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Tsuchiya M, Hashimoto M, Takenaka Y, Motoike IN, Yoshikawa K. Global genetic response in a cancer cell: self-organized coherent expression dynamics. PLoS One 2014; 9:e97411. [PMID: 24831017 PMCID: PMC4022610 DOI: 10.1371/journal.pone.0097411] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 04/18/2014] [Indexed: 12/19/2022] Open
Abstract
Understanding the basic mechanism of the spatio-temporal self-control of genome-wide gene expression engaged with the complex epigenetic molecular assembly is one of major challenges in current biological science. In this study, the genome-wide dynamical profile of gene expression was analyzed for MCF-7 breast cancer cells induced by two distinct ErbB receptor ligands: epidermal growth factor (EGF) and heregulin (HRG), which drive cell proliferation and differentiation, respectively. We focused our attention to elucidate how global genetic responses emerge and to decipher what is an underlying principle for dynamic self-control of genome-wide gene expression. The whole mRNA expression was classified into about a hundred groups according to the root mean square fluctuation (rmsf). These expression groups showed characteristic time-dependent correlations, indicating the existence of collective behaviors on the ensemble of genes with respect to mRNA expression and also to temporal changes in expression. All-or-none responses were observed for HRG and EGF (biphasic statistics) at around 10–20 min. The emergence of time-dependent collective behaviors of expression occurred through bifurcation of a coherent expression state (CES). In the ensemble of mRNA expression, the self-organized CESs reveals distinct characteristic expression domains for biphasic statistics, which exhibits notably the presence of criticality in the expression profile as a route for genomic transition. In time-dependent changes in the expression domains, the dynamics of CES reveals that the temporal development of the characteristic domains is characterized as autonomous bistable switch, which exhibits dynamic criticality (the temporal development of criticality) in the genome-wide coherent expression dynamics. It is expected that elucidation of the biophysical origin for such critical behavior sheds light on the underlying mechanism of the control of whole genome.
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Affiliation(s)
- Masa Tsuchiya
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, School of Media and Governance, Keio University, Fujisawa, Japan
- * E-mail: (MT); (KY)
| | - Midori Hashimoto
- Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Japan
| | - Yoshiko Takenaka
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Ikuko N. Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
- * E-mail: (MT); (KY)
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Abstract
The mechanism of the self-regulation of gene expression in living cells is generally explained by considering complicated networks of key-lock relationships, and in fact there is a large body of evidence on a hugenumber of key-lock relationships. However, in the present article we stress that with the network hypothesis alone it is impossible to fully explain the mechanism of self-regulation in life. Recently, it has been established that individual giant DNA molecules, larger than several tens of kilo base pairs, undergo a large discrete transition in their higher-order structure. It has become clear that nonspecific weak interactions with various chemicals, suchas polyamines, small salts, ATP and RNA, cause on/off switching in the higher-order structure of DNA. Thus, the field parameters of the cellular environment should play important roles in the mechanism of self-regulation, in addition to networks of key and locks. This conformational transition induced by field parameters may be related to rigid on/off regulation, whereas key-lock relationships may be involved in a more flexible control of gene expression.
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Affiliation(s)
- K Yoshikawa
- Department of Physics, Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
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3
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Large system in a small cell: A hypothetical pathway from a microscopic stochastic process towards robust genetic regulation. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.05.083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Song Z, Parker KJ, Enoh I, Zhao H, Olubajo O. Elucidation of spermidine interaction with nucleotide ATP by multiple NMR techniques. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48:123-128. [PMID: 19960498 PMCID: PMC2909874 DOI: 10.1002/mrc.2554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Interaction of polyamines with nucleotides plays a key role in many biological processes. Here we use multiple NMR techniques to characterize interaction of spermidine with adenosine 5'-triphosphate (ATP). Two-dimensional (1)H-(15)N spectra obtained from gs-HMBC experiments at varied pH show significant shift of N-1 peak around pH 2.0-7.0 range, suggesting that spermidine binds to N-1 site of ATP base. The binding facilitates N-1 deprotonation, shifting its pK(a) from 4.3 to 3.4. By correlating (15)N and (31)P chemical shift data, it is clear that spermidine is capable of concurrently binding to ATP base and phosphate sites around pH 4.0-7.0. The self-diffusion constants derived from (1)H PFG-diffusion measurements provide evidence that binding of spermidine to ATP is in 1:1 ratio, and pH variations do not induce significant nucleotide self-association in our samples. (31)P spectral analysis suggests that at neutral pH, Mg(2+) ion competes with spermidine and shows stronger binding to ATP phosphates. From (31)P kinetic measurements of myosin-catalyzed ATP hydrolysis, it is found that binding of spermidine affects the stability and reactivity of ATP. These NMR results are important for advancing the studies on nucleotide-polyamine interaction and its impact on nucleotide structures and activities under varied conditions.
