A guide for the perplexed: Systems biology, transcriptional modeling, and the Drosophila embryo
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1 A guide for the perplexed: Systems biology, trnscriptionl modeling, nd the Drosophil embryo Dvid Arnosti Deprtment of Biochemistry nd Moleculr Biology Michign Stte University
2 Wht is systems biology?
3 Wht is systems biology? Biologicl theory of everything
4 Wht is systems biology? Biologicl theory of everything Excuse not to think before doing experiments
5 Wht is systems biology? Biologicl theory of everything Excuse not to think before doing experiments Wy to glen good insights from bd dt
6 Wht is systems biology? Biologicl theory of everything Excuse not to think before doing experiments Wy to glen good insights from bd dt Integrtion of quntittive tools nd lrgescle dtsets to bring us to the next level of understnding of systems
7 I wonder how tht works
8 Development strts with few ordered mnifoldnesses; but the mnifoldnesses crete, by interctions, new mnifoldnesses, nd these re ble, by cting bck on the originl ones, to provoke new differences, nd so on. With ech new response, new cuse is immeditely provided, nd new specific rectivity for further specific responses. Hns Driesch (1894) Anlytische Theorie der orgnischen Entwicklung (
9 Wieschus & Nusslein-Volhrd, Levine nd others: We need to know something bout trnscription
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11 eve stripe 2 enhncer
12 Kreitmn, Eisen, nd others we need to know something bout evolution
13 Functionl Output Fitness Lndscpe Billbord Enhncer Model Arnosti nd Kulkrni, 2005
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20 Empiricl identifiction of cis regultory element grmmr wht mtters for enhncer output? Spcing (coopertivity, quenching) Activtor/repressor stoichiometry Site rrngement Binding site ffinity Abundnce of fctors
21 Appliction of Predictive Model
22 Some pproches involving modeling
23 Thermodynmic model Uses DNA sequence informtion Subtle modifictions spcing, ffinity, overlps Snpshot equilibrium sitution
24 Differentil Eqution model Promoter treted s blck box Incorportes post-trnscriptionl processes Movie provides dynmic pictures
25 Boolen model Promoter - blck box Post-trnscriptionl processes Movie Interctions simplified to +/- Computtions simpler, output corser
26 1. For DNA-level modeling, thermodynmic pproches re especilly pt 2. If you re fstidious, you must collect your own dt Nture Genetics 38: 1159 (2006)
27 Focusing specificlly on properties of short-rnge trnscriptionl repressors: Wlid Fkhouri
28 Empiricl Testing of Trnscriptionl Grmmr Spcing Arrngement nd Promoter Proximity Activtor Number nd Affinity Alterntive Repressors Stoichiometry nd Spcing Wlid Fkhouri nd Rupinder Syl
29 Gene expression s function of [Gint] [Gint]
30 Exmple of modeling for one construct
31 Root men squre error Repressor Scling Fctor Gint-Gint coopertivity Quenching Activtor specificity
32 Ip, Gry nd Levine
33 Rupinder Syl
34 Enhncer robustness Wild-Type Dl3 Twi1 Dl1 Dl4 Twi2 Dl2 bhlh duo
35 Probing the limits to enhncer robustness Wild-Type Dl1, Twi2 Dl2, Twi2 Dl1, Dl2 Dl2, Dl3 Dl3, Twi2 Dl1, Dl3 Dl2, Twi1 Dl1, bhlh Duo
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37 Test specific hypotheses bout protein interctions on the enhncer
38 Two-lyer model to incorporte cisregultory nd temporl informtion How does vrition in cis-regultory informtion ffect development? Jcqueline Dresch
