezaei, V., Swain, P. S. & Michnick, S. W. 2010. The scaffold protein Ste5 directly controls a switch-like mating decision in yeast. Nature 465, 101105.
  • Martin, S. E., Shabanowitz, J., Hunt, D. F. & Marto, J. A. 2000. Subfemtomole MS and MS/MS peptide sequence analysis using nano-HPLC micro-ESI fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 72, 42664274.
  • Moens, P. B. 1976. Spindle and kinetochore morphology of Dictyostelium discoideum. J. Cell Biol. 68, 113122.
  • Muramoto, T. & Chubb, J. R. 2008. Live imaging of the Dictyostelium cell cycle reveals widespread S phase during development, a G2 bias in spore differentiation and a premitotic checkpoint. Development 135, 16471657.
  • Muramoto, T., Muller, I., Thomas, G., Melvin, A. & Chubb, J. R. 2010. Methylation of H3K4 Is required for inheritance of active transcriptional states. Curr. Biol. 20, 397406.
  • Ng, R. K. & Gurdon, J. B. 2008. Epigenetic memory of an active gene state depends on histone H3.3 incorporation into chromatin in the absence of transcription. Nat. Cell Biol. 10, 102109.
  • Ozbudak, E. M., Thattai, M., Kurtser, I., Grossman, A. D. & van Oudenaarden, A. 2002. Regulation of noise in the expression of a single gene. Nat. Genet. 31, 6973.
  • Pare, A., Lemons, D., Kosman, D., Beaver, W., Freund, Y. & Mcginnis, W. 2009. Visualization of individual Scr mRNAs during Drosophila embryogenesis yields evidence for transcriptional bursting. Curr. Biol. 19, 20372042.
  • Perkins, D. N., Pappin, D. J., Creasy, D. M. & Cottrell, J. S. 1999. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 35513567.
  • Raj, A., Peskin, C. S., Tranchina, D., Vargas, D. Y. & Tyagi, S. 2006. Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 4, e309.
  • Raj, A., Rifkin, S. A., Andersen, E. & van Oudenaarden, A. 2010. Variability in gene expression underlies incomplete penetrance. Nature 463, 913918.
  • Raj, A., Van Den Bogaard, P., Rifkin, S. A., van Oudenaarden, A. & Tyagi, S. 2008. Imaging individual mRNA molecules using multiple singly labeled probes. Nat. Methods 5, 877879.
  • Raj, A. & van Oudenaarden, A. 2008. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135, 216226.
  • Raser, J. M. & O’shea, E. K. 2004. Control of stochasticity in eukaryotic gene expression. Science 304, 18111814.
  • Raser, J. M. & O’shea, E. K. 2005. Noise in gene expression: origins, consequences, and control. Science 309, 20102013.
  • Ringrose, L. & Paro, R. 2004. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu. Rev. Genet. 38, 413443.
  • Roesch, A., Fukunaga-Kalabis, M., Schmidt, E. C., Zabierowski, S. E., Brafford, P. A., Vultur, A., Basu, D., Gimotty, P., Vogt, T. & Herlyn, M. 2010. A temporarily distinct subpopulation of slow-cycling melanoma cells is required for continuous tumor growth. Cell 141, 583594.
  • Rutter, G. A., White, M. R. & Tavare, J. M. 1995. Involvement of MAP kinase in insulin signalling revealed by non-invasive imaging of luciferase gene expression in single living cells. Curr. Biol. 5, 890899.
  • Santos-Rosa, H., Schneider, R., Bernstein, B. E., Karabetsou, N., Morillon, A., Weise, C., Schreiber, S. L., Mellor, J. & Kouzarides, T. 2003. Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin. Mol. Cell 12, 13251332.
  • Sharma, S. V., Lee, D. Y., Li, B., Quinlan, M. P., Takahashi, F., Maheswaran, S., Mcdermott, U., Azizian, N., Zou, L., Fischbach, M. A., Wong, K. K., Brandstetter, K., Wittner, B., Ramaswamy, S., Classon, M. & Settleman, J. 2010. A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations. Cell 141, 6980.
