An analytical framework for studying transcriptional regulation
Doctoral thesis, 2020
The state and behavior of any living cell is controlled by a complex interplay of different regulatory processes, with the regulation of transcription playing a major role. When a cell adapts to a new environment it often does that by modulating gene transcript levels, mainly through changes in transcription factor binding events. Therefore, understanding the transcriptional regulation is vital for many biological research fields ranging from understanding cancer metabolism to metabolic engineering.
In this thesis, I present and apply an analytical framework for studying transcriptional regulation in a well-characterized eukaryotic model organism, the yeast S. cerevisiae. The framework is a combination of advanced sequencing methods like Chromatin Immunoprecipitation followed by DNA sequencing (ChIP-seq / ChIP-exo) and Cap Analysis of Gene Expression (CAGE) with bioinformatic approaches.
The relative binding location of transcription factors in relation to the transcription start site is important for interpretation, therefore the transcription start sites of all genes active in multiple controlled growth environments were determined using CAGE. To use and analyze the gathered data in a reliable and efficient way a high-quality bioinformatics pipeline was established.
After establishing the required analytical framework, I employed it in various projects, all aimed to gain a better understanding of yeast transcriptional regulation. In a detailed study of a single transcription factor, I investigated Leu3, the main regulator of leucine biosynthesis. Here, I was able to show that its binding behavior is affected by the availability of leucine in the media, an adaptive behavior that has not been reported before.
Metabolic engineering will be increasingly important to support the needs of our society and in order to help with this, I developed a tool for fine tuning conditional gene expression levels using hybrid promoters. This tool is based on a machine learning approach and can be used to improve productivity in large scale fermentations.
In conclusion, this thesis lays the foundation for future large-scale studies of transcriptional regulation in S. cerevisiae and can also serve as a blueprint on how to study it in different organisms.
In this thesis, I present and apply an analytical framework for studying transcriptional regulation in a well-characterized eukaryotic model organism, the yeast S. cerevisiae. The framework is a combination of advanced sequencing methods like Chromatin Immunoprecipitation followed by DNA sequencing (ChIP-seq / ChIP-exo) and Cap Analysis of Gene Expression (CAGE) with bioinformatic approaches.
The relative binding location of transcription factors in relation to the transcription start site is important for interpretation, therefore the transcription start sites of all genes active in multiple controlled growth environments were determined using CAGE. To use and analyze the gathered data in a reliable and efficient way a high-quality bioinformatics pipeline was established.
After establishing the required analytical framework, I employed it in various projects, all aimed to gain a better understanding of yeast transcriptional regulation. In a detailed study of a single transcription factor, I investigated Leu3, the main regulator of leucine biosynthesis. Here, I was able to show that its binding behavior is affected by the availability of leucine in the media, an adaptive behavior that has not been reported before.
Metabolic engineering will be increasingly important to support the needs of our society and in order to help with this, I developed a tool for fine tuning conditional gene expression levels using hybrid promoters. This tool is based on a machine learning approach and can be used to improve productivity in large scale fermentations.
In conclusion, this thesis lays the foundation for future large-scale studies of transcriptional regulation in S. cerevisiae and can also serve as a blueprint on how to study it in different organisms.
transcription factor
ChIP-exo
S. cerevisiae
transcriptional regulation
Author
Christoph Sebastian Börlin
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions
FEMS Yeast Research,; Vol. 19(2019)
Journal article
A bioinformatic pipeline to analyze ChIP-exo datasets
Biology Methods and Protocols,; Vol. 4(2019)
Journal article
Predictive models of eukaryotic transcriptional regulation reveals changes in transcription factor roles and promoter usage between metabolic conditions
Nucleic Acids Research,; Vol. 47(2019)p. 4986-5000
Journal article
Börlin CS, Bergenholm D, Kerkhoven EJ, Siewers V & Nielsen J. Analyzing and predicting conditional gene expression changes using transcription factor binding data.
The transcription factor Leu3 shows differential binding behavior in response to changing leucine availability
FEMS Microbiology Letters,; Vol. 367(2020)
Journal article
Bergenholm D, Börlin CS, Holland P & Nielsen J. T-rEx: A Saccharomyces cerevisiae transcription factor explorer.
A living cell is exposed to a constantly changing environment and therefore has to continuously adapt. It also has to periodically change between growth and cell division to survive and proliferate in nature. How can such a dynamic response be achieved and regulated? The main determinant for the cellular responses is the concentration of different proteins inside the cell, which are the little machines that perform most tasks. One key mechanism that influences the protein levels is a regulatory process called transcriptional regulation.
Because transcriptional regulation plays such a central role in determining the fate and state of living cells, understanding it is vital for many biological research fields ranging from understanding cancer metabolism to metabolic engineering.
In this thesis, I present the development of a framework to study transcriptional regulation in the yeast Saccharomyces cerevisiae, also known as Baker’s yeast. The framework is based on gathering data on the exact start sites of transcription in different environmental conditions using state-of-the-art sequencing technologies combined with a custom build bioinformatics analytical pipeline.
Additionally, I also highlight how one can use this framework to study the complex mechanisms involved in transcriptional regulation using machine learning. The results from this can then be used to develop online tools for metabolic engineering applications, a field of research that is vital for the transition towards a bio-based economy and a reduced dependency on non-renewable resources.
In conclusion, this thesis lays the foundation for future large-scale studies of transcriptional regulation in S. cerevisiae based on transcription factor binding data and can also serve as a blueprint on how to study this regulatory process in different organisms.
Because transcriptional regulation plays such a central role in determining the fate and state of living cells, understanding it is vital for many biological research fields ranging from understanding cancer metabolism to metabolic engineering.
In this thesis, I present the development of a framework to study transcriptional regulation in the yeast Saccharomyces cerevisiae, also known as Baker’s yeast. The framework is based on gathering data on the exact start sites of transcription in different environmental conditions using state-of-the-art sequencing technologies combined with a custom build bioinformatics analytical pipeline.
Additionally, I also highlight how one can use this framework to study the complex mechanisms involved in transcriptional regulation using machine learning. The results from this can then be used to develop online tools for metabolic engineering applications, a field of research that is vital for the transition towards a bio-based economy and a reduced dependency on non-renewable resources.
In conclusion, this thesis lays the foundation for future large-scale studies of transcriptional regulation in S. cerevisiae based on transcription factor binding data and can also serve as a blueprint on how to study this regulatory process in different organisms.
Subject Categories
Biological Sciences
Infrastructure
C3SE (Chalmers Centre for Computational Science and Engineering)
ISBN
978-91-7905-332-1
Doktorsavhandlingar vid Chalmers tekniska högskola. Ny serie: 4799
Publisher
Chalmers
Opponent: Associate Professor Christopher Workman, Technical University Denmark