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Temporal Partitioning of the Yeast Cellular Network

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Book cover Systems Biology of Metabolic and Signaling Networks

Part of the book series: Springer Series in Biophysics ((BIOPHYSICS,volume 16))

Abstract

A plethora of data is accumulating from high throughput methods on metabolites, coenzymes, proteins, lipids and nucleic acids and their interactions as well as the signalling and regulatory functions and pathways of the cellular network. The frozen moment viewed in a single discrete time sample requires frequent repetition and updating before any appreciation of the dynamics of component interaction becomes possible. Even then in a sample derived from a cell population, time-averaging of processes and events that occur in out-of-phase individuals blur the detailed complexity of single cell.

Continuously grown cultures of yeast spontaneously self-synchronise and provide resolution of detailed temporal structure. Continuous online monitoring (O2 electrode and membrane-inlet mass spectrometry for O2, CO2 and H2S; direct fluorimetry for NAD(P)H and flavins) gives dynamic information from timescales of minutes to hours. When these data are supplemented with mass spectrometry-based metabolomics and transcriptomics, the predominantly oscillatory behaviour of network components becomes evident, where respiration cycles between increased oxygen consumption (oxidative phase) and decreased oxygen consumption (reductive phase). This ultradian clock provides a coordinating function that links mitochondrial energetics and redox balance to transcriptional regulation, mitochondrial structure and organelle remodelling, DNA duplication and chromatin dynamics. Ultimately, anabolism and catabolism become globally partitioned: mediation is by direct feedback loops between the energetic and redox state of the cell and chromatin architecture via enzymatic co-factors and co-enzymes.

Multi-oscillatory outputs were observed in dissolved gases with 12-h, 40-min and 4-min periods, and statistical self-similarity in Power Spectral and Relative Dispersional analyses: i.e. complex non-linear behaviour and a functional scale-free network operating simultaneously on several timescales. Fast sampling (at 10 or 1 Hz) of NAD(P)H fluorescence revealed subharmonic components of the 40-min signal at 20,10 and 3–5 min. The latter corresponds to oscillations directly observed and imaged by 2-photon microscopy in surface-attached cells. Signalling between time domains is suggested by studies with protonophore effectors of mitochondrial energetics. Multi-oscillatory states impinge on the complex reactome (where concentrations of most chemical species oscillate) and network functionality is made more comprehensible when in vivo time structure is taken into account.

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References

  • Akiyama S, Tsurugi K (2003) The GTS1 gene product facilitates the self-organization of the energy metabolism oscillation in the continuous culture of the yeast Saccharomyces cerevisiae. FEMS Microbiol Lett 228:105–10

    Article  PubMed  CAS  Google Scholar 

  • Aon MA, Cortassa S (1997) Dynamic biological organization: fundamentals as applied to cellular systems. Springer, New York

    Book  Google Scholar 

  • Aon MA, Cortassa S, Marbán E, O’Rourke B (2003) Synchronized whole cell oscillations in mitochondrial metabolism triggered by a local release of reactive oxygen species in cardiac myocytes. J Biol Chem 278:44735–44

    Article  PubMed  CAS  Google Scholar 

  • Aon MA, Cortassa S, Lemar KM, Hayes AJ, Lloyd D (2007) Single and cell population respiratory oscillations in yeast: a 2-photon scanning laser microscopy study. FEBS Lett 581:8–14

    Article  PubMed  CAS  Google Scholar 

  • Aon MA, Roussel MR, Cortassa S, O’Rourke B, Murray DB, Beckmann M, Lloyd D (2008) The scale free network organization of yeast and heart systems biology. PLoS One 3:e3624

    Article  PubMed  Google Scholar 

  • Basehoar AD, Zanton SJ, Pugh BF (2004) Identification and distinct regulation of yeast TATA box-containing genes. Cell 116:699–709

    Article  PubMed  CAS  Google Scholar 

  • Boorsma A, Foat BC, Vis D, Klis FM, Bussemaker HJ (2005) T-profiler: scoring the activity of predefined groups of genes using gene expression data. Nucleic Acids Res 33:W592–W595

    Article  PubMed  CAS  Google Scholar 

  • Brauer MJ, Huttenhower C, Airoldi EM et al (2008) Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast. Mol Biol Cell 19:352–67

