Lecture 4: Statistical Mechanics of Gene RegulationThe Single Molecule Census Continued: Gene ExpressionAll Together Now: The Lac OperonSlide 4Slide 5Beta-Galactosidase ActivitySlide 7Real-Time PCRMeasuring Promoter Occupancy:ChIPSlide 10Lecture 4: Statistical Mechanics of Lecture 4: Statistical Mechanics of Gene RegulationGene RegulationRob 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+mRNALac RepressorCRP and DNAProducts of the Lac OperonAll Together Now: The Lac OperonAll Together Now: The Lac OperonOur 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 ActivityIan 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 PCRCYCLE NUMBER AMOUNT OF DNA0 11 22 43 84 165 326 647 1288 2569 51210 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 1,580,000,000www.biorad.com2a. excitation flters2b. emission filters1. halogen tungsten lamp4. sample plate3. intensifier5. ccd detector 350,000 pixelsMeasuring Promoter Occupancy:ChIPMeasuring Promoter Occupancy:ChIPhttp://www.vincibiochem.it/ChIP-IT.htm)()0((L) RepressionboundboundLpLp Repression in the Lac Operon: The Repression in the Lac Operon: The Experimental Backdrop Experimental Backdrop (Muller et
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