??? His Central Dogma: DNA is a Read-Only-Memory. Who manages the - PowerPoint PPT Presentation

At 桂林 ; June 19, 2007 京都大学 吉川研一 Novel Hypothesis on the Self-Regulation of Genetic Information: Scenario from One-Dimensional DNA into Spatio-Temporal Order Protein Conclusion: The concept of “network” is insufficint. What is Cell necessary for additional? Arg ??? His Central Dogma: “DNA is a Read-Only-Memory.”

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

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!

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

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

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

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

Most Experimental Studies Reported As Continuous Monomolecular Condensation of λ -DNA Induced by Cobalt Hexammine J. Widom and R. L. Baldwin, Biopolymers, 22, 1595-1620 (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 Condensing Chemical R

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

Free Energy density

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

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

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

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”)

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

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

Structural transition and transcriptional activity of DNA DNA DNA mRNA only Coil state ⇒ Transcriptional activity ON Globule state ⇒ Transcriptional activity OFF I n the region larger than 100 kbp (more than 10 ～ 100 不連続転移は、 100 kbp 以上の領域 (10 ～ 100 以上の 遺伝子を含む ) で初めて起こる。 genes), discrete transition occurs. Yamada et al., APL, 2005

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

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

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.

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

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.

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

∂ u ∂ v ( ) + ∇ ( ) + d ∇ ∂ t = γ f u , v ∂ t = γ g u , v 2 u , 2 v ( ) = a − u − h u , v ( ) , g u , v ( ) = α b − v ( ) − h u , v ( ) f u , v ρ uv ( ) = h u , v 1 + u + Ku 2

Soma is generated with traveling waves. Tail Head Mouse Zebrafish Periodicity: 90-120min Periodicity: 30min Y. Bessho, R. Kageyama Curr.Opinion Gene.Dev., 13 , 379, (2003).

⎧ ⎪ = − + − + ∇ & 2 x k xz k y k x D x 1 2 3 ⎪ ⎪ k = − + + ⎨ & 5 y k y k + 4 6 2 1 x ⎪ ⎪ k = − + − & 7 ⎪ z k xz k z ⎩ + 1 8 2 1 x x: Hes1 protein y: hes1 mRNA z: E2A(?) protein

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

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

Numerical Example 1-D Couples Cells Isolated Cells

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 far- from-equilibrium conditions

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.

謝謝 馬 劉 Research Colleagues at Kyoto Univ.