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The Combinatorics of Transcriptional Regulation


Rydenfelt, Mattias Sven Olof (2014) The Combinatorics of Transcriptional Regulation. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/PNX5-Y638.


The ability to regulate gene expression is of central importance for the adaptability of living organisms to changes in their internal and external environment. At the transcriptional level, binding of transcription factors (TFs) in the vicinity of promoters can modulate the rate at which transcripts are produced, and as such play an important role in gene regulation. TFs with regulatory action at multiple promoters is the rule rather than the exception, with examples ranging from TFs like the cAMP receptor protein (CRP) in <i>E. coli</i> that regulates hundreds of different genes, to situations involving multiple copies of the same gene, such as on plasmids, or viral DNA. When the number of TFs heavily exceeds the number of binding sites, TF binding to each promoter can be regarded as independent. However, when the number of TF molecules is comparable to the number of binding sites, TF titration will result in coupling ("entanglement") between transcription of different genes. The last few decades have seen rapid advances in our ability to quantitatively measure such effects, which calls for biophysical models to explain these data. Here we develop a statistical mechanical model which takes the TF titration effect into account and use it to predict both the level of gene expression and the resulting correlation in transcription rates for a general set of promoters. To test these predictions experimentally, we create genetic constructs with known TF copy number, binding site affinities, and gene copy number; hence avoiding the need to use free fit parameters. Our results clearly prove the TF titration effect and that the statistical mechanical model can accurately predict the fold change in gene expression for the studied cases. We also generalize these experimental efforts to cover systems with multiple different genes, using the method of mRNA fluorescence in situ hybridization (FISH). Interestingly, we can use the TF titration affect as a tool to measure the plasmid copy number at different points in the cell cycle, as well as the plasmid copy number variance. Finally, we investigate the strategies of transcriptional regulation used in a real organism by analyzing the thousands of known regulatory interactions in <i>E. coli</i>. We introduce a "random promoter architecture model" to identify overrepresented regulatory strategies, such as TF pairs which coregulate the same genes more frequently than would be expected by chance, indicating a related biological function. Furthermore, we investigate whether promoter architecture has a systematic effect on gene expression by linking the regulatory data of <i>E. coli</i> to genome-wide expression censuses.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Transcriptional regulation; Statistical mechanics; Transcription factor titration; Sequestration; Promoter architectures
Degree Grantor:California Institute of Technology
Division:Physics, Mathematics and Astronomy
Major Option:Physics
Systems Biology
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Phillips, Robert B.
Thesis Committee:
  • Phillips, Robert B. (chair)
  • Murray, Richard M.
  • Refael, Gil
  • Tirrell, David A.
Defense Date:28 April 2014
Funding AgencyGrant Number
National Institutes of HealthR01 GM085286, R01 GM085286-01S
Fulbright Science & Technology AwardUNSPECIFIED
Record Number:CaltechTHESIS:05162014-140751409
Persistent URL:
Related URLs:
URLURL TypeDescription DOIArticle adapted for ch. 2 adapted for ch. 3
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:8239
Deposited By: Mattias Rydenfelt
Deposited On:20 May 2014 16:56
Last Modified:08 Nov 2023 00:41

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