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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.


Related in: MedlinePlus

TI gives rise to a switch-like response.(A, B) Reciprocal switch in expression of full-length x transcript level (A) and full-length y transcript level (B). x and y expression is inversely correlated, while x levels decrease as α increases, y levels increase. H denotes the value of Hill coefficient (see Methods) (C, D) Expression maps for full-length (ηx, ηy) and truncated () transcripts from pX (C) and pY (D) respectively. Fraction of rounds of transcription which failed to fire (due to occlusion or sitting duck interference, SDI) are depicted at positions xk/L = 0 and yh/L = 0. Production of truncated RNA transcripts due to survival of SDCs at pY and pX promoter is represented at positions xk/L = 0.95 and yh/L = 0.95, respectively. Fraction of successful full-length transcripts (ηx, ηy) appears at positions xk/L>1 and yh/L>1. (E) Mechanistic representation of occlusion at pY for α = 0.4. Middle panel shows representative trajectories of ECs along the DNA when occlusion at pY is the dominant mechanism. Horizontal green dashed lined at pY region (middle panel) indicate rounds of transcription that were occluded. Top and bottom panels show transcriptional fraction of full-length (ηx, ηy) and truncated RNA transcripts () originated at pX (top panel) and pY (bottom panel), respectively. Fraction of rounds of transcription which failed to fire (due to occlusion or sitting duck interference) are depicted at positions xk/L = 0 (top panel) and yh/L = 0 (bottom panel). (F, G) Analogous representations showing RNAP collision for α = 0.8 (F) and SDI at pX for α = 1.7 (G) as the dominant mechanism, respectively. For E, F, and G panels, opaque ellipses represent RNAPs that continued transcribing after TI occurred while translucent ellipses denote RNAPs that were not able to bind or remain bound to DNA. The simulations shown in panels A-G correspond to L = 400 bp, τBX = 20 s, τIX = 12 s and τIY = 9.5 s, and α values varied from 0.1 to 2 by varying τBY from 2 to 40 s. Initiation time always remained smaller than binding times in order to avoid self-occlusion.
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pone.0133873.g003: TI gives rise to a switch-like response.(A, B) Reciprocal switch in expression of full-length x transcript level (A) and full-length y transcript level (B). x and y expression is inversely correlated, while x levels decrease as α increases, y levels increase. H denotes the value of Hill coefficient (see Methods) (C, D) Expression maps for full-length (ηx, ηy) and truncated () transcripts from pX (C) and pY (D) respectively. Fraction of rounds of transcription which failed to fire (due to occlusion or sitting duck interference, SDI) are depicted at positions xk/L = 0 and yh/L = 0. Production of truncated RNA transcripts due to survival of SDCs at pY and pX promoter is represented at positions xk/L = 0.95 and yh/L = 0.95, respectively. Fraction of successful full-length transcripts (ηx, ηy) appears at positions xk/L>1 and yh/L>1. (E) Mechanistic representation of occlusion at pY for α = 0.4. Middle panel shows representative trajectories of ECs along the DNA when occlusion at pY is the dominant mechanism. Horizontal green dashed lined at pY region (middle panel) indicate rounds of transcription that were occluded. Top and bottom panels show transcriptional fraction of full-length (ηx, ηy) and truncated RNA transcripts () originated at pX (top panel) and pY (bottom panel), respectively. Fraction of rounds of transcription which failed to fire (due to occlusion or sitting duck interference) are depicted at positions xk/L = 0 (top panel) and yh/L = 0 (bottom panel). (F, G) Analogous representations showing RNAP collision for α = 0.8 (F) and SDI at pX for α = 1.7 (G) as the dominant mechanism, respectively. For E, F, and G panels, opaque ellipses represent RNAPs that continued transcribing after TI occurred while translucent ellipses denote RNAPs that were not able to bind or remain bound to DNA. The simulations shown in panels A-G correspond to L = 400 bp, τBX = 20 s, τIX = 12 s and τIY = 9.5 s, and α values varied from 0.1 to 2 by varying τBY from 2 to 40 s. Initiation time always remained smaller than binding times in order to avoid self-occlusion.

Mentions: Biological conditions can cause the relative strengths of pX and pY promoters, α, to change from α<1 to α>1, giving rise to a switch response in gene expression (see Methods). For the chosen system of convergent promoters with a given length of overlapping DNA between them (here L = 400 bp, S1 Table), we obtained the production of truncated and full-length transcripts over a range of α values between 0.1 and 2 (Fig 3A and 3B). We assume pX is a constitutive promoter with fixed average RNAP binding and initiation times (τBX = 20 s, τIX = 12 s), whereas pY is an inducible promoter with a variable RNAP binding time (τBY = ατBX), but a fixed RNAP initiation time (τIY = 9.5 s). These parameter values are used hereafter unless otherwise stated. The condition tested here assumes EC’s do not pause and move with an average velocity of 50 bp/s (⟨vx⟩ = ⟨vy⟩ = 50 bp/s) from pX and pY promoters.


