Self-organization of domain structures by DNA-loop-extruding enzymes

The long chromosomal DNAs of cells are organized into loop domains much larger in size than individual DNA-binding enzymes, presenting the question of how formation of such structures is controlled. We present a model for generation of defined chromosomal loops, based on molecular machines consisting of two coupled and oppositely directed motile elements which extrude loops from the double helix along which they translocate, while excluding one another sterically. If these machines do not dissociate from DNA (infinite processivity), a disordered, exponential steady-state distribution of small loops is obtained. However, if dissociation and rebinding of the machines occurs at a finite rate (finite…

• NS
  National Science Foundation

  Awards: 1206868, DMR-1206868, 1022117, 0715099, MCB-1022117
• NI
  National Institutes of Health

  Awards: MCB-1022117, 1U54CA143869-01, DMR-1206868, 1U54CA143869
• DO
  Division of Materials Research

  Award: DMR-1206868