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Mechanisms of Gene Expression


Mechanisms of Gene Expression

Zach Hensel


  1. To familiarize students with some mechanisms of regulating gene expression at the transcription and post-transcription levels including production and degradation processes;
  2. To offer study of selected topics at the cutting edge of advancing knowledge on prokaryotic and eukaryotic gene expression;
  3. To teach critical analysis of original experimental data and the scientific literature;
  4. To familiarize students with peer review of gene expression literature;
  5. To introduce stochastic simulation techniques from systems from systems biology that can easily be applied by non-expert scientists;
  6. To demonstrate how knowledge of gene expression mechanisms is being deployed in synthetic biology.


  1. Introduction, prehistory, and the cutting edge: Foundations in genetics and evolution for molecular studies and recent developments in post-transcriptional regulation
  2. The operon and transcriptional regulation: Transcription factors and other aspects of gene regulation in bacteriophage lysis/lysogeny
  3. Eukaryotic gene regulation: promoter architecture, enhancers and histone modifications
  4. Eukaryotic genome conformation: chromatin folding at different scales – from loops to topologically associated domains to chromosomal compartments – and its impact on gene regulation
  5. Bacterial gene expression mechanisms – size, activation, translation, degradation
  6. Post-SCAN discussion
  7. Insights into gene expression from single-molecule studies
  8. Stochastic simulations: a method that can be applied to almost any problem in biology
  9. Synthetic biology: how do we get from simple gene circuits to engineering synthetic organisms?
  10. Project: Preprint journal club

Students are evaluated both by the instructor and by each other on the basis of their contributions to the team project. The instructor gives feedback on the project at 3 stages throughout the week.


Main Bibliography

  1. Ptashne, Mark. A Genetic Switch : Phage Lambda Revisited. 3rd ed. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press, 2004. Table of contents
  2. Philips, Ron Milo & Ron. “Cell Biology by the Numbers.” Accessed November 25, 2019.
  3. “BioRxiv.Org - the Preprint Server for Biology.” Accessed November 25, 2019.
  4. Course contents adapted from selected manuscripts from the scientific literature.



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