How are compartments formed?

red ballEquilibrium (passive)?  Motivated by energy landscape models of protein folding,

B Zhang et AL. (2015) PNAS. 112, 427,M Di Pietro et AL. (2016) PNAS. 113, 12168,J Monarchic et AL. (1997) Anny. Rev. Phys. Chem. 48, 545

yellow ball a prevailing hypothesis is chromatin configurations are due to biochemical affinities between distinct chromatin types:

M Falk et AL. (2019) Nature. 570, 395-3.99

yellow ball More complex interactions can reproduce observed contact maps:

     

G. Le Trent, F. Képès, & H. Orland, BioPhysics 115, 2286 (2018)

red ball But the genome is intrinsically out of equilibrium, dependent on ATP for function and activity:

... 

yellow ballChromosomal loci diffuse slower in ATP-depleted cells:

Weber et.al (2012) PNAS 109 (19), 7338-7343

yellow ballCorrelated chromatim motion across different length and time scales:

Zidovska, Weitz, Mitchison (2013) PNAS 110 (39) 15555-15560

yellow ball How do sequence-dependent active processes affect chromatin folding?