Exploring chromatin hierarchical organization via Markov State Modelling
Fig 1
The toy model of a chromosome with a hierarchical energy landscape.
(A) The energy landscape with three levels of hierarchy considered here. (B) Pairwise contact energy landscape for the toy model of a chromosome of length 500. (C) Illustration of the effect of annealing on the mean-first passage time (MFPT) between the states. (D) Optimization of the metastability index results in profiles, revealing three levels of hierarchy corresponding to three hub sets , and
, respectively. (E, top) A network representation of the toy chromosome interactions with nodes colored according to the partitions associated with the hub set
; (E, bottom) reduced network constructed from the partitions associated with the hub set
, with links depicting effective interactions between partitions calculated via Eq 11 in Materials and methods.