??? Central Dogma: DNA is a Read-Only-Memory.

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1 京 都 大 学 吉 川 研 一 At 桂 林 ; June 19, 2007 Novel Hypothesis on the Self-Regulation of Genetic Information: Scenario from One-Dimensional DNA into Spatio-Temporal Order Conclusion: The concept of Protein network is insufficint. What is necessary Cell for additional? Arg His??? Central Dogma: DNA is a Read-Only-Memory.

2 Who manages the expression of 20,000 genes? Current network hypothesis gives the answer: Hypothesis of Jacob & Monod (1961)

3 Difficulties in Complicated Network 1. Fluctuation in the number of key-lock interactions diminishes the stability of the fix points in the network: Difficulty of robust on/off switching. 2. Almost impossible to explain the simultaneous switching on hundreds of senes. 3. Are there 10 3 regulatory factors to control 10 4 genes? Effect of cross-talk 4. Appearance of a large number of metastable states: Difficulty of simultaneous switching on many genes. 5. Who can choose the certain fix point? And how? Absence of CPU. We should think of something else!

4 T4DNA: 155 kbp Fluorescence Microscopy AFM Microscopy 1.5μm 1.5μm Broadening with Gaussian (~300 nm) 1.5μm Yoshinaga, et al., J.Chem.Phy.2002.

5 Short DNA is a stiff rod. All of the genomic DNAs are giant (above 1 mm). Giant DNA is a Persistence Length; 50 nm (170 base pairs) flexible rope. DNA above several kilo base pairs is giant.

6 Helix-Coil Transition Melting Transition of Double Stranded DNA Continuous Transition Coil-Globule Transition Folding Transition of Giant DNA On/Off Transition

7 Coil (Unfolded) R c ~ λn 3/5 N: Number of segments λ: Kuhn length s: Cross section of segment Globule (Folded) R g ~ (λsn) 1/3 Coil Ratio on the Density When N = 100 (30kbp), λ= 100nm, s = 4nm 2 ρ g /ρ c ~ R c3 /R g3 ~ 10 5 Continuous Large Change or Discrete? in Density Globule

8 Most Experimental Studies Reported As Continuous Monomolecular Condensation of λ-dna Induced by Cobalt Hexammine J. Widom and R. L. Baldwin, Biopolymers, 22, (1983). In Abstract: "Some interesting properties of monomolecular condensation are noted. (1) The transition is not a two-state reaction, as judged by measurements of the diffusion coefficient through the transition zone. (2) The transition for monomolecular condenstation is diffuse. " Current concept R R Condensing Chemical

9 See e.g.; JCP,102,6595( 95); PRL, 76,3029( 96); JPCB, 101, 9396 ( 97). Observation on Single DNA Molecules Discrete: Single chain Continuous: Ensemble of chains Folding transition induced by spermine (4+) T4DNA(166kbp) Contour length:57μm

10 Free Energy density

11 1 n ~ 10 2 n ~ 10 Liquid Solid Always Continuous First-Order Phase Transition Cf: Ar-Cluster, H 2 O-cluster N=100 corresponds to DNA with 30kbp, where Kuhn length is 100nm (300bp)

12 Nucleation & Growth in a Single Chain Simulation Experiment Sakaue, et al., JCP( 02) Single DNA Observation (T4DNA: 57μm) 10μm Time Interval : 2s Matsuzawa, et al., JACS( 96)

13 Switching of DNA conformation by environment parameters ATP RNA low low high high ph Acid Alkaline

14 Network: key-lock interactions Recognition of specific base-sequences on DNA by individual regulatory factors. Variable: Finite number (discrete; the density of N ) Field: Environment Nonspecific abundant chemicals such as ATP; Na,K-ions; RNA; ph; etc. Environmental species: Large number (concentration is almost given by the density of R )

15 Environment causes on/off switching. Dr. Makita Makita, et al., FEBS Letters, 460 (1999)

16 Compaction of DNA completely inhibits the transcriptional activity of genes Luckel, Tsumoto, et al., Biophys. Chem.(2003).

17 Structural transition and transcriptional activity of DNA DNA mrna DNA only Coil state Transcriptional activity ON Globule state Transcriptional activity OFF In the 不 連 region 続 転 移 は 100 larger than kbp 100 以 上 の kbp 領 域 (more (10 than ~ 以 ~上 100 の genes), 遺 伝 子 discrete を 含 む)で transition 初 めて 起 こる occurs. Yamada et al., APL, 2005

18 Switching of the Transcriptional Activity is Caused by the changa of Energy State Giant DNA Short DNA Biomacromol.(2003)

19 Shindo, et al., J.Biotech.(2007).

20 Summary on Genetic Regulation 1) Environmental parameters induce On/Off switching on the conformation of giant DNA. 2) The correlation length in intra-chain segregation is determined by the cross-talk between DNA and environment. 3) On/Off switching of gene expression is driven by the conformational transition of giant DNA. 4) Network hypothesis may stand for the soft control of gene expression. Robust control will be managed by the conformational transition in giant DNA.

21 Network: Fluctuating pairs of key-locks Environment: Robust owe to large number Metabolic Network Expression Genetic Regulators Unfolded DNA Transcription Intra-cellular Network Nuclear Environment Loose Packing Outer Environment Folder of genes Tight Packing Life is a hybrid system between network and environment.

22 Missing Link between DNA and Spatio-Temporal Order in Life 1) Selective on/off switching on a large number of genes Cell Differentiation, Cancer, AIDS, etc. 2) Construction of the own body Turing Pattern, Apoptosis, etc.

23 Current Model on the Construction of Own Body 1. Positioning through chemical gradient 2. Cell automaton 3. Neighboring Interaction 4. Reaction-Diffusion System (Turing Pattern) 1.Positioning 2.Cell Automaton 3.Neighboring Interaction

24 u = γf u,v t ( )+ 2 u, v t = γg ( u,v )+ d 2 v f( u, v) = a u hu,v ( ), gu,v ( ) = α( b v) hu,v ( ) ρuv hu,v ( )= 1 + u + Ku 2

25 Soma is generated with traveling waves. Tail Head Mouse Periodicity: min Zebrafish Periodicity: 30min Y. Bessho, R. Kageyama Curr.Opinion Gene.Dev., 13, 379, (2003).

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27 + + = = + + = z k x k xz k z k x k y k y x D x k y k xz k x & & & x: Hes1 protein y: hes1 mrna z: E2A(?) protein

28 Somite Segmentation is Generated through Traveling Waves Experiment Numerical Oscillation is robust.

29 Fluctuating rhythm on single cells Oscillation of Hes-1 Individual Cells Ensemble of Cells

30 Numerical Example Isolated Cells 1-D Couples Cells

31 Missing Link between DNA and Spatio-Temporal Order in Life 1) Selective on/off switching on a large number of genes Cell Differentiation, Cancer, AIDS, etc. 2) Construction of the own body Turing Pattern, Apoptosis, etc. Nonlinear dynamics under farfrom-equilibrium conditions

32 Message for the young scientists: Fusion between Physico-Mathmatics and Bioscience will open the next era. What is Life? 20th Century: Accumulation of the knowledge on Elements. 21th Century: Understanding of System Dynamics.

33 謝 謝 劉 馬 Research Colleagues at Kyoto Univ.