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Cis-Antisense Transcription Gives Rise to Tunable Genetic Switch Behavior: A Mathematical Modeling Approach.

Bordoy AE, Chatterjee A - PLoS ONE (2015)

Bottom Line: Here, we present a mathematical modeling framework for antisense transcription that combines the effects of both transcriptional interference and cis-antisense regulation.We identify important parameters affecting the cellular switch response in order to provide the design principles for tunable gene expression using antisense transcription.This presents an important insight into functional role of antisense transcription and its importance towards design of synthetic biological switches.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, United States of America.

ABSTRACT
Antisense transcription has been extensively recognized as a regulatory mechanism for gene expression across all kingdoms of life. Despite the broad importance and extensive experimental determination of cis-antisense transcription, relatively little is known about its role in controlling cellular switching responses. Growing evidence suggests the presence of non-coding cis-antisense RNAs that regulate gene expression via antisense interaction. Recent studies also indicate the role of transcriptional interference in regulating expression of neighboring genes due to traffic of RNA polymerases from adjacent promoter regions. Previous models investigate these mechanisms independently, however, little is understood about how cells utilize coupling of these mechanisms in advantageous ways that could also be used to design novel synthetic genetic devices. Here, we present a mathematical modeling framework for antisense transcription that combines the effects of both transcriptional interference and cis-antisense regulation. We demonstrate the tunability of transcriptional interference through various parameters, and that coupling of transcriptional interference with cis-antisense RNA interaction gives rise to hypersensitive switches in expression of both antisense genes. When implementing additional positive and negative feed-back loops from proteins encoded by these genes, the system response acquires a bistable behavior. Our model shows that combining these multiple-levels of regulation allows fine-tuning of system parameters to give rise to a highly tunable output, ranging from a simple-first order response to biologically complex higher-order response such as tunable bistable switch. We identify important parameters affecting the cellular switch response in order to provide the design principles for tunable gene expression using antisense transcription. This presents an important insight into functional role of antisense transcription and its importance towards design of synthetic biological switches.

No MeSH data available.


Antisense transcription coupled with protein feedback gives rise to bistability.(A) Successful full-length x and y transcripts that do not undergo antisense interaction are free to be translated into proteins X and Y respectively. Production of inducer molecule, Z, is indirectly activated by protein Y. Protein X implements a negative feed-back loop by binding to operator site OY and repressing promoter pY. Z binds to X and relieves the repression of pY promoter. (B-D) These multiple regulatory layers enable cells to demonstrate a higher-order a bistable switch response to different rates of production of W (denoted by kWZ). ON state is characterized by production of proteins Y and Z while OFF state is characterized by production of protein X. Threshold kWZ value to switch between OFF to ON states is 11.5 nM/s whereas the threshold for the inverse switch between ON to OFF states occurs at kWZ = 8.8 nM/s.
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pone.0133873.g006: Antisense transcription coupled with protein feedback gives rise to bistability.(A) Successful full-length x and y transcripts that do not undergo antisense interaction are free to be translated into proteins X and Y respectively. Production of inducer molecule, Z, is indirectly activated by protein Y. Protein X implements a negative feed-back loop by binding to operator site OY and repressing promoter pY. Z binds to X and relieves the repression of pY promoter. (B-D) These multiple regulatory layers enable cells to demonstrate a higher-order a bistable switch response to different rates of production of W (denoted by kWZ). ON state is characterized by production of proteins Y and Z while OFF state is characterized by production of protein X. Threshold kWZ value to switch between OFF to ON states is 11.5 nM/s whereas the threshold for the inverse switch between ON to OFF states occurs at kWZ = 8.8 nM/s.

Mentions: We next consider regulation of the transcriptional process when protein products X and Y, encoded by genes x and y respectively, exert negative and positive feedback to create a gene regulatory network based on cis-antisense transcription (see Methods). We consider that protein X implements a negative feed-back loop by controlling pY strength. Protein Y in turn acts as an antagonist of protein X, and through the indirect activation of protein Z production implements a positive feed-back loop by relieving pY repression via binding of Z to X (Fig 6A). In this and following section, α only varies from α = fY,min/fX = 0.37 to α = fY,max/fX = 1.74, corresponding to the repressed state and de-repressed state of pY, respectively (S1 Table). We numerically solved equations 5–18 to analyze the steady state behavior of the system in response to different rates of production (kWZ) of transcriptional activator/signaling molecule Z. Steady state solutions show that coupling TI and AR with feedback from regulatory proteins give rise to a characteristic bistable switch response. When bistability is present, cells can adopt two experimentally observable distinct states depending on the production rate of Z (Fig 6B) [73]. The bistable curve comprises the characteristic S-shaped section where multiple steady states reside. Two of these are stable steady states that correspond to ON (lower curve, Fig 6B) and OFF state of the switch (upper curve, Fig 6B), whereas the unstable steady state in the middle is not observed experimentally. At low rates of production of Z the systems exists in an OFF state which is characterized by low expression levels of Y and Z (Fig 6C and 6D), but high expression levels of repressor X (Fig 6B). As kWZ increases the system continues to be in the OFF state until it reaches a threshold rate of 11.5 nM/s, where the systems transitions to the ON state characterized by nearly two orders of magnitude increase in Z and Y levels and decrease in repressor X level. Conversely, once the switch is turned ON, the system continues to be in the ON state until the production rate kWZ drops below 8.8 nM/s. The system thus demonstrates a sophisticated hysteresis response to Z production rate, marked by well separated ON to OFF states occurring at different threshold rates. It is important to note that both hypersensitive and bistable switches are considered higher-order because their non-linearity indicates cooperation between different mechanisms integrating the system. In the model proposed here interactions arise between the three regulatory layers: TI, AR and protein regulation.


