Erez Aiden’s team of Baylor researchers discover a CTCF protein controlling 3D formation of 10,000 loops. Only 1 of 4 orientations is found. Challenges for evolution:
1) How did this essential CTCF protein develop to loop DNA when the DNA is essential for its production.
2) How was the 1 orientation in 4 selected?
See: There’s a Mystery Machine That Sculpts the Human Genome
. . .In 2014, a team led by Erez Lieberman Aiden at Baylor College of Medicine took important steps towards this goal by creating an unprecedentedly detailed 3-D map of the human genome. These genetic cartographers used a technique called Hi-C to embalm the genome and identify regions that interact with one another. Using this method, they identified a grand total of 10,000 loops—far fewer than the millions that were thought to exist. . . .
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.”
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. . . .
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? . . .
There’s a growing appreciation that some diseases are related to how the genome is oriented rather than just a mutation,” adds Rao. . . .
Rao et al., A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping, Cell (2014), http://dx.doi.org/10.1016/j.cell.2014.11.021
Curiouser and curioser for stochastic theoriests.
Obvious design components for ID.