Scientists use CRISPR to reveal DNA folding secrets

Scientists have used 'genome surgery' to change the way DNA is packed inside human cells.

The DNA that makes up a human genome is two metres long, and to fit a copy inside the nucleus of every cell of the body means that it must be condensed, folded and specially ordered. One of the ways in which this happens is that around 10,000 loops of DNA are formed. These loops also allow different stretches of DNA which may be a long way apart to be brought together and interact at close quarters, but it is not clear how these loops are made.

'In the old model, scientists thought that a loop formed when two bits of the genome wiggled around and then met inside the cell nucleus,' said co-lead author of the study, Dr Erez Lieberman Aiden of the Baylor College of Medicine, Texas. 'But this process would lead to interweaving loops and highly entangled chromosomes.' Instead, the study, published in PNAS, finds evidence for a different system of loop formation, called extrusion.

The team likens this system to the plastic sliding buckles that adjust the length of the straps of a rucksack. 'Extrusion is the process you use when you're manipulating the plastic adjustors on your backpack: you feed the strap through on each side, and the slack forms a loop.' said Adrian Sanborn of Stanford University, California, also co-lead author.

The researchers found that this extrusion stops when the proteins forming the 'adjustors' encounter a short specific sequence of DNA called an anchor motif, where they bind tightly. They subsequently used the recently developed CRISPR/Cas9 gene-editing technique, which allows the changing of a DNA sequence in a targeted manner, on the genomes of a lab-grown human cell line.

'Using CRISPR allowed us to go in with a "molecular scalpel" to add or remove a small number of genetic letters. By knowing exactly which letters we needed to target, we found that it was possible to change how the genome folded in a highly predictable fashion,' said co-lead author, Suhas Rao, also of Stanford.

They aimed to alter the anchor motifs, and cause the proteins to bind in a different place, or not at all. They found that they could destroy, move, or create new anchor motifs, and so make changes in how loops were formed. They were able to predict these changes with high accuracy, using mathematical and computer models.

'The ability to read out the 3D structure of a genome is improving rapidly. As shown by our genome-editing experiments, it may now be possible not only to read genome folding patterns but also to write them,' the team concludes.