A Modelling Framework for Gene Regulatory Networks Including Transcription and Translation

Bulletin of Mathematical Biology
R EdwardsP van den Driessche

Abstract

Qualitative models of gene regulatory networks have generally considered transcription factors to regulate directly the expression of other transcription factors, without any intermediate variables. In fact, gene expression always involves transcription, which produces mRNA molecules, followed by translation, which produces protein molecules, which can then act as transcription factors for other genes (in some cases after post-transcriptional modifications). Suppressing these multiple steps implicitly assumes that the qualitative behaviour does not depend on them. Here we explore a class of expanded models that explicitly includes both transcription and translation, keeping track of both mRNA and protein concentrations. We mainly deal with regulation functions that are steep sigmoids or step functions, as is often done in protein-only models. We find that flow cannot be constrained to switching domains, though there can still be asymptotic approach to singular stationary points (fixed points in the vicinity of switching thresholds). This avoids the thorny issue of singular flow, but leads to somewhat more complicated possibilities for flow between threshold crossings. In the infinitely fast limit of either mRNA or protein rates...Continue Reading

References

Dec 1, 1973·Journal of Theoretical Biology·R Thomas
Apr 1, 1973·Journal of Theoretical Biology·L Glass, S A Kauffman
Feb 5, 2000·Nature·M B Elowitz, S Leibler
Feb 5, 2000·Nature·T S GardnerJ J Collins
Jul 18, 2002·Proceedings of the National Academy of Sciences of the United States of America·Jonathan A BernsteinStanley N Cohen
Jul 17, 2004·Proceedings of the National Academy of Sciences of the United States of America·Jordi Garcia-OjalvoSteven H Strogatz
Oct 1, 2005·Journal of Mathematical Biology·Richard CaseyJean-Luc Gouzé
Dec 31, 2005·Journal of Mathematical Biology·Etienne Farcot
Mar 1, 2006·Theoretical Biology & Medical Modelling·Verner PaetkauReinhard Illner
Aug 12, 2009·Journal of Theoretical Biology·A PolynikisM di Bernardo
May 23, 2012·Bulletin of Mathematical Biology·Tomáš GedeonJeffrey J Heys
Jul 5, 2013·Chaos·A MachinaP van den Driessche

❮ Previous
Next ❯

Citations

Oct 27, 2016·Chaos·Otti D'HuysDaniel J Gauthier
Feb 6, 2018·Experimental and Therapeutic Medicine·Fen Hu, Yunfeng Zhang
Jun 8, 2018·Frontiers in Physiology·Bree CumminsKonstantin Mischaikow
Mar 17, 2017·Physical Review. E·Johannes LohmannDaniel J Gauthier
Jan 1, 2016·SIAM Journal on Applied Dynamical Systems·Bree CumminsKafung Mok
Nov 18, 2018·Journal of Theoretical Biology·Madalena ChavesJean-Luc Gouzé
Jan 1, 2019·SIAM Journal on Applied Dynamical Systems·Peter Crawford-KahrlTomas Gedeon
Apr 11, 2017·Physica D. Nonlinear Phenomena·Tomáš GedeonHiroe Oka
Jun 6, 2018·Physica D. Nonlinear Phenomena·Zane HuttingaKonstantin Mischaikow

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.