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Affiliation(s)
- Zhiyan Song
- Department of Natural Sciences, Savannah State University, Savannah, GA 31404, USA.
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Modern Atomic Force Microscopy and Its Application to the Study of Genome Architecture. SCANNING PROBE MICROSCOPY IN NANOSCIENCE AND NANOTECHNOLOGY 2010. [DOI: 10.1007/978-3-642-03535-7_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Takenaka Y, Nagahara H, Kitahata H, Yoshikawa K. Large-scale on-off switching of genetic activity mediated by the folding-unfolding transition in a giant DNA molecule: an hypothesis. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 77:031905. [PMID: 18517420 DOI: 10.1103/physreve.77.031905] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Indexed: 05/26/2023]
Abstract
We present a model to describe the on-off switching of transcriptional activity in a genetic assembly by considering the intrinsic characteristics of a giant genomic DNA molecule which can undergo a discrete structural transition between coiled and compact states. We propose a model in which the transition in the higher-order structure of DNA plays an essential role in regulating stable on-off switching and/or the oscillation of a large number of genes under the fluctuations in a living cell, where such a structural transition is caused by environmental factors. This model explains the rapid and broad transcriptional response in a genetic assembly as well as its robustness against fluctuations.
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Affiliation(s)
- Yoshiko Takenaka
- Department of Physics, Graduate School of Science, Kyoto University, and Spatio-temporal Order Project, ICORP, JST, Kyoto 606-8502, Japan.
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Lomozik L, Gasowska A, Bregier-Jarzebowska R, Jastrzab R. Coordination chemistry of polyamines and their interactions in ternary systems including metal ions, nucleosides and nucleotides. Coord Chem Rev 2005. [DOI: 10.1016/j.ccr.2005.05.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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NISHIKAWA A, TSUKAHARA S, FUJIWARA T. Microscopic Dielectrophoresis of Single DNA in the Presence of Some Substances in Aqueous Solutions. BUNSEKI KAGAKU 2005. [DOI: 10.2116/bunsekikagaku.54.459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Ayaka NISHIKAWA
- Department of Chemistry, Graduate School of Science, Hiroshima University
| | - Satoshi TSUKAHARA
- Department of Chemistry, Graduate School of Science, Hiroshima University
| | - Terufumi FUJIWARA
- Department of Chemistry, Graduate School of Science, Hiroshima University
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Tsumoto K, Luckel F, Yoshikawa K. Giant DNA molecules exhibit on/off switching of transcriptional activity through conformational transition. Biophys Chem 2004; 106:23-9. [PMID: 14516909 DOI: 10.1016/s0301-4622(03)00138-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We found that the transcriptional activity of large DNAs (40 kbp) can be completely inhibited by adding condensing agents, spermine and poly(ethylene glycol), whereas under the same conditions short fragments (140 bp) still show active transcription. Fluorescence microscopic observations of large DNAs revealed clear correlation between the higher-order structure of templates and their transcriptional activity. The steep decrease in transcriptional activity leading to complete inhibition, or on/off switching, is interpreted in terms of conformational transition of the ensemble of DNA molecules.
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Affiliation(s)
- Kanta Tsumoto
- Department of Chemistry for Materials, Faculty of Engineering, Mie University, Tsu, Mie 514-8507, Japan.