    Article  PubMed  CAS  Google Scholar 

  • Brown DA, Aon MA, Akar FG, Liu T, Sorarrain N, O’Rourke B (2008) Effects of 4′-chlorodiazepam on cellular excitation-contraction coupling and ischaemia-reperfusion injury in rabbit heart. Cardiovasc Res 79:141–9

    Article  PubMed  CAS  Google Scholar 

  • Chance B, Williams GR (1955) Respiratory enzymes in oxidative phosphorylation. III. The steady state. J Biol Chem 217:409–27

    PubMed  CAS  Google Scholar 

  • Chance B, Nioka S, Warren W, Yurtsever G (2005) Mitochondrial NADH as the bellwether of tissue O2 delivery. Adv Exp Med Biol 566:231–42

    Article  PubMed  CAS  Google Scholar 

  • Chin SL, Marcus IM, Klevecz RR, Li CM (2012) Dynamics of oscillatory phenotypes in Saccharomyces cerevisiae reveal a network of genome-wide transcriptional oscillators. FEBS J 279:119–30

    Article  Google Scholar 

  • Cortassa S, Aon MA, O’Rourke B, Winslow RL (2011) Metabolic control analysis applied to mitochondrial networks. Conf Proc IEEE Eng Med Biol Soc 2011:4673–6

    PubMed  Google Scholar 

  • Delini-Stula A, Radeke E, Waldmeier PC (1988) Basic and clinical aspects of the activity of the new monoamine oxidase inhibitors. Psychopharmacol Ser 5:147–58

    PubMed  CAS  Google Scholar 

  • Edwards SW, Lloyd D (1978) Oscillations of respiration and adenine nucleotides in synchronous cultures of Acanthamoeba castellanii: mitochondrial respiratory control in vivo. Microbiology 108:197–204

    CAS  Google Scholar 

  • Edwards SW, Lloyd D (1980) Oscillations in protein and RNA content during synchronous growth of Acanthamoeba castellanii. Evidence for periodic turnover of macromolecules during the cell cycle. FEBS Lett 109:21–6

    Article  PubMed  CAS  Google Scholar 

  • Engelman W, Bollig I, Hartmann R (1976) [The effects of lithium ions on circadian rhythms (author’s transl.)]. Arzneimittelforschung 26(6):1085–6

    Google Scholar 

  • Finn RK, Wilson RE (1954) Fermentation process control, population dynamics of a continuous propagator for microorganisms. J Agric Food Chem 2:66–69

    Article  Google Scholar 

  • Fu M, Zhang W, Wu L, Yang G, Li H, Wang R (2012) Hydrogen sulfide (H2S) metabolism in mitochondria and its regulatory role in energy production. Proc Natl Acad Sci USA 109:2943–8

    Article  PubMed  CAS  Google Scholar 

  • Gasch AP, Werner-Washburne M (2002) The genomics of yeast responses to environmental stress and starvation. Funct Integr Genomics 2:181–92

    Article  PubMed  CAS  Google Scholar 

  • Gavin A-C, Aloy P, Grandi P et al (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440:631–6

    Article  PubMed  CAS  Google Scholar 

  • Hackenbrock CR (1966) Ultrastructural bases for metabolically linked mechanical activity in mitochondria. I. Reversible ultrastructural changes with change in metabolic steady state in isolated liver mitochondria. J Cell Biol 30:269–97

    Article  PubMed  CAS  Google Scholar 

  • Hackenbrock CR (1968) Ultrastructural bases for metabolically linked mechanical activity in mitochondria. II. Electron transport-linked ultrastructural transformations in mitochondria. J Cell Biol 37:345–69

    Article  PubMed  CAS  Google Scholar 

  • Harbison CT, Gordon DB, Lee TI et al (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431:99–104

    Article  PubMed  CAS  Google Scholar 

  • Henson MA (2004) Modeling the synchronization of yeast respiratory oscillations. J Theor Biol 231:443–58

    Article  PubMed  Google Scholar 

  • Hiroi N, Funahashi A (2006) Kinetics of dimension restricted conditions. Humana, NJ, USA

    Google Scholar 

  • Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 98:4569–74

    Article  PubMed  CAS  Google Scholar 

  • Jarmuszkiewicz W, Woyda-Ploszczyca A, Antos-Krzeminska N, Sluse FE (2009) Mitochondrial uncoupling proteins in unicellular eukaryotes. Biochim Biophys Acta 1797:792–9

