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Center for Models of Life
Niels Bohr Institute
University of Copenhagen
Blegdamsvej 17
2100 Copenhagen Ø

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Transcription dynamics and regulation

Transcription is a dynamic process dealing with RNA polymerase (RNAP), Promoters, and movement of RNAP interference along the DNA. Transcription initiation can be regulated by a number of proteins, including transcription factors and RNAP from convergent promoters. We build physical/mathematical models of this regulation in order to understand limits and possibilities af this essential nano-mechanical part of RNA polymerase traffic in Escherichia coli.


Sneppen K, Dodd IB, Shearwin KE, Palmer AC, Schubert RA, Callen BP, Egan JB
A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coli
J. Mol. Biol. 346 (2005)

Peter Horvath, Alexander Hunziker, Janos Erdossy, Sandeep Krishna and Szabolcs Semsey
Timing of gene transcription in the galactose utilization system of Escherichia coli
JBC 285 (2010)

Ala Trusina and Chao Tang
The unfolded protein response and translation attenuation: a modelling approach
Diabetes, Obesity and Metabolism 12 (2010)

Ala Trusina, Feroz Papa and Chao Tang
Translation Attenuation Mechanism in Unfolded Protein Response
Evolution from Cellular to Social Scales NATO Science for Peace and Security Series B: Physics and Biophysics 0 (2008)

Ilaria Cataudella, Ala Trusina, Kim Sneppen, Kenn Gerdes, and Namiko Mitarai
Conditional cooperativity in toxin–antitoxin regulation prevents random toxin activation and promotes fast translational recovery
Nuc. Acids Res. 40 (2012)

Kamilla Norregaard, Magnus Andersson, Kim Sneppen, Peter Eigil Nielsen, Stanley Brown, and Lene B. Oddershede
DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch
Proc. Natl. Acad. Sct. USA 110 (2013)

Kamilla Norregaard, Magnus Andersson, Kim Sneppen, Peter Eigil Nielsen, Stanley Brown, Lene B Oddershede
Effect of supercoiling on the lambda switch
Bacteriophage 4 (2014)

Namiko Mitarai, Mogens Høgh Jensen, Szabolcs Semsey
Coupled Positive and Negative Feedbacks Produce Diverse Gene Expression Patterns in Colonies
mBio 6 (2015)

Namiko Mitarai, Szabolcs Semsey, Kim Sneppen
Dynamic competition between transcription initiation and repression: Role of non-equilibrium steps in cell-to-cell heterogeneity
Phys. Rev. E 92 (2015)

Sabine Hansen, Sandeep Krishna, Szabolcs Semsey, and Sine Lo Svenningsen
Effects of Four Different Regulatory Mechanisms on the Dynamics of Gene Regulatory Cascades
Scientific Reports 5 (2015)

Kristian Moss Bendtsen, Mogens H. Jensen, Sandeep Krishna, Szabolcs Semsey
The role of mRNA and protein stability in the function of coupled positive and negative feedback systems in eukaryotic cells
Scientific Reports 5 (2015)

Nan Hao, Kim Sneppen, Keith E. Shearwin, and Ian B. Dodd
Efficient chromosomal-scale DNA looping in Escherichia coli using multiple DNA-looping elements
Nucleic Acids Res 1 (2017)

Alexander Hunziker, Mogens H Jensen, Sandeep Krishna
Stress-specific response of the p53-Mdm2 feedback loop
BMC Systems Biology 4 (2010)

Alexander Hunziker, Csaba Tuboly, Péter Horváth, Sandeep Krishna, and Szabolcs Semsey
Genetic flexibility of regulatory networks
Proc. Natl. Acad. Sci. USA 107 (2010)

Christian Garde, Thomas Bjarnsholt, Michael Givskov, Tim Holm Jakobsen, Morten Hentzer, Anetta Claussen, Kim Sneppen, Jesper Ferkinghoff-Borg and Thomas Sams
Quorum Sensing Regulation in Aeromonas hydrophila
J. Mol. Biol. 396 (2010)

I.B. Dodd, K.E. Shearwin and K. Sneppen
Modelling transcriptional interference and DNA looping in gene regulation
J. Mol. Biol. 369 (2007)

Jacob Bock Axelsen, Sebastian Bernhardsson, Kim Sneppen
One Hub-One Process: A Tool Based View on Regulatory Network Topology
BMC Systems Biology 2 (2008)

Kim Sneppen, Mille A Micheelsen & Ian B Dodd
Ultrasensitive gene regulation by positive feedback loops in nucleosome modification
Molecular Systems Biology 4 (2008)

Namiko Mitarai, Ian B. Dodd, Michael T. Crooks, Kim Sneppen
The Generation of Promoter-Mediated Transcriptional Noise in Bacteria
PLoS Comput. Biol. 4 (2008)

Sandeep Krishna, Szabolcs Semsey, Kim Sneppen
Combinatorics of feedback in cellular uptake and metabolism of small molecules
Proc. Natl. Acad. Sci. USA 104 (2007)

Simone Pigolotti, Sandeep Krishna, Mogens H. Jensen
Symbolic dynamics of biological feedback networks
Phys. Rev. Lett. 102 (2009)

Hiizu Nakanishi, Margit Pedersen, Anne K. Alsing and Kim Sneppen
Modeling of the Genetic Switch of Bacteriophage TP901-1: A Heteromer of CI and MOR Ensures Robust Bistability
J. Mol. Biol. 394 (2009)

Szabolcs Semsey, Sandeep Krishna, Janos Erdssy, Peter Horvath, Laszlo Orosz, Kim Sneppen and Sankar Adhya
Dominant Negative Autoregulation Limits Steady-State Repression Levels in Gene Networks
Journal of Bacteriology 191 (2009)

Sandeep Krishna, Laszlo Orosz, Kim Sneppen, Sankar Adhya and Szabolcs Semsey
Relation of Intracellular Signal Levels and Promoter Activities in the gal Regulon of Escherichia coli
Journal of Molecular Biology 391 (2009)

Mille A. Micheelsen, Namiko Mitarai, Kim Sneppen, Ian. B. Dodd
Theory for stability and regulation of epigenetic landscapes
Phys. Biol. 7 (2010)

Kim Sneppen, Sandeep Krishna, Szabolcs Semsey
Simplified Models of Biological Networks
Annual Review of Biophysics 39 (2010)

Yusuke Himeoka, Namiko Mitarai
Modeling slow-processing of toxin messenger RNAs in type-I Toxin-Antitoxin systems: post-segregational killing and noise filtering
BioRxiv 0 (2018)