1. 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
2. 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

2022 lecture notes