    PubMed  Google Scholar 

  • Keulers M, Kuriyama H (1998) Extracellular signalling in an oscillatory yeast culture. In: Holcombe WML, Paton R, Holcombe M (eds) Information processing in cells and tissues. Plenum, New York, pp 85–94

    Chapter  Google Scholar 

  • Keulers M, Asaka T, Kuriyama H (1994) A versitile data acquisition system for physiological modelling of laboratory fermentation processes. Biotechnol Tech 8:879–84

    Article  CAS  Google Scholar 

  • Keulers M, Satroutdinov AD, Suzuki T, Kuriyama H (1996a) Synchronization affector of autonomous short-period-sustained oscillation of Saccharomyces cerevisiae. Yeast 12:673–82

    Article  PubMed  CAS  Google Scholar 

  • Keulers M, Suzuki T, Satroutdinov AD, Kuriyama H (1996b) Autonomous metabolic oscillation in continuous culture of Saccharomyces cerevisiae grown on ethanol. FEMS Microbiol Lett 142:253–8

    Article  PubMed  CAS  Google Scholar 

  • Klevecz RR, Murray DB (2001) Genome wide oscillations in expression. Wavelet analysis of time series data from yeast expression arrays uncovers the dynamic architecture of phenotype. Mol Biol Rep 28:73–82

    Article  PubMed  CAS  Google Scholar 

  • Klevecz RR, Bolen J, Forrest G, Murray DB (2004) A genomewide oscillation in transcription gates DNA replication and cell cycle. Proc Natl Acad Sci U S A 101:1200–05

    Article  PubMed  CAS  Google Scholar 

  • Krogan NJ, Cagney G, Yu H et al (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440:637–43

    Article  PubMed  CAS  Google Scholar 

  • Kwak WJ, Kwon G-S, Jin I, Kuriyama H, Sohn H-Y (2003) Involvement of oxidative stress in the regulation of H2S production during ultradian metabolic oscillation of Saccharomyces cerevisiae. FEMS Microbiol Lett 219:99–104

    Article  PubMed  CAS  Google Scholar 

  • Li CM, Klevecz RR (2006) A rapid genome-scale response of the transcriptional oscillator to perturbation reveals a period-doubling path to phenotypic change. Proc Natl Acad Sci U S A 103:16254–59

    Article  PubMed  CAS  Google Scholar 

  • Lloyd D (2003) Effects of uncoupling of mitochondrial energy conservation on the ultradian clock-driven oscillations in Saccharomyces cerevisiae continuous culture. Mitochondrion 3:139–46

    Article  PubMed  CAS  Google Scholar 

  • Lloyd D (2006a) The ultradian clock: not to be confused with the cell cycle. Nat Rev Mol Cell Biol. doi:10.1038/nrm1980-c1

    PubMed  Google Scholar 

  • Lloyd D (2006b) Hydrogen sulfide: clandestine microbial messenger? Trends Microbiol 14:456–62

    Article  PubMed  CAS  Google Scholar 

  • Lloyd D (2008) Respiratory oscillations in yeasts. Adv Exp Med Biol 641:118–40

    Article  PubMed  CAS  Google Scholar 

  • Lloyd D, Edwards SW (1984) Epigenetic oscillations during the cell cycles of lower eukaryotes are coupled to a clock: life’s slow dance to the music of time. In: Edmunds L (ed) Cell cycle clocks. Marcel Dekker, New York, pp 27–46

    Google Scholar 

  • Lloyd AL, Lloyd D (1995) Chaos: its significance and detection in biology. Biol Rhythm Res 26:233–52

    Article  Google Scholar 

  • Lloyd D, Murray DB (2005) Ultradian metronome: timekeeper for orchestration of cellular coherence. Trends Biochem Sci 30:373–7

    Article  PubMed  CAS  Google Scholar 

  • Lloyd D, Murray DB (2006) The temporal architecture of eukaryotic growth. FEBS Lett 580:2830–35

    Article  PubMed  CAS  Google Scholar 

  • Lloyd D, Murray DB (2007) Redox rhythmicity: clocks at the core of temporal coherence. Bioessays 29:465–73

    Article  PubMed  CAS  Google Scholar 

  • Lloyd D, Rossi EL (1992) Ultradian rhythms in life processes: an inquiry into fundamental principles. Springer, London