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Akitaya T, Tsumoto K, Yamada A, Makita N, Kubo K, Yoshikawa K. NTP concentration switches transcriptional activity by changing the large-scale structure of DNA. Biomacromolecules 2003; 4:1121-5. [PMID: 12959573 DOI: 10.1021/bm034017w] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is becoming clearer that genetic activity is closely associated with the intracellular energy state. However, the mechanisms of this association are still unclear. In this study, we focused on large-scale changes in the structure of DNA to examine the effect of the NTP concentration on the transcription reaction with T7 RNA polymerase and compared the results with long duplex DNA to those with a short persistent-length(1) fragment. The transcriptional activity dramatically changed only for long duplex DNA within a narrow range of NTP concentrations associated with changes in the large-scale structure of DNA. This result suggests that the energy state may play an essential role in regulating ON/OFF switching on transcriptional activity.
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Affiliation(s)
- Tatsuo Akitaya
- Department of Physics, Graduate School of Science, Kyoto University, and CREST, Kyoto 606-8502, Japan
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11
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Iwaki T, Yoshikawa K. Competition between interchain and intrachain phase segregation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2003; 68:031902. [PMID: 14524798 DOI: 10.1103/physreve.68.031902] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2003] [Indexed: 05/24/2023]
Abstract
Single-molecule observations of giant DNA have clarified that individual molecules undergo a marked discrete transition between an elongated coil state and a compact globule state. There is a relatively wide region of coexistence between the coil and the globule states, i.e., interchain phase segregation, with a change in intensive variables such as the concentration of the condensing agent, salt concentration, temperature. Very recently, the coexistence of coil and globule conformations within a single long DNA chain, i.e., intrachain phase segregation, has been reported under certain experimental conditions. In this study, we investigated general conditions for intrachain phase segregation in a single polyelectrolyte molecule, based on a simple statistical model. We consider the contribution of condensed counterions and the interaction energy of a charged coiled region. Intrachain phase segregation is stable with regard to free energy within a suitable parameter region. Our results suggest that intrachain phase segregation occurs when the electrostatic screening effect by the salt solution is negligible or when the screening effect is large and there is attractive interaction between polyelectrolyte segments.
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Affiliation(s)
- T Iwaki
- Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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HARADA T, YOSHIKAWA K. 生命現象と非線形科学. ELECTROCHEMISTRY 2003. [DOI: 10.5796/electrochemistry.71.341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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13
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Effects of ATP, Mg2+ and a mixture of the two on the formation of large DNA aggregates induced by spermidine. J Biosci Bioeng 2003. [DOI: 10.1016/s1389-1723(03)80021-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Makita N, Yoshikawa K. Proton concentration (pH) switches the higher-order structure of DNA in the presence of spermine. Biophys Chem 2002; 99:43-53. [PMID: 12223238 DOI: 10.1016/s0301-4622(02)00110-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Single-chain observations on the conformational change of giant DNA (T4 DNA) molecules were performed using fluorescence microscopy at different values of pH in the presence of spermine. Individual DNA molecules undergo a large discrete change, or all-or-none transition, in conformation from a folded compact state to an unfolded coil state with an increase in pH. This abrupt unfolding of DNA with an increase in pH is attributed to a decrease in the concentration of the tetravalent form in spermine [SPM(4+)]. We propose a scheme for the folding transition of single DNAs, where the manner of spermine binding changes dramatically from weak loose binding in the elongated coil state to strong tight binding in the folded compact state. We discuss the hierarchical nature of the transition, i.e. cooperative continuous change on the ensemble vs. all-or-none switching on individual DNAs.
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Affiliation(s)
- Naoko Makita
- Graduate School of Human Informatics, Nagoya University, Nagoya 464-8601, Japan
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Nomura SM, Yoshikawa Y, Yoshikawa K, Dannenmuller O, Chasserot-Golaz S, Ourisson G, Nakatani Y. Towards proto-cells: "primitive" lipid vesicles encapsulating giant DNA and its histone complex. Chembiochem 2001; 2:457-9. [PMID: 11828477 DOI: 10.1002/1439-7633(20010601)2:6<457::aid-cbic457>3.0.co;2-f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- S M Nomura
- Department of Physics, Graduate School of Science, Kyoto University & CREST, 606-8502 Kyoto, Japan
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Affiliation(s)
- Jurij Reščič
- Physical Chemisty 1, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, S-221 00 Lund, Sweden
| | - Per Linse
- Physical Chemisty 1, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, S-221 00 Lund, Sweden
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