When dense assemblies of proteins form, they can create distinct compartments that lack a membrane. Some behave as droplets, with millions of molecules. Others are small, contain thousands of molecules, and form on the surface of DNA. Now, using optical tweezers, researchers demonstrate that some condensates form on DNA as a type of surface condensation. The findings suggest that the formation and positioning of these droplets of transcription factors wet a surface and reveal regulatory DNA regions.
This work is published in Nature Physics, in the article, “Sequence dependent surface condensation of a pioneer transcription factor on DNA.”
For this study, the researchers employed optical tweezers—a technology that uses lasers to isolate and manipulate very small objects such as single DNA molecules—combined with confocal microscopy, to look at molecules individually.
“With optical tweezers, it is possible to capture a single DNA molecule and with confocal microscopy, we can observe transcription factors binding and forming protein condensates at their preferred DNA sequences,” noted Jose A. Morin, PhD, a post-doc at Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBI). “The fact that we can study this process one molecule at the time allowed us to detect interactions otherwise blurred by the complexity of the living cell.”
The researchers investigated condensates using the transcription factor Krüppel-like factor 4 (Klf4). They wrote that “Klf4 can phase separate on its own at high concentrations, but at low concentrations, Klf4 only forms condensates on DNA.”
Using optical tweezers, they showed that the Klf4 condensates form on DNA as a type of surface condensation. This surface condensation, they wrote, “involves a switch-like transition from a thin adsorbed layer to a thick condensed layer, which shows hallmarks of a prewetting transition.”
The team went on to illustrate that the localization of condensates on DNA correlates with sequence, suggesting that the condensate formation of Klf4 on DNA is a sequence-dependent form of surface condensation.
With the help of physicists, noted Sina Wittmann, PhD, a postdoc in the Hyman lab at the MPI-CBI, “we were able to understand how transcription factors communicate with each other and assemble through teamwork. They undergo what is called a prewetting transition to form liquid-like droplets, which are similar to the drops on a mirror in your bathroom after a shower. These condensates are filled with thousands of transcription factors. Assembled in this way, the transcription factors can now identify the correct DNA region by reading out DNA sequence.”
“We now have a possible mechanistic explanation for the localization of transcription factors along the genome,” noted Stephan Grill, PhD, director and research group leader at the MPI-CBI. “This is essential to understand how gene expression is regulated. Since we know that this regulation breaks down in developmental diseases and cancer, these new results give us a clearer picture of how these diseases occur. This knowledge is important to think about new therapeutic options that take the teamwork of transcription factors into account.”