    Book  Google Scholar 

  • Lloyd D, Rossi EL (2008) Ultradian rhythms from molecules to mind: a new vision of life. Springer, New York

    Book  Google Scholar 

  • Lloyd D, Edwards SW, Fry JC (1982a) Temperature-compensated oscillations in respiration and cellular protein content in synchronous cultures of Acanthamoeba castellanii. Proc Natl Acad Sci U S A 79:3785–8

    Article  PubMed  CAS  Google Scholar 

  • Lloyd D, Poole RK, Edwards SW (1982b) The cell division cycle: temporal organization control of cellular growth and reproduction. Academic, London

    Google Scholar 

  • Lloyd D, Salgado EJ, Murray DB, Eshantha L, Salgado J, Turner MP (2002a) Respiratory oscillations in yeast: clock-driven mitochondrial cycles of energization. FEBS Lett 519:41–4

    Article  PubMed  CAS  Google Scholar 

  • Lloyd D, Salgado LEJ, Turner MP, Suller MTE, Murray DB (2002b) Cycles of mitochondrial energization driven by the ultradian clock in a continuous culture of Saccharomyces cerevisiae. Microbiology 148:3715–24

    PubMed  CAS  Google Scholar 

  • Lloyd D, Lemar KM, Salgado LE, Gould TM, Murray DB (2003) Respiratory oscillations in yeast: mitochondrial reactive oxygen species, apoptosis and time; a hypothesis. FEMS Yeast Res 3:333–9

    Article  PubMed  CAS  Google Scholar 

  • Lloyd D, Cortassa S, O’Rourke B, Aon MA (2012) What yeast and cardiomyocytes share: ultradian oscillatory redox mechanisms of cellular coherence and survival. Integr Biol (Camb) 4(1):65–74

    Article  CAS  Google Scholar 

  • Lorch Y, Cairns BR, Zhang M, Kornberg RD (1998) Activated RSC-nucleosome complex and persistently altered form of the nucleosome. Cell 94:29–34

    Article  PubMed  CAS  Google Scholar 

  • Machné R, Murray DB (2012) The yin and yang of yeast transcription: elements of a global feedback system between metabolism and chromatin. PLoS One 7:e37906

    Article  PubMed  Google Scholar 

  • MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E (2006) An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 7:113

    Article  PubMed  Google Scholar 

  • Mano Y (1977) Interaction between glutathione and the endoplasmic reticulum in cyclic protein synthesis in sea urchin embryos. Dev Biol 61:273–86

    Article  PubMed  CAS  Google Scholar 

  • Marques N, Edwards SW, Fry JC, Halberg F, Lloyd D (1987) Temperature-compensated ultradian variation in cellular protein content of Acanthamoeba castellanii revisited. Prog Clin Biol Res 227A:105–19

    PubMed  CAS  Google Scholar 

  • McCord RP, Berger MF, Philippakis AA, Bulyk ML (2007) Inferring condition-specific transcription factor function from DNA binding and gene expression data. Mol Syst Biol 3:100

    Article  PubMed  Google Scholar 

  • Métivier R, Penot G, Hübner MR et al (2003) Estrogen receptor-α directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115:751–63

    Article  PubMed  Google Scholar 

  • Mitchell P, Moyle J (1969) Estimation of membrane potential and pH difference across the cristae membrane of rat liver mitochondria. Eur J Biochem 7:471–84

    Article  PubMed  CAS  Google Scholar 

  • Mueller S, Machné R, Murray DB (2012) A new dynamic model for highly efficient mass transfer in aerated bioreactors and consequences for kLa. Biotechnol Bioeng 109(12):2997–3006. doi:10.1002/bit.24594

    Article  CAS  Google Scholar 

  • Murray DB (2004) On the temporal self-organisation of Saccharomyces cerevisiae. Curr Genomics 5:665–7

    Article  CAS  Google Scholar 

  • Murray DB (2006) The respiratory oscillation in yeast phase definitions and periodicity. Nat Rev Mol Cell Biol. doi:10.1038/nrm1980-c2

    Google Scholar 

  • Murray DB, Lloyd D (2006) A tuneable attractor underlies yeast respiratory dynamics. Biosystems 90:287–94

    Article  PubMed  Google Scholar 

  • Murray DB, Engelen FA, Keulers M, Kuriyama H, Lloyd D (1998) NO+, but not NO., inhibits respiratory oscillations in ethanol-grown chemostat cultures of Saccharomyces cerevisiae. FEBS Lett 26:297–99