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

Bordoy AE, Chatterjee A - PLoS ONE (2015)

TI gives rise to a switch-like response.(A, B) Reciprocal switch in expression of full-length x transcript level (A) and full-length y transcript level (B). x and y expression is inversely correlated, while x levels decrease as α increases, y levels increase. H denotes the value of Hill coefficient (see Methods) (C, D) Expression maps for full-length (ηx, ηy) and truncated () transcripts from pX (C) and pY (D) respectively. Fraction of rounds of transcription which failed to fire (due to occlusion or sitting duck interference, SDI) are depicted at positions xk/L = 0 and yh/L = 0. Production of truncated RNA transcripts due to survival of SDCs at pY and pX promoter is represented at positions xk/L = 0.95 and yh/L = 0.95, respectively. Fraction of successful full-length transcripts (ηx, ηy) appears at positions xk/L>1 and yh/L>1. (E) Mechanistic representation of occlusion at pY for α = 0.4. Middle panel shows representative trajectories of ECs along the DNA when occlusion at pY is the dominant mechanism. Horizontal green dashed lined at pY region (middle panel) indicate rounds of transcription that were occluded. Top and bottom panels show transcriptional fraction of full-length (ηx, ηy) and truncated RNA transcripts () originated at pX (top panel) and pY (bottom panel), respectively. Fraction of rounds of transcription which failed to fire (due to occlusion or sitting duck interference) are depicted at positions xk/L = 0 (top panel) and yh/L = 0 (bottom panel). (F, G) Analogous representations showing RNAP collision for α = 0.8 (F) and SDI at pX for α = 1.7 (G) as the dominant mechanism, respectively. For E, F, and G panels, opaque ellipses represent RNAPs that continued transcribing after TI occurred while translucent ellipses denote RNAPs that were not able to bind or remain bound to DNA. The simulations shown in panels A-G correspond to L = 400 bp, τBX = 20 s, τIX = 12 s and τIY = 9.5 s, and α values varied from 0.1 to 2 by varying τBY from 2 to 40 s. Initiation time always remained smaller than binding times in order to avoid self-occlusion.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4519249&req=5

pone.0133873.g003: TI gives rise to a switch-like response.(A, B) Reciprocal switch in expression of full-length x transcript level (A) and full-length y transcript level (B). x and y expression is inversely correlated, while x levels decrease as α increases, y levels increase. H denotes the value of Hill coefficient (see Methods) (C, D) Expression maps for full-length (ηx, ηy) and truncated () transcripts from pX (C) and pY (D) respectively. Fraction of rounds of transcription which failed to fire (due to occlusion or sitting duck interference, SDI) are depicted at positions xk/L = 0 and yh/L = 0. Production of truncated RNA transcripts due to survival of SDCs at pY and pX promoter is represented at positions xk/L = 0.95 and yh/L = 0.95, respectively. Fraction of successful full-length transcripts (ηx, ηy) appears at positions xk/L>1 and yh/L>1. (E) Mechanistic representation of occlusion at pY for α = 0.4. Middle panel shows representative trajectories of ECs along the DNA when occlusion at pY is the dominant mechanism. Horizontal green dashed lined at pY region (middle panel) indicate rounds of transcription that were occluded. Top and bottom panels show transcriptional fraction of full-length (ηx, ηy) and truncated RNA transcripts () originated at pX (top panel) and pY (bottom panel), respectively. Fraction of rounds of transcription which failed to fire (due to occlusion or sitting duck interference) are depicted at positions xk/L = 0 (top panel) and yh/L = 0 (bottom panel). (F, G) Analogous representations showing RNAP collision for α = 0.8 (F) and SDI at pX for α = 1.7 (G) as the dominant mechanism, respectively. For E, F, and G panels, opaque ellipses represent RNAPs that continued transcribing after TI occurred while translucent ellipses denote RNAPs that were not able to bind or remain bound to DNA. The simulations shown in panels A-G correspond to L = 400 bp, τBX = 20 s, τIX = 12 s and τIY = 9.5 s, and α values varied from 0.1 to 2 by varying τBY from 2 to 40 s. Initiation time always remained smaller than binding times in order to avoid self-occlusion.
Mentions: Biological conditions can cause the relative strengths of pX and pY promoters, α, to change from α<1 to α>1, giving rise to a switch response in gene expression (see Methods). For the chosen system of convergent promoters with a given length of overlapping DNA between them (here L = 400 bp, S1 Table), we obtained the production of truncated and full-length transcripts over a range of α values between 0.1 and 2 (Fig 3A and 3B). We assume pX is a constitutive promoter with fixed average RNAP binding and initiation times (τBX = 20 s, τIX = 12 s), whereas pY is an inducible promoter with a variable RNAP binding time (τBY = ατBX), but a fixed RNAP initiation time (τIY = 9.5 s). These parameter values are used hereafter unless otherwise stated. The condition tested here assumes EC’s do not pause and move with an average velocity of 50 bp/s (⟨vx⟩ = ⟨vy⟩ = 50 bp/s) from pX and pY promoters.

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.


Related in: MedlinePlus