Fundamentals of Transcription
How Number of TF binding sites affects transcription
- increase binding rate
- increase probability > n TFs are bound
- increase probability an enhancer promoter interaction activates the gene.
Affinity:
- relation from multiple weak sites to strong sites
- predicting real target sites vs non-functional sites (probability off-target effects in a therapy treatment)
Geometry/Topology/Grammar
- when are sites working together vs. independently
- length scale for cooperation?
- length scale for independence?
Interactions of Genes and the Environment (Explaining variable outcomes of identical genetics)
Temperature Adaptations
- sharp thresholds -> high sensitivities to external variation
- mall differences in binding allow large differences in development
- which genetic mechanisms are more sensitive / what are the trade-offs?
Feasibility of DNA-TF FRET? Not enough molecules?