39 Perry et l, Current Biology 2010 Comprehensively incorporte cis-regultory informtion
40 Bieler et l, Biophysicl Journl 2011 Comprehensively incorporte cis-regultory informtion Incorporte GRNs nd protein interctions
41 Mrkstein et l, PNAS 2002 Comprehensively incorporte cis-regultory informtion Incorporte GRNs nd protein interctions Predict chnges through time
42 Comprehensively incorporte cis-regultory informtion Incorporte GRNs nd protein interctions Predict chnges through time Understnd the impct of evolution on gene expression
43 1. Thermodynmic Model Zinzen et l, Current Biology Differentil Eqution Model Perkins et l, PLoS Comp Bio 2006
44 Simple Gene Network: Dl Twi Sn rho
45 Dorsl, twist, snil, nd rhomboid + + _ (trget) Dorsl levels reltively invrint during modeled intervl Feedbck loop Dl Twi Sn Coherent nd incoherent feed-forwrd loops rho
46 twi Predicted binding sites on ech enhncer Dl Twi Sn sn rho
47 Expression Profiles
48 Expression Nuclei (Ventrl-Dorsl)
49 Two-Lyer Model mrna rte of chnge m i t S p i D m, m i 1 m i m i 1 m i m, m i p i t T m i D p, p i 1 p i p i 1 p i p, p i protein rte of chnge
50 m i t S p i D m, m i 1 m i m i 1 m i m, m i Thermo Model p i t T m i D p, p i 1 p i p i 1 p i p, p i mrna
51 Thermodynmic synthesis term (similr to those of Fkhouri & Ay 2010 nd Jnssens 2006) gene Twi Dl Sn S p i successful sttes ll possible sttes S K T p i T K D CK K T D D T D 1 K T T D S Q K K T S Q K K D S CQ K K K T D S T T S D D S D T D S K D K S CK T K D T D K T K S T S K D K S D S K T K D K S T D S
52 m i t S p i D m, m i 1 m i m i 1 m i m, m i p i t T m i D p, mrna Diffusion rte p i 1 p i p i 1 mrna Decy rte p i p, p i
53 mrna m i t S Trnsltion rte protein m i D m, m i 1 m i protein Diffusion rte m i 1 m i m, m i protein Decy rte p i t T m i D p, p i 1 p i p i 1 p i p, p i
54 Expression Preliminry Results Dt Used for Fitting: (from BDTNP) Dorsl Twist Snil Rhomboid Predictions fter Fitting: Nuclei (DV) t = 0 min t = 10 min t = 0 min t = 10 min t = 20 min t = 30 min t = 20 min t = 30 min t = 40 min t = 50 min t = 40 min t = 50 min
55 Sensitivity nlysis of biologicl models: (How much model output chnges s prticulr prmeters re tweked) Thermodynmic trnscription models hve not been similrly nlyzed Jckie Dresch, Xiozhou Liu, Ahmet Ay
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57 C u r
58 Zinzen et l. model shows low sensitivity for coopertivity
59 globl bioinformtic nlysis/chip dt phylogenetic comprisons Cis regultory grmmr expression ptterns trns-cting fctors
60 Retinoblstom (RB) corepressors E2F RB DP DNA pol PCNA RNR3
61 RB regultion by phosphoryltion Cyclin /CDK P E2F RB DP DNA pol PCNA RNR3
62 Developmentl- nd tissue-specific expression of Rbf1 Keller et l. (2004)
63 Rbf1 binds close to trnscriptionl strt sites 1
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65 cyclins/cdks Rbf1 Rbf2 corepressors SWI/SNF remodelers dream, l(3)mbt E2F
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67 dilp Incresed Rbf repression IRS (Chico) PIP2 PIP3 Akt Rheb Pi3K59F PTEN TSC1 TORC step TOR FOXO melt
68 dilp Decresed Rbf repression InR IRS (Chico) Pi3K68D Pi3K92E Pi3K21B Pi3K59F step PIP2 PTEN PP2A PIP3 PDK1 TSC2 TSC1 L (PRAS40) S6K Rheb SIK2 TORC CrebB TOR SREBP melt Thor (4E-BP)
69 Shingleton et l. (2009) Proc Biol Sci 276:2625.
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72 Arnosti lb nd friend Bill Henry Nitin Rj Styke Sengupt Kevin White Nicols Negre Funding from NIH, MSU Foundtion MSU icer: John Johnston
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