    Article  Google Scholar 

  • Murray DB, Engelen FA, Lloyd D, Kuriyama H (1999) Involvement of glutathione in the regulation of respiratory oscillation during a continuous culture of Saccharomyces cerevisiae. Microbiology 145:2739–45

    PubMed  CAS  Google Scholar 

  • Murray DB, Roller S, Kuriyama H, Lloyd D (2001) Clock control of ultradian respiratory oscillation found during yeast continuous culture. J Bacteriol 183:7253–59

    Article  PubMed  CAS  Google Scholar 

  • Murray DB, Klevecz RR, Lloyd D (2003) Generation and maintenance of synchrony in Saccharomyces cerevisiae continuous culture. Exp Cell Res 287:10–15

    Article  PubMed  CAS  Google Scholar 

  • Murray DB, Beckmann M, Kitano H (2007) Regulation of yeast oscillatory dynamics. Proc Natl Acad Sci U S A 104:2241–6

    Article  PubMed  CAS  Google Scholar 

  • Murray DB, Haynes K, Tomita M (2011) Redox regulation in respiring Saccharomyces cerevisiae. Biochim Biophys Acta 1810:945–58

    Article  PubMed  CAS  Google Scholar 

  • Nagaich AK, Walker DA, Wolford R, Hager GL (2004) Rapid periodic binding and displacement of the glucocorticoid receptor during chromatin remodeling. Mol Cell 14:163–74

    Article  PubMed  CAS  Google Scholar 

  • Naiki N, Yamagata S (1976) Isolation and some properties of copper-binding proteins found in a copper-resistant strain of yeast. Plant Cell Physiol 17:1281–95

    CAS  Google Scholar 

  • Rapkine L (1931) Chemical processes during cellular division. Ann Physiol Physicochem 7:382

    CAS  Google Scholar 

  • Roussel MR, Lloyd D (2007) Observation of a chaotic multioscillatory metabolic attractor by real-time monitoring of a yeast continuous culture. FEBS J 274:1011–18

    Article  PubMed  CAS  Google Scholar 

  • Salgado LE, Murray DB, Lloyd D (2002) Some antidepressant agents (Li+, monoamine oxidase type A inhibitors) perturb the ultradian clock in Saccharomyces cerevisiae. Biol Rhythm Res 33:351–61

    Article  CAS  Google Scholar 

  • Sasidharan K, Tomita M, Aon MA, Lloyd D, Murray DB (2012) Time structure of the yeast metabolism in vivo. Adv Exp Med Biol 736:359–79

    Article  PubMed  CAS  Google Scholar 

  • Satroutdinov AD, Kuriyama H, Kobayashi H (1992) Oscillatory metabolism of Saccharomyces cerevisiae in continuous culture. FEMS Microbiol Lett 77:261–7

    Article  PubMed  CAS  Google Scholar 

  • Slavov N, Botstein D (2011) Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast. Mol Biol Cell 22:1997–2009

    Article  PubMed  CAS  Google Scholar 

  • Slavov N, Macinskas J, Caudy A, Botstein D (2011) Metabolic cycling without cell division cycling in respiring yeast. Proc Natl Acad Sci USA 108:19090–5

    Article  PubMed  CAS  Google Scholar 

  • Sohn H-Y, Kuriyama H (2001a) Ultradian metabolic oscillation of Saccharomyces cerevisiae during aerobic continuous culture: hydrogen sulphide, a population synchronizer, is produced by sulphite reductase. Yeast 18:125–35

    Article  PubMed  CAS  Google Scholar 

  • Sohn H-Y, Kuriyama H (2001b) The role of amino acids in the regulation of hydrogen sulfide production during ultradian respiratory oscillation of Saccharomyces cerevisiae. Arch Microbiol 176:69–78

    Article  PubMed  CAS  Google Scholar 

  • Sohn H-Y, Murray DB, Kuriyama H (2000) Ultradian oscillation of Saccharomyces cerevisiae during aerobic continuous culture: hydrogen sulphide mediates population synchrony. Yeast 16:1185–90

    Article  PubMed  CAS  Google Scholar 

  • Sohn H-Y, Kum E-J, Kwon G-S, Jin I, Adams CA, Kuriyama H (2005a) GLR1 plays an essential role in the homeodynamics of glutathione and the regulation of H2S production during respiratory oscillation of Saccharomyces cerevisiae. Biosci Biotechnol Biochem 69:2450–4

