Volume 5, Issue 2
A Novel Computational Method for Two-State Transcription Model with Non-Exponential ON and OFF Durations

Manyi Zheng, Zhishan Qiu, Feng Jiao & Qiwen Sun

CSIAM Trans. Appl. Math., 5 (2024), pp. 295-319.

Published online: 2024-05

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  • Abstract

The fluctuation of mRNA molecule numbers within an isogenic cell population is primarily attributed to randomly switching between active (ON) and inactive (OFF) periods of gene transcription. In most studies the waiting-times for ON or OFF states are modeled as exponential distributions. However, increasing data suggest that the residence durations at ON or OFF are non-exponential distributed for which the traditional master equations cannot be presented. By combining Kolmogorov forward equations with alternating renewal processes, we present a novel method to compute the average transcription level and its noise by circumventing the bottleneck of master equations under gene ON and OFF switch. As an application, we consider lifetimes of OFF and ON states having Erlang distributions. We show that: (i) multiple steps from OFF to ON force the oscillating transcription while multiple steps from ON to OFF accelerate the transcription, (ii) the increase of steps between ON and OFF rapidly reduces the transcription noise to approach its minimum value. This suggests that a large number of steps between ON and OFF are not needed in the model to capture the stochastic transcription data. Our computation approach can be further used to treat a series of transcription cycles which are non-lattice distributed.

  • AMS Subject Headings

60K05, 34A35, 34A38, 92B05

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COPYRIGHT: © Global Science Press

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@Article{CSIAM-AM-5-295, author = {Zheng , ManyiQiu , ZhishanJiao , Feng and Sun , Qiwen}, title = {A Novel Computational Method for Two-State Transcription Model with Non-Exponential ON and OFF Durations}, journal = {CSIAM Transactions on Applied Mathematics}, year = {2024}, volume = {5}, number = {2}, pages = {295--319}, abstract = {

The fluctuation of mRNA molecule numbers within an isogenic cell population is primarily attributed to randomly switching between active (ON) and inactive (OFF) periods of gene transcription. In most studies the waiting-times for ON or OFF states are modeled as exponential distributions. However, increasing data suggest that the residence durations at ON or OFF are non-exponential distributed for which the traditional master equations cannot be presented. By combining Kolmogorov forward equations with alternating renewal processes, we present a novel method to compute the average transcription level and its noise by circumventing the bottleneck of master equations under gene ON and OFF switch. As an application, we consider lifetimes of OFF and ON states having Erlang distributions. We show that: (i) multiple steps from OFF to ON force the oscillating transcription while multiple steps from ON to OFF accelerate the transcription, (ii) the increase of steps between ON and OFF rapidly reduces the transcription noise to approach its minimum value. This suggests that a large number of steps between ON and OFF are not needed in the model to capture the stochastic transcription data. Our computation approach can be further used to treat a series of transcription cycles which are non-lattice distributed.

}, issn = {2708-0579}, doi = {https://doi.org/10.4208/csiam-am.SO-2023-0049}, url = {http://global-sci.org/intro/article_detail/csiam-am/23123.html} }
TY - JOUR T1 - A Novel Computational Method for Two-State Transcription Model with Non-Exponential ON and OFF Durations AU - Zheng , Manyi AU - Qiu , Zhishan AU - Jiao , Feng AU - Sun , Qiwen JO - CSIAM Transactions on Applied Mathematics VL - 2 SP - 295 EP - 319 PY - 2024 DA - 2024/05 SN - 5 DO - http://doi.org/10.4208/csiam-am.SO-2023-0049 UR - https://global-sci.org/intro/article_detail/csiam-am/23123.html KW - Stochastic gene transcription, two-state transcription model, master equations, non-Markov process, alternating renewal processes. AB -

The fluctuation of mRNA molecule numbers within an isogenic cell population is primarily attributed to randomly switching between active (ON) and inactive (OFF) periods of gene transcription. In most studies the waiting-times for ON or OFF states are modeled as exponential distributions. However, increasing data suggest that the residence durations at ON or OFF are non-exponential distributed for which the traditional master equations cannot be presented. By combining Kolmogorov forward equations with alternating renewal processes, we present a novel method to compute the average transcription level and its noise by circumventing the bottleneck of master equations under gene ON and OFF switch. As an application, we consider lifetimes of OFF and ON states having Erlang distributions. We show that: (i) multiple steps from OFF to ON force the oscillating transcription while multiple steps from ON to OFF accelerate the transcription, (ii) the increase of steps between ON and OFF rapidly reduces the transcription noise to approach its minimum value. This suggests that a large number of steps between ON and OFF are not needed in the model to capture the stochastic transcription data. Our computation approach can be further used to treat a series of transcription cycles which are non-lattice distributed.

Manyi Zheng, Zhishan Qiu, Feng Jiao & Qiwen Sun. (2024). A Novel Computational Method for Two-State Transcription Model with Non-Exponential ON and OFF Durations. CSIAM Transactions on Applied Mathematics. 5 (2). 295-319. doi:10.4208/csiam-am.SO-2023-0049
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