Genome complexity: DNA Looping mechanisms (Introduction)

by David Turell , Saturday, October 24, 2015, 01:30 (3107 days ago) @ David Turell

DNA is six feet/ 2 meters long and has to be packed into the nucleus, just so. No knots, and genes need to be placed near modifiers and controllers, even if quite a distance away when stretched out:-http://www.theatlantic.com/science/archive/2015/10/theres-a-mystery-machine-that-sculpts-the-human-genome/411199/-"In the 1970s, biochemists showed that this feat of extreme origami begins when DNA is wrapped around proteins called histones, creating what looks like a string of beads. This reduces the packing problem, but doesn't come close to solving it. The wrapped DNA must be folded and twisted in ever more complicated (and as yet unknown) ways. Eventually, it forms large loops.-***-"They also bring genes into close contact with distant sequences that turn them on or off. So, the 3-D form of the genome also dictates its function. -***-"They also showed that the loops obey certain rules. Most tend to be short. They occur in the same places whether you're looking at a neuron or a skin cell, or a human cell or mouse cell. And they almost always associate with a protein called CTCF, which acts as a fastener. In theory, two CTCF proteins will bind to separate stretches of DNA and then lock together, creating a loop and holding it in place.-"But when Aiden's team looked at CTCF more closely, they found a huge surprise. The protein recognizes and sticks to specific DNA sequences, which act as its landing pads. These sequences point in a particular direction, which means that a pair of them can line up in four possible ways. They don't. In reality, they almost always line up in just one of the four orientations, pointing towards each other in what study co-leader Eric Lander described as “a genomic yin and yang.”-“'That was a total bombshell,” says student Suhas Rao who worked on the project. He, like many others, had assumed that loops form when two stretches of free-floating DNA randomly find each other and are fastened by a pair of CTCF proteins. But that can't be right. If it was, the CTCF landing sequences would align in all four possible orientations, rather than the very specific one that Rao saw in his data. The loops must be forming in a completely different way, one that's deliberate and controlled.-"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.-"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."-Comment: I've indicated the 3-D importance when studying the functionality of DNA. And then there is a chicken and egg problem: How did this essential CTCF protein develop to loop DNA when the DNA is essential for its production? Again, design is a good answer.