microcosmic reality mechanics and rao's hyparchic folding machine...,

theatlantic |  Rao and fellow student Adrian Sanborn think that the key to this process is a cluster of proteins called an “extrusion complex,” which looks like a couple of Polo mints stuck together. The complex assembles on a stretch of DNA so that the long molecule threads through one hole, forms a very short loop, and then passes through the other one. Then, true to its name, the complex extrudes the DNA, pushing both strands outwards so that the loop gets longer and longer. And when the complex hits one of the CTCF landing sites, it stops, but only if the sites are pointing in the right direction.

This explanation is almost perfect. It accounts for everything that the team have seen in their work: why the loops don’t get tangled, and why the CTCF landing sites align the way they do. “This is an important milestone in understanding the three dimensional structure of chromosomes, but like most great papers, it raises more questions than it provides answers,” says Kim Nasmyth, a biochemist at the University of Oxford who first proposed the concept of an extrusion complex in 2001.

The big mystery, he says, is how the loops actually grow. Is there some kind of ratcheting system that stops the DNA from sliding back? Is such a system even necessary? And “even when we understand how loops are created, we still need to understand what they are doing for the genome,” Nasmyth adds. “It’s very early days.”

And then there’s the really big problem: No one knows if the extrusion complex exists.

Since Nasmyth conceived of it, no one has yet proved that it’s real, let alone worked out which proteins it contains. CTCF is probably part of it, as is a related protein called cohesin. Beyond that, it’s a mystery. It’s like a ghostly lawnmower, whose presence is inferred by looking at a field of freshly shorn grass, or the knife that we only know about by studying the stab wounds. It might not actually be a thing.

Except: The genome totally behaves as if the extrusion complex was a thing. Rao and Sanborn created a simulation that predicts the structure of the genome on the basis that the complex is real and works they way they think it does.

These predictions were so accurate that the team could even re-sculpt the genome at will. They started playing around with the CTCF landing pads, deleting, flipping, and editing these sequences using a powerful gene-editing technique called CRISPR. In every case, their simulation predicted how the changes would alter the 3-D shape of the genome, and how it would create, move, or remove the existing loops. And in every case, it was right.

“Our model requires very little knowledge beyond where CTCF is binding, but it tells us where the loops will be,” says Rao. “It now allows us to do genome surgery, where we can reengineer the genome on a large scale.”

This predictive power has several applications. Remember that loops allow seemingly innocuous stretches of DNA to control the activity of distant genes. If biologists can understand the principles behind these interactions, and predict their outcomes, they can more efficiently engineer new genetic circuits.

“There’s a growing appreciation that some diseases are related to how the genome is oriented rather than just a mutation,” adds Rao. “This is a little speculative, but there might be diseases where you could go in, put a loop back, and fix the problem.”