8.592 - HST.452J (Fall 2025)

Statistical Physics in Biology

Lecture 25

Chromatin Organization (part II)

Determinants of nucleosome position
- Sequence dependent positioning
  - AAATTT... repels nucleosomes, possibly due to rigidity
  - Nucleosome attracting sequences; typically composed of AA, TT, AT and more flexible(and possibly bent) in one direction
- Statistical positioning
  - Erlang distribution for probability of k non-overlapping nucleosomes in an interval
Genome packing
- Wrapping aroud nucleosomes of persistent DNA provides a compression factor of roughly 5
- Chromatin fibre packed into nucleus (size 7-25\mu m)
- Persistence length of the chromatin fibre should be of the order of 3-5 nuclesomes (each around 10nm in size) for 30-50nm
- Treated as a random walk, a chromosome of 10^9 would occupy a size of around 30\mu m, possible in large oocytes
- Expectations for the size of a polymer segment of size s in the random walk, and when confined to a size D
- However, measurements of R(s)~s^{1/3} appear to indicate a different behavior for chromatin
- Chromosome Conformation Capture (Job Dekker) provides a measure of connectivity
- Hi Glass (viewer of Hi-C data)
- The hard problem is to infer 3d structure from Hi-C data, can instead look at statistical properties
- The fractal globule model seems to fit some statistical aspects of the data

8.592 lecture- last update 12/1/2025 by M. Kardar