Revision 1

Accepted · first revision · record

Title: What physical interactions create A and B compartments?
Plain: Active and inactive parts of the genome separate into two spatial groups, somewhat as oil separates from water. Which molecular interactions cause this, and how it competes with loop extrusion, is not settled.
Precise: Identify the effective interactions (HP1-mediated heterochromatin bridging, histone-mark-dependent attraction, transcription-linked activity, tethering to the nuclear lamina) that produce the checkerboard compartment pattern in Hi-C, and build a polymer model with measured interaction strengths that reproduces compartment strength and its observed increase upon cohesin depletion.
Settled by: A polymer model with independently measured interaction energies that predicts compartment patterns and their changes under targeted depletion of each candidate factor.
Kind: phenomenon
Answer type: mechanism
References: (empty)
Literature status: open
Status note: (empty)
Posed since: 2009