Lecture 4: Statistical Mechanics of Gene Regulation Rob Phillips California Institute of Technology (Beautiful work of David Goodsell)

Lecture 4: Statistical Mechanics of Lecture 4: Statistical Mechanics of Gene RegulationGene Regulation

Rob PhillipsCalifornia Institute of Technology

(Beautiful work of David Goodsell)

The Single Molecule Census Continued: The Single Molecule Census Continued:

Gene Expression Gene Expression

(Beautiful work of David Goodsell)

RNAP+DNA+mRNA

Lac Repressor

CRP and DNA

Products of the Lac Operon

All Together Now: The Lac OperonAll Together Now: The Lac Operon

Our goal: mathematize the story told by all of these cartoons.In particular, compute the probability of RNAP binding as a function of concentration of all the other molecular actors.

Measure the Concentration of the Gene Measure the Concentration of the Gene

Product: Fluorescence Product: Fluorescence

(Elowitz and Leibler)

Repression in the Lac Operon: the Role of Repression in the Lac Operon: the Role of

Looping Looping

(Elowitz et al.)

Beta-Galactosidase ActivityBeta-Galactosidase Activity

Ian B. Dodd et al. Genes Dev. 2004; 18: 344-354

(Dove et al.)

(Lawrence et al.)

Measuring the mRNA Content of a Cell Measuring the mRNA Content of a Cell

(Yeast microarray data – Brown Group at Stanford)

Real-Time PCRReal-Time PCR

CYCLE NUMBER AMOUNT OF DNA0 11 22 43 84 165 326 647 1288 2569 512

10 1,02411 2,04812 4,09613 8,19214 16,38415 32,76816 65,53617 131,07218 262,14419 524,28820 1,048,57621 2,097,15222 4,194,30423 8,388,60824 16,777,21625 33,554,43226 67,108,86427 134,217,72828 268,435,45629 536,870,91230 1,073,741,82431 1,400,000,00032 1,500,000,00033 1,550,000,00034 1,580,000,000

www.biorad.com

2a. excitation flters

2b. emission filters

1. halogen tungsten lamp

4. sample plate

3. intensifier

5. ccd detector 350,000 pixels

Measuring Promoter Occupancy:ChIPMeasuring Promoter Occupancy:ChIP

http://www.vincibiochem.it/ChIP-IT.htm

)(

)0((L) Repression

bound

bound

Lp

Lp

Repression in the Lac Operon: The Repression in the Lac Operon: The

Experimental Backdrop Experimental Backdrop

(Muller et al.)