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Gene regulation in Escherichia coli beyond the “rate” approximation

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Title: Gene regulation in Escherichia coli beyond the “rate” approximation
Author(s): So, Lok-hang
Director of Research: Golding, Ido
Doctoral Committee Chair(s): Clegg, Robert M.
Doctoral Committee Member(s): Golding, Ido; Aksimentiev, Aleksei; Stack, John D.
Department / Program: Physics
Discipline: Physics
Degree Granting Institution: University of Illinois at Urbana-Champaign
Degree: Ph.D.
Genre: Dissertation
Subject(s): Systems Biology Quantitative Biology Biophysics Stochastic Gene Expression Escherichia coli Transcriptional Time-Series Fluorescence in situ Hybridization Single-Cell
Abstract: The blueprint of a living cell is inscribed in its DNA. A region of DNA encoding a protein is called a gene. The cell reads the DNA and makes molecular machines made up of proteins to carry out all cellular functions required for survival. All cells live in ever-changing environments, and have different needs at different times. The control of when and how often each protein is produced from a gene is called gene regulation. Transcription, the copying of a DNA sequence into a complementary mRNA molecule, is the first step in the information flow from DNA to proteins, and most regulation is already done at the transcription level to avoid the production of superfluous intermediates. A living cell takes environmental stimuli as input, and regulates the activity of genes through DNA-binding proteins called transcription factors. The activity of a gene is described by its time-series of discrete mRNA production events. The events constituting this transcriptional time-series are stochastic and exhibit intermittent, bursty behavior, in bacteria as well as higher organisms. Thus the transcriptional time-series cannot be fully described by a simple chemical “rate”—the probability per unit time of transcribing an mRNA molecule. An important consequence of this temporal complexity is that gene expression level can be tuned by varying different features of the time-series. It is then natural to ask: What modulation scheme is used by the cell to change expression levels of genes? Furthermore, if we look at the transcriptional time-series of multiple genes, would we see different modulation schemes for different genes, or a common modulation scheme shared by all genes? Last but not least, what is the molecular mechanism leading to bursty transcriptional time-series? What are the biophysical states that correspond to the active and inactive periods in a bursty transcriptional time-series? To answer these questions, I characterized the mRNA copy-number statistics from multiple promoters in the model organism Escherichia coli under various growth conditions using single-molecule fluorescence in situ hybridization. The kinetics of the underlying transcriptional time-series was then inferred using the two-state model, a simple stochastic mathematical model that describes bursty transcription time-series. I found that the degree of burstiness depends only on the gene expression level, while being independent of the details of gene regulation. The observed behavior is explained by the underlying variation in the duration of bursting events. At this stage, there is no mechanistic, molecular-level understanding of what gives rise to the bursty behavior of gene activity in bacteria. However, my finding here, that the properties of the transcriptional time-series are gene-independent rather than gene-specific, is contrary to the most common theoretical model used to explain bursty transcriptional time-series in bacteria, which involves the binding and unbinding of transcription factors at the promoter. My data suggests that the observed bursty kinetics arises from gene-nonspecific mechanisms such as DNA topology modulation, RNA polymerase dynamics, or regulation by broad-target DNA-binding proteins. Further investigation would narrow down the source of bursty transcriptional time-series.
Issue Date: 2011-05-25
URI: http://hdl.handle.net/2142/24231
Rights Information: Copyright 2011 Lok-hang So
Date Available in IDEALS: 2011-05-25
Date Deposited: 2011-05
 

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