On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation

C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, IST Austria, 2019.

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Thesis | Published | English
Department
Series Title
IST Austria Thesis
Abstract
Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. i) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. ii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. iii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. iv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. We demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation.
Publishing Year
Date Published
2019-05-03
Page
152
ISSN
IST-REx-ID

Cite this

Igler C. On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation. IST Austria; 2019. doi:10.15479/AT:ISTA:6371
Igler, C. (2019). On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. IST Austria. https://doi.org/10.15479/AT:ISTA:6371
Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation. IST Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371.
C. Igler, On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. IST Austria, 2019.
Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation, IST Austria, 152p.
Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation. IST Austria, 2019, doi:10.15479/AT:ISTA:6371.
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IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf 12.60 MB
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2019-05-03T11:54:52Z
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IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx 34.64 MB
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2019-05-03T11:54:54Z


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