Long-range genomic loci cooperatively form hierarchal chromosome skeleton

How a polypeptide (with ~ 300 monomers) folds into a protein has been a century problem and attracts enormous public attention with the advent of AlphaFold. It is a more challenging problem how chromosomes (with up to ~10^8 monomers and a total length ~ 2 meters for 46 human chromosomes) fold and form segregated territories within a nucleus with size ~ 10 microns or less. Based on an original work of de Gennes, a dominating model is that chromosomes fold into a crumpled state, which explains experimental data up to 5M bp, only deviates at intermediate range due to formation of loops (within 1kb or less), and the latter is explained by a loop-extrusion model. However, from analyzing HiC and chromosome tracing by DNA FISH, we identified unexpected highly conserved structures formed by genomic regions separated by 100M bp or further. Our (2-10) hour-long CRISPR-dCas9 guided live-cell imaging confirmed that the structures are stable. Statistical analyses reveal the structures are stabilized through cooperative binding. Our work suggests chromosomes fold through coordination of mechanisms at three scales: the identified structures reduce the state space and facilitate formation of crumpled state and short-ranged loops. This work also emphasizes the importance of physical intuition even in the time of big data era.