Cis-Antisense Transcription Gives Rise to Tunable Genetic Switch Behavior: A Mathematical Modeling Approach.

Bordoy AE, Chatterjee A - PLoS ONE (2015)

Antisense transcription coupled with protein feedback gives rise to bistability.(A) Successful full-length x and y transcripts that do not undergo antisense interaction are free to be translated into proteins X and Y respectively. Production of inducer molecule, Z, is indirectly activated by protein Y. Protein X implements a negative feed-back loop by binding to operator site OY and repressing promoter pY. Z binds to X and relieves the repression of pY promoter. (B-D) These multiple regulatory layers enable cells to demonstrate a higher-order a bistable switch response to different rates of production of W (denoted by kWZ). ON state is characterized by production of proteins Y and Z while OFF state is characterized by production of protein X. Threshold kWZ value to switch between OFF to ON states is 11.5 nM/s whereas the threshold for the inverse switch between ON to OFF states occurs at kWZ = 8.8 nM/s.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4519249&req=5

pone.0133873.g006: Antisense transcription coupled with protein feedback gives rise to bistability.(A) Successful full-length x and y transcripts that do not undergo antisense interaction are free to be translated into proteins X and Y respectively. Production of inducer molecule, Z, is indirectly activated by protein Y. Protein X implements a negative feed-back loop by binding to operator site OY and repressing promoter pY. Z binds to X and relieves the repression of pY promoter. (B-D) These multiple regulatory layers enable cells to demonstrate a higher-order a bistable switch response to different rates of production of W (denoted by kWZ). ON state is characterized by production of proteins Y and Z while OFF state is characterized by production of protein X. Threshold kWZ value to switch between OFF to ON states is 11.5 nM/s whereas the threshold for the inverse switch between ON to OFF states occurs at kWZ = 8.8 nM/s.
Mentions: We next consider regulation of the transcriptional process when protein products X and Y, encoded by genes x and y respectively, exert negative and positive feedback to create a gene regulatory network based on cis-antisense transcription (see Methods). We consider that protein X implements a negative feed-back loop by controlling pY strength. Protein Y in turn acts as an antagonist of protein X, and through the indirect activation of protein Z production implements a positive feed-back loop by relieving pY repression via binding of Z to X (Fig 6A). In this and following section, α only varies from α = fY,min/fX = 0.37 to α = fY,max/fX = 1.74, corresponding to the repressed state and de-repressed state of pY, respectively (S1 Table). We numerically solved equations 5–18 to analyze the steady state behavior of the system in response to different rates of production (kWZ) of transcriptional activator/signaling molecule Z. Steady state solutions show that coupling TI and AR with feedback from regulatory proteins give rise to a characteristic bistable switch response. When bistability is present, cells can adopt two experimentally observable distinct states depending on the production rate of Z (Fig 6B) [73]. The bistable curve comprises the characteristic S-shaped section where multiple steady states reside. Two of these are stable steady states that correspond to ON (lower curve, Fig 6B) and OFF state of the switch (upper curve, Fig 6B), whereas the unstable steady state in the middle is not observed experimentally. At low rates of production of Z the systems exists in an OFF state which is characterized by low expression levels of Y and Z (Fig 6C and 6D), but high expression levels of repressor X (Fig 6B). As kWZ increases the system continues to be in the OFF state until it reaches a threshold rate of 11.5 nM/s, where the systems transitions to the ON state characterized by nearly two orders of magnitude increase in Z and Y levels and decrease in repressor X level. Conversely, once the switch is turned ON, the system continues to be in the ON state until the production rate kWZ drops below 8.8 nM/s. The system thus demonstrates a sophisticated hysteresis response to Z production rate, marked by well separated ON to OFF states occurring at different threshold rates. It is important to note that both hypersensitive and bistable switches are considered higher-order because their non-linearity indicates cooperation between different mechanisms integrating the system. In the model proposed here interactions arise between the three regulatory layers: TI, AR and protein regulation.

Bottom Line: Here, we present a mathematical modeling framework for antisense transcription that combines the effects of both transcriptional interference and cis-antisense regulation.We identify important parameters affecting the cellular switch response in order to provide the design principles for tunable gene expression using antisense transcription.This presents an important insight into functional role of antisense transcription and its importance towards design of synthetic biological switches.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, United States of America.

ABSTRACT
Antisense transcription has been extensively recognized as a regulatory mechanism for gene expression across all kingdoms of life. Despite the broad importance and extensive experimental determination of cis-antisense transcription, relatively little is known about its role in controlling cellular switching responses. Growing evidence suggests the presence of non-coding cis-antisense RNAs that regulate gene expression via antisense interaction. Recent studies also indicate the role of transcriptional interference in regulating expression of neighboring genes due to traffic of RNA polymerases from adjacent promoter regions. Previous models investigate these mechanisms independently, however, little is understood about how cells utilize coupling of these mechanisms in advantageous ways that could also be used to design novel synthetic genetic devices. Here, we present a mathematical modeling framework for antisense transcription that combines the effects of both transcriptional interference and cis-antisense regulation. We demonstrate the tunability of transcriptional interference through various parameters, and that coupling of transcriptional interference with cis-antisense RNA interaction gives rise to hypersensitive switches in expression of both antisense genes. When implementing additional positive and negative feed-back loops from proteins encoded by these genes, the system response acquires a bistable behavior. Our model shows that combining these multiple-levels of regulation allows fine-tuning of system parameters to give rise to a highly tunable output, ranging from a simple-first order response to biologically complex higher-order response such as tunable bistable switch. We identify important parameters affecting the cellular switch response in order to provide the design principles for tunable gene expression using antisense transcription. This presents an important insight into functional role of antisense transcription and its importance towards design of synthetic biological switches.

No MeSH data available.