MODEL1202270001
type: SBMLModel
species: 304152
species: 304092
rule: 304225
reaction: 304345
is described by: http://identifiers.org/pubmed/22453733
species: 304189
substance units: 291211
volume units: 291259
area units: area
units def: 303935
species: 304116
compartment: 304044
reaction: 304430
species: 304177
notes: This model is from the article: A regulatory role for repeated decoy transcription factor binding sites in target gene expression. Lee TH, Maheshri N. Mol Syst Biol. 2012 Mar 27;8:576. 22453733 , Abstract: Tandem repeats of DNA that contain transcription factor (TF) binding sites could serve as decoys, competitively binding to TFs and affecting target gene expression. Using a synthetic system in budding yeast, we demonstrate that repeated decoy sites inhibit gene expression by sequestering a transcriptional activator and converting the graded dose-response of target promoters to a sharper, sigmoidal-like response. On the basis of both modeling and chromatin immunoprecipitation measurements, we attribute the altered response to TF binding decoy sites more tightly than promoter binding sites. Tight TF binding to arrays of contiguous repeated decoy sites only occurs when the arrays are mostly unoccupied. Finally, we show that the altered sigmoidal-like response can convert the graded response of a transcriptional positive-feedback loop to a bimodal response. Together, these results show how changing numbers of repeated TF binding sites lead to qualitative changes in behavior and raise new questions about the stability of TF/promoter binding. Note: This model corresponds to the comprehensive model encompassing the basic model (MODEL1202270000) as well as the tTA/dox (tet-transcriptional activator/doxycycline) interaction, described in the paper. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N,…
rule: 304237
species: 304164
species: 304068
reaction: 304515
curated: false
species: 304140
units def: 303959
species: 304080
rule: 304213
reaction: 304601
time units: 291235
species: 304128
species: 304104
length unit: length
rule: 304249
reaction: 304261
units def: 304008
species: 304201
species: 304056
name: Lee2012_GeneExpression_tTA-doxInteraction

304152
type: Species
constant: false
boundary condition: false
has only substance units: true
substance units: 303935
initial concentration: NaN
initial amount: 30.0
in compartment: 304044
name: decoy sites balance

303935
type: SBMLUnitsDef
unit: 303947
name: molecule

303947
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.66053872801495E-24
kind: MOLE

304044
type: Compartment
constant: true
size: 10000.0
spatial dimensions: 3.0
name: nucleus

304092
type: Species
constant: false
boundary condition: false
has only substance units: true
substance units: 303935
initial concentration: NaN
initial amount: 0.0
in compartment: 304044
name: TF activator_dox complex1

304345
type: Reaction
kinetic law: 304394
product: 304382
reactant: 304370
reactant: 304358
fast: false
reversible: true
name: reaction xTx

304418
type: LocalParameter
units: 304008
value: 0.0021
name: ks-

304008
type: SBMLUnitsDef
unit: 304032
unit: 304020
name: 1/minute

304032
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 0.0166666666666667
kind: DIMENSIONLESS

304020
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

304406
type: LocalParameter
units: 303959
value: 0.01
name: ks+

303959
type: SBMLUnitsDef
unit: 303996
unit: 303983
unit: 303971
name: 1/(molecule*minute)

303996
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.00369033166667E22
kind: DIMENSIONLESS

303983
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

303971
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: MOLE

304382
type: SpeciesReference
stoichiometry: 1.0
species: 304104

304104
type: Species
constant: false
boundary condition: false
has only substance units: true
substance units: 303935
initial concentration: NaN
initial amount: 0.0
in compartment: 304044
name: TF activator_dox complex3

304370
type: SpeciesReference
stoichiometry: 1.0
species: 304080

304080
type: Species
constant: false
boundary condition: false
has only substance units: true
substance units: 303935
initial concentration: NaN
initial amount: 50.0
in compartment: 304044
name: free dox

