DNA has been known to form loops, and these loops have been thought to influence gene expression, recombination, and DNA repair. But according to a new study, DNA loops are rare and fleeting. Consequently, their functional role may need to be rethought.
DNA loops were subjected to live-cell imaging by researchers at the Massachusetts Institute of Technology (MIT). Using computational analysis to make sense of their observations, the researchers determined that in one stretch of the genome, fully formed loops exist for just 20–45 minutes, or about 3–6% of the time.
“If the loop is only present for such a tiny period of the cell cycle and very short-lived, we shouldn’t think of this fully looped state as being the primary regulator of gene expression,” said Anders Sejr Hansen, PhD, an assistant professor of biological engineering at MIT and one of the leaders of the new study. “We think we need new models for how the 3D structure of the genome regulates gene expression, DNA repair, and other functional downstream processes.”
Detailed findings from the study appeared in the journal Science, in an article titled, “Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging.”
“Animal genomes are folded into loops and topologically associating domains (TADs) by CTCF and loop extruding cohesins, but the live dynamics of loop formation and stability remain unknown,” the article’s authors wrote. “Here, we directly visualize chromatin looping at the Fbn2 TAD in mouse embryonic stem cells using super-resolution live-cell imaging and quantify looping dynamics by Bayesian inference.”
Besides establishing the rare and dynamic nature of full chromatin loops, the researchers found that partially extruded loops were present about 92% of the time. Indeed, by integrating their experimental data with polymer simulations, the researchers were able to quantify the relative extents of the unlooped, partially extruded, and fully looped states.
The researchers hypothesize that partial loops may play more important roles in gene regulation than fully formed loops. Strands of DNA run along each other as loops begin to form and then fall apart, and these interactions may help regulatory elements such as enhancers and gene promoters find each other.
“More than 90% of the time, there are some transient loops, and presumably what’s important is having those loops that are being perpetually extruded,” said a co-leader of the study, Leonid Mirny, PhD, a professor in MIT’s Institute for Medical Engineering and Science and the department of physics. “The process of extrusion itself may be more important than the fully looped state that only occurs for a short period of time.”
Since most of the other loops in the genome are weaker than the one the researchers studied in this paper, they suspect that many other loops will also prove to be highly transient. They now plan to use their new technique to study some of those other loops, in a variety of cell types.
“There are about 10,000 of these loops, and we’ve looked at one,” Hansen said. “We have a lot of indirect evidence to suggest that the results would be generalizable, but we haven’t demonstrated that. Using the technology platform that we’ve set up, which combines new experimental and computational methods, we can begin to approach other loops in the genome.”
“This method was crucial for us to distinguish signal from noise in our experimental data and quantify looping,” added Christoph Zechner, PhD, another co-leader of the study and a group leader at the Max Planck Institute of Molecular Cell Biology and Genetics. “We believe that such approaches will become increasingly important for biology as we continue to push the limits of detection with experiments.”
The researchers plan to investigate the role of specific loops in disease. Many diseases, including a neurodevelopmental disorder called FOXG1 syndrome, could be linked to faulty loop dynamics. The researchers are now studying how both the normal and mutated form of the FOXG1 gene, as well as the cancer-causing gene MYC, are affected by genome loop formation.