  • Sigal, A., Milo, R., Cohen, A., Geva-Zatorsky, N., Klein, Y., Liron, Y., Rosenfeld, N., Danon, T., Perzov, N. & Alon, U. 2006. Variability and memory of protein levels in human cells. Nature 444, 643646.
  • Spencer, S. L., Gaudet, S., Albeck, J. G., Burke, J. M. & Sorger, P. K. 2009. Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Nature 459, 428432.
  • Stathopoulos, A., Van Drenth, M., Erives, A., Markstein, M. & Levine, M. 2002. Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo. Cell 111, 687701.
  • Stevense, M., Muramoto, T., Muller, I. & Chubb, J. R. 2010. Digital nature of the immediate-early transcriptional response. Development 137, 579584.
  • Sucgang, R., Chen, G., Liu, W., Lindsay, R., Lu, J., Muzny, D., Shaulsky, G., Loomis, W., Gibbs, R. & Kuspa, A. 2003. Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium. Nucleic Acids Res. 31, 23612368.
  • Tan-Wong, S. M., Wijayatilake, H. D. & Proudfoot, N. J. 2009. Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex. Genes Dev. 23, 26102624.
  • Urushihara, H., Morio, T. & Tanaka, Y. 2006. The cDNA sequencing project. Methods Mol. Biol. 346, 3149.
  • Verkerke-Van Wijk, I., Brandt, R., Bosman, L. & Schaap, P. 1998. Two distinct signaling pathways mediate DIF induction of prestalk gene expression in Dictyostelium. Exp. Cell Res. 245, 179185.
  • Vermeulen, M., Mulder, K. W., Denissov, S., Pijnappel, W. W., Van Schaik, F. M., Varier, R. A., Baltissen, M. P., Stunnenberg, H. G., Mann, M. & Timmers, H. T. 2007. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 131, 5869.
  • Vilar, J. M., Guet, C. C. & Leibler, S. 2003. Modeling network dynamics: the lac operon, a case study. J. Cell Biol. 161, 471476.
  • Voliotis, M., Cohen, N., Molina-Paris, C. & Liverpool, T. B. 2008. Fluctuations, pauses, and backtracking in DNA transcription. Biophys. J. 94, 334348.
  • Walters, M. C., Fiering, S., Eidemiller, J., Magis, W., Groudine, M. & Martin, D. I. 1995. Enhancers increase the probability but not the level of gene expression. Proc. Natl Acad. Sci. USA 92, 71257129.
  • Weijer, C. J., Duschl, G. & David, C. N. 1984. A revision of the Dictyostelium discoideum cell cycle. J. Cell Sci. 70, 111131.
  • Wysocka, J., Swigut, T., Xiao, H., Milne, T. A., Kwon, S. Y., Landry, J., Kauer, M., Tackett, A. J., Chait, B. T., Badenhorst, P., Wu, C. & Allis, C. D. 2006. A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. Nature 442, 8690.
  • Xiong, H., Rivero, F., Euteneuer, U., Mondal, S., Mana-Capelli, S., Larochelle, D., Vogel, A., Gassen, B. & Noegel, A. A. 2008. Dictyostelium Sun-1 connects the centrosome to chromatin and ensures genome stability. Traffic 9, 708724.
  • Yao, J., Munson, K. M., Webb, W. W. & Lis, J. T. 2006. Dynamics of heat shock factor association with native gene loci in living cells. Nature 442, 10501053.
  • Yunger, S., Rosenfeld, L., Garini, Y. & Shav-Tal, Y. 2010. Single-allele analysis of transcription kinetics in living mammalian cells. Nat. Methods 7, 631633.
  • Zacharioudakis, I., Gligoris, T. & Tzamarias, D. 2007. A yeast catabolic enzyme controls transcriptional memory. Curr. Biol. 17, 20412046.
  • Zeitlinger, J., Zinzen, R. P., Stark, A., Kellis, M., Zhang, H., Young, R. A. & Levine, M. 2007. Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes Dev. 21, 385390.
  • Zenklusen, D., Larson, D. R. & Singer, R. H. 2008. Single-RNA counting reveals alternative modes of gene expression in yeast. Nat. Struct. Mol. Biol. 15, 12631271.