304358
type: SpeciesReference
stoichiometry: 1.0
species: 304092

304189
type: Species
constant: false
boundary condition: false
has only substance units: true
substance units: 303935
initial concentration: NaN
initial amount: 7.0
in compartment: 304044
name: promotor balance

304116
type: Species
constant: false
boundary condition: false
has only substance units: true
substance units: 303935
initial concentration: NaN
initial amount: 50.0
in compartment: 304044
name: total intracellular dox

304430
type: Reaction
kinetic law: 304479
product: 304467
reactant: 304455
reactant: 304443
fast: false
reversible: true
name: reaction TN

304503
type: LocalParameter
units: 304008
value: 0.42
name: kn-

304491
type: LocalParameter
units: 303959
value: 0.01
name: kn+

304467
type: SpeciesReference
stoichiometry: 1.0
species: 304140

304140
type: Species
constant: false
boundary condition: false
has only substance units: true
substance units: 303935
initial concentration: NaN
initial amount: 0.0
in compartment: 304044
name: total decoy sites

304455
type: SpeciesReference
stoichiometry: 1.0
species: 304128

304128
type: Species
constant: false
boundary condition: false
has only substance units: true
substance units: 303935
initial concentration: NaN
initial amount: 30.0
in compartment: 304044
name: decoy sites

304443
type: SpeciesReference
stoichiometry: 1.0
species: 304068

304068
type: Species
constant: false
boundary condition: false
has only substance units: true
substance units: 303935
initial concentration: NaN
initial amount: 100.0
in compartment: 304044
name: free TF activator

304177
type: Species
constant: false
boundary condition: false
has only substance units: true
substance units: 303935
initial concentration: NaN
initial amount: 0.0
in compartment: 304044
name: total promotor

304164
type: Species
constant: false
boundary condition: false
has only substance units: true
substance units: 303935
initial concentration: NaN
initial amount: 7.0
in compartment: 304044
name: promotor

304515
type: Reaction
kinetic law: 304564
product: 304552
reactant: 304539
reactant: 304527
fast: false
reversible: true
name: reaction TP

304589
type: LocalParameter
units: 304008
value: 0.42
name: kp-

304577
type: LocalParameter
units: 303959
value: 0.01
name: kp+

304552
type: SpeciesReference
stoichiometry: 1.0
species: 304177

304539
type: SpeciesReference
stoichiometry: 1.0
species: 304164

304527
type: SpeciesReference
stoichiometry: 1.0
species: 304068

304601
type: Reaction
kinetic law: 304649
product: 304637
reactant: 304625
reactant: 304613
fast: false
reversible: true
name: reaction xT

304673
type: LocalParameter
units: 304008
value: 0.0021
name: ks-

304661
type: LocalParameter
units: 303959
value: 0.01
name: ks+

304637
type: SpeciesReference
stoichiometry: 1.0
species: 304201

304201
type: Species
constant: false
boundary condition: false
has only substance units: true
substance units: 303935
initial concentration: NaN
initial amount: 0.0
in compartment: 304044
name: TF activator_dox complex2

304625
type: SpeciesReference
stoichiometry: 1.0
species: 304080

304613
type: SpeciesReference
stoichiometry: 1.0
species: 304068

304261
type: Reaction
kinetic law: 304309
product: 304297
reactant: 304285
reactant: 304273
fast: false
reversible: true
name: reaction Tx

304333
type: LocalParameter
units: 304008
value: 0.0021
name: ks-

304321
type: LocalParameter
units: 303959
value: 0.01
name: ks+

304297
type: SpeciesReference
stoichiometry: 1.0
species: 304092

304285
type: SpeciesReference
stoichiometry: 1.0
species: 304080

304273
type: SpeciesReference
stoichiometry: 1.0
species: 304068

304056
type: Species
constant: false
boundary condition: false
has only substance units: true
substance units: 303935
initial concentration: NaN
initial amount: 100.0
in compartment: 304044
name: total TF level