    Article  PubMed  CAS  Google Scholar 

  • Sohn H-Y, Kum E-J, Kwon G-S, Jin I, Kuriyama H (2005b) Regulation of branched-chain, and sulfur-containing amino acid metabolism by glutathione during ultradian metabolic oscillation of Saccharomyces cerevisiae. J Microbiol 43:375–80

    PubMed  CAS  Google Scholar 

  • Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ (2010) The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 8:e1000414

    Article  PubMed  Google Scholar 

  • Tu BP, Kudlicki A, Rowicka M, McKnight SL (2005) Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 310:1152–8

    Article  PubMed  CAS  Google Scholar 

  • Vincent JA, Kwong TJ, Tsukiyama T (2008) ATP-dependent chromatin remodeling shapes the DNA replication landscape. Nat Struct Mol Biol 15:477–84

    Article  PubMed  CAS  Google Scholar 

  • von Bertalanffy L (1952) Problems of life: an evaluation of modern biological thought. C. A. Watts & Company, London

    Google Scholar 

  • von Meyenburg HK (1969) Energetics of the budding cycle of Saccharomyces cerevisiae during glucose limited aerobic growth. Arch Microbiol 66:289–303

    Google Scholar 

  • Watson JD, Crick FH (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171:737–8

    Article  PubMed  CAS  Google Scholar 

  • Whitehouse I, Rando OJ, Delrow J, Tsukiyama T (2007) Chromatin remodelling at promoters suppresses antisense transcription. Nature 450:1031–5

    Article  PubMed  CAS  Google Scholar 

  • Wolf J, Sohn H-Y, Heinrich R, Kuriyama H (2001) Mathematical analysis of a mechanism for autonomous metabolic oscillations in continuous culture of Saccharomyces cerevisiae. FEBS Lett 499:230–4

    Article  PubMed  CAS  Google Scholar 

  • Yates FE (1992) Fractal applications in biology: scaling time in biochemical networks. Methods Enzymol 210:636–75

    Article  PubMed  CAS  Google Scholar 

  • Yeung KS, Hoare M, Thornhill NF, Williams T, Vaghjiani JD (1999) Near-infrared spectroscopy for bioprocess monitoring and control. Biotechnol Bioeng 63:684–93

    Article  PubMed  CAS  Google Scholar 

  • Zhang Z, Wippo CJ, Wal M, Ward E, Korber P, Pugh BF (2011) A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science 332:977–80

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

DL and DBM are grateful to the Royal Society and the Japan Society for the Promotion of Science for supporting this work. RM and DBM are grateful to the Vienna Science and Technology Fund (WWTF), for funding an exchange grant (MA07-30). KS, DBM and CA are supported in part by funds from Yamagata Prefectural Government and Tsuruoka-city. DBM is also supported by a Japan partnering award (Japan Science and Technology agency and the Biotechnology and Biological Sciences Research Council, UK) and a Japan Society for the Promotion of Science Grant-in-aid.

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Authors and Affiliations

  1. Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan

    Douglas B. Murray, Cornelia Amariei & Kalesh Sasidharan

  2. Institute for Theoretical Biochemistry, University of Vienna, Vienna, Austria

    Rainer Machné

  3. School of Medicine, Johns Hopkins University, Baltimore, MD, USA

    Miguel A. Aon

  4. School of Biosciences, Cardiff University, Wales, UK

    David Lloyd

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  1. Douglas B. Murray
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Correspondence to Douglas B. Murray .

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  1. School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA

    Miguel A. Aon

  2. Laboratory of Fundamental and Applied Bi, Inserm U1055 and University Joseph Fourier, Grenoble, Grenoble cedex 9, France

    Valdur Saks

  3. Laboratory of Fundamental and Applied Bi, Inserm U1055 and University Joseph Fourier, Grenoble, Grenoble cedex 9, France

    Uwe Schlattner

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Murray, D.B., Amariei, C., Sasidharan, K., Machné, R., Aon, M.A., Lloyd, D. (2014). Temporal Partitioning of the Yeast Cellular Network. In: Aon, M., Saks, V., Schlattner, U. (eds) Systems Biology of Metabolic and Signaling Networks. Springer Series in Biophysics, vol 16. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38505-6_12

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