BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1611030000?filename=MODEL1611030000.pdfhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1611030000?filename=MODEL1611030000-biopax3.owlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1611030000?filename=MODEL1611030000-biopax2.owlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1611030000?filename=MODEL1611030000_urn.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1611030000?filename=MODEL1611030000_url.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1611030000?filename=MODEL1611030000.mhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1611030000?filename=MODEL1611030000.vcmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1611030000?filename=MODEL1611030000.xpphttps://www.ebi.ac.uk/biomodels/model/download/MODEL1611030000?filename=MODEL1611030000.scihttps://www.ebi.ac.uk/biomodels/model/download/MODEL1611030000?filename=MODEL1611030000.pngprimaryOK200Luis DiambraNon-curatedordinary differential equation modelL3V1https://www.ebi.ac.uk/biomodels/MODEL161103000026958852falseBioModelsModelsSBMLGuisoni2016 Cis regulatory system (CRS) can drive sustained oscillations2016MODEL1611030000Guisoni N, Monteoliva D, Diambra LGuisoni N26958852,
It is well known that single-gene circuits with negative feedback loop can lead to oscillatory gene expression when they operate with time delay. In order to generate these oscillations many processes can contribute to properly timing such delay. Here we show that the time delay coming from the transitions between internal states of the cis-regulatory system (CRS) can drive sustained oscillations in an auto-repressive single-gene circuit operating in a small volume like a cell. We found that the cooperative binding of repressor molecules is not mandatory for a oscillatory behavior if there are enough binding sites in the CRS. These oscillations depend on an adequate balance between the CRS kinetic, and the synthesis/degradation rates of repressor molecules. This finding suggest that the multi-site CRS architecture can play a key role for oscillatory behavior of gene expression. Finally, our results can also help to synthetic biologists on the design of the promoters architecture for new genetic oscillatory circuits.. null, 11.
Instituto de Física de Líquidos y Sistemas Biológicos, Universidad Nacional de La Plata, La Plata, Argentina.ldiambra@gmail.comIt is well known that single-gene circuits with negative feedback loop can lead to oscillatory gene expression when they operate with time delay. In order to generate these oscillations many processes can contribute to properly timing such delay. Here we show that the time delay coming from the transitions between internal states of the cis-regulatory system (CRS) can drive sustained oscillations in an auto-repressive single-gene circuit operating in a small volume like a cell. We found that the cooperative binding of repressor molecules is not mandatory for a oscillatory behavior if there are enough binding sites in the CRS. These oscillations depend on an adequate balance between the CRS kinetic, and the synthesis/degradation rates of repressor molecules. This finding suggest that the multi-site CRS architecture can play a key role for oscillatory behavior of gene expression. Finally, our results can also help to synthetic biologists on the design of the promoters architecture for new genetic oscillatory circuits.Promoters Architecture-Based Mechanism for Noise-Induced Oscillations in a Single-Gene Circuit.Guisoni N N, Monteoliva D D, Diambra L Lcarcinoma in situ, ahl4, SCS, mother-to-child transmission of rubella syndrome, craniosynostosis 1, malignant, 2610511A05Rik, body system, BB234005, fetal rubella syndrome, Congenital, Drives., CIS, Cis, G18, Rubella Syndrome, system, congenital rubella, intraepithelial carcinoma, connected anatomical system, Congenital Rubella, congenital rubella syndrome, foetal rubella syndrome, Congenital Rubella syndrome, CIS-1, rubella congenital, CRS, anatomical systems, craniostenosis, TWIST, 9030605P22Rik, stage 0 disease, non-invasive carcinoma, CSO, Gestational rubella syndrome (disorder), organ system, TWIST1-related craniosynostosis, SOCS, in situ, BPES3, Protein G18, craniosynostosis type 1, BPES2, CRS1, bHLHa38, carcinoma, epithelial tumor, Suppressor of cytokine signaling, BACTS2, ACS3, Congenital rubella syndromeprojections, multicellular organismal catabolic process, single-organism catabolic process, SCS, small volume, craniosynostosis 1, artificial sequence, neutral molecular compounds, 2610511A05Rik, Long Term, binding site, BB234005, dmTAF[[II]]230, Roles, Rubella Syndrome, Concepts, Effect, molecule, hereditary., IKKg, multicellular organismal biosynthetic process, KEY, Key, molecula, single-organism biosynthetic process, molecules, Gene Expressions, craniostenosis, TFIID TAF250, cel, catabolism, anabolism, Molekuel, behavioral response to stimulus, non-invasive carcinoma, genetic, papilla, Role Concepts, Protein G18, bHLHa38, Long-Term Effects, single-organism behavior, carcinoma in situ, mother-to-child transmission of rubella syndrome, dTAF[[II]]230, anatomical protrusion, Process, lamina, familial, Longterm Effect, TAF200, flanges, TAFII-250, TAF250/230, results, Acceptance Processes, Binding, Congenital, Acceptance Process, DmIKKgamma, TAFII250, Role Concept, dIKK, CIS, Cis, shelf, G18, Kenny, Role, intraepithelial carcinoma, Congenital Rubella, region, CIS-1, breakdown, Drives, positional polypeptide feature, shelves, IKK-gamma, 9030605P22Rik, INSDC_feature:gene, stage 0 disease, CG17603, projection, TAF[[II]], ridge, organ system, SYNTHETIC CONSTRUCT sequences, DmelCG16910, Taf250, spine, SR3-5, CRS1, artificial, inherited genetic, Feedbacks, time, TAF230, d230, Effects, region or site annotation, lamellae, Processes, Gene, dTAFII250, biosynthesis, EfW1, process of organ, body system, dIKK-gamma, protrusion, period, lamella, dmTAF1, Taf230, DmIKK-gamma, Sites, system, dmIKKgamma, synthetic genetic interaction (sensu inequality), IKK[[gamma]], TAF250, Site, Taf200, positional, anatomical systems, dTAF[[II]]250, Longterm, formation, cell, ligand, synthetic genetic interaction defined by inequality, Taf1p, ridges, Long-Term, Expressions, TWIST1-related 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SOCS, BPES3, BPES2, processus, epithelial tumor, Suppressor of cytokine signaling, ACS3, Congenital rubella syndrome, TAF1projections, extent, multicellular organismal catabolic process, single-organism catabolic process, SCS, small volume, craniosynostosis 1, artificial sequence, Public Sectors, 2610511A05Rik, Long Term, binding site, BB234005, dmTAF[[II]]230, Roles, Rubella Syndrome, Concepts, Public Enterprise, Effect, multicellular organismal biosynthetic process, single-organism biosynthetic process, Gene Expressions, craniostenosis, TFIID TAF250, cel, catabolism, anabolism, Public Domains, behavioral response to stimulus, non-invasive carcinoma, genetic, papilla, Role Concepts, Protein G18, bHLHa38, Long-Term Effects, single-organism behavior, carcinoma in situ, mother-to-child transmission of rubella syndrome, Noise, dTAF[[II]]230, anatomical protrusion, Process, completeness, lamina, familial, Pollution, Longterm Effect, TAF200, flanges, TAFII-250, TAF250/230, results, Acceptance Processes, Binding, Congenital, Acceptance Process, TAFII250, Role Concept, Playthings and Play, Public Domain, CIS, Cis, G18, shelf, Role, Domains, Plaything, intraepithelial carcinoma, Congenital Rubella, region, Domain, CIS-1, breakdown, Drives, positional polypeptide feature, shelves, Toys, 9030605P22Rik, INSDC_feature:gene, stage 0 disease, CG17603, projection, TAF[[II]], ridge, organ system, SYNTHETIC CONSTRUCT sequences, Sector, Taf250, spine, SR3-5, CRS1, artificial, inherited genetic, Noise Pollution, Feedbacks, time, TAF230, d230, Sectors, Plays, Effects, region or site annotation, lamellae, Processes, number, Gene, dTAFII250, Copyrights, biosynthesis, EfW1, body system, process of organ, presence, protrusion, period, lamella, dmTAF1, Taf230, Sites, system, synthetic genetic interaction (sensu inequality), Enterprises, TAF250, Toy, Site, Taf200, positional, anatomical systems, dTAF[[II]]250, Playthings, Longterm, formation, cell, ligand, synthetic genetic interaction defined by inequality, Taf1p, ridges, Long-Term, Public Enterprises, Expressions, TWIST1-related craniosynostosis, synthesis, dTAF250, Combining Site, Abstract, Puppets, in situ, craniosynostosis type 1, Play, site, Long-Term Effect, carcinoma, Expression, TAF, Behaviors, Enterprise, laminae, Combining Sites, constitutitional genetic, behaviour, BACTS2, Puppet, ahl4, TAF[[II]]250, adequate, degradation, malignant, synthesize, anatomical process, l(3)84Ab, artificial gene, BG:DS00004.13, Binding Site, synthetic DNA, Cell, low volume, dTAF230, Concept, fetal rubella syndrome, count in organism, Public, p230, Long Term Effects, TAF[[II]]250/230, synthetic, TFIID, congenital rubella, connected anatomical system, congenital rubella syndrome, flange, organ process, Data Base, foetal rubella syndrome, Taf[[II]]250, Congenital Rubella syndrome, Acceptance, rubella congenital, CRS, TAF[[II]]230, INSDC_feature:misc_binding, TWIST, Combining, TAF[II]250, synthetic constructs, CSO, Gestational rubella syndrome (disorder), Noises, Longterm Effects, processes, process, DmelCG17603, behavioural response to stimulus, binding_or_interaction_site, SOCS, BPES3, BPES2, processus, Public., epithelial tumor, quantitative, Suppressor of cytokine signaling, hereditary, ACS3, Congenital rubella syndrome, TAF1, presence or absence in organismPollution, Noise Pollution, Noise, INSDC_feature:gene., NoisesfalseGuisoni2016 - Cis-regulatory system (CRS) can drive sustained oscillations
Guisoni2016 - Cis-regulatory system (CRS) can
drive sustained oscillations
This model is described in the article:
Promoters Architecture-Based
Mechanism for Noise-Induced Oscillations in a Single-Gene
Circuit.
Guisoni N, Monteoliva D, Diambra
L.
PLoS ONE 2016; 11(3): e0151086
Abstract:
It is well known that single-gene circuits with negative
feedback loop can lead to oscillatory gene expression when they
operate with time delay. In order to generate these
oscillations many processes can contribute to properly timing
such delay. Here we show that the time delay coming from the
transitions between internal states of the cis-regulatory
system (CRS) can drive sustained oscillations in an
auto-repressive single-gene circuit operating in a small volume
like a cell. We found that the cooperative binding of repressor
molecules is not mandatory for a oscillatory behavior if there
are enough binding sites in the CRS. These oscillations depend
on an adequate balance between the CRS kinetic, and the
synthesis/degradation rates of repressor molecules. This
finding suggest that the multi-site CRS architecture can play a
key role for oscillatory behavior of gene expression. Finally,
our results can also help to synthetic biologists on the design
of the promoters architecture for new genetic oscillatory
circuits.
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2016-11-032016-11-032016-11-03MODEL161103000026958852