8.592 - HST.452J (Spring 2025)

Statistical Physics in Biology

Lecture 15

Protein-DNA interactions

1. Deducing interaction of transcription factor to protein
• additive energy model described by a 4xL matrix
• ChIP sequencing
• Berg & von Hippel 
  • Binding energy should be in a particular range
  • Micro-canonical to canonical transition
  • Constraints on L and binding energy for genome of length M
2. Not enough information in TF of eucaryotes
   • Need more copies of TF in eucaryotes compared to bacteria
   • Need multiple TF per regulatory site
3. Kinetics

(Lecture slides from 2025)

(Lecture note from 2022)

Nature article (2025) on low overlap