Scientists capture first detailed look inside droplet-like structures of compacted DNA

Inside human cells, biology has pulled off the ultimate packing job, figuring out how to fit six feet of DNA into a nucleus about one-tenth as wide as a human hair while making sure the all-important molecules can still function.

To compress itself, DNA wraps around proteins to form nucleosomes that are linked together like beads on a string. These strings coil into compact chromatin fibers, which are further condensed inside the nucleus.

It was unclear how this additional compaction process happened. Then, in 2019, HHMI Investigator Michael Rosen and his team at UT Southwestern Medical Center reported that synthetic nucleosomes created in the lab congregate into membrane-less blobs called condensates. This happens through a process called phase separation – akin to oil droplets forming in water – that the researchers think mimics how chromatin compacts inside cells.

Looking Inside Chromatin Condensates

These chromatin condensates, made up of hundreds of thousands of rapidly moving molecules, have emergent properties — behaviors that aren’t present in the individual molecules but appear only when they work together as one. These properties dictate how the droplets form and maintain their physical characteristics.

To better understand these qualities, which could help researchers learn how chromatin compacts inside cells, scientists need to peer deep inside the droplets to examine individual chromatin fibers and nucleosomes.

Now, Rosen and his team, along with researchers led by HHMI Investigator Elizabeth Villa at the University of California, San Diego; Rosana Collepardo-Guevara at the University of Cambridge; and Zhiheng Yu at HHMI’s Janelia Research Campus; have figured out how to do just that.

Using advanced imaging performed at Janelia, they’ve captured the most detailed images yet of the molecules inside synthetic chromatin condensates, seeing first-hand how the chromatin fibers and nucleosomes are packaged inside the droplet-like structures. Using the same techniques, the team also imaged and analyzed native chromatin in cells.

Understanding Condensate Formation

These visualizations, combined with computer simulations and light microscopy, enabled the team to examine the structures and interactions of the individual molecules inside the synthetic chromatin condensates, allowing them to start to figure out how the droplets form and function.  

The team found that the length of linker DNA connecting the nucleosomes affects how the structures are arranged, which in turn dictates the interactions between chromatin fibers and the network structure of the condensates.

These physical features helped explain why some chromatin fibers undergo phase separation better than others and why condensates formed by different kinds of chromatin have different emergent material properties. They also found that synthetic condensates produced in the lab structurally mimic compacted DNA inside cells.

“The work has allowed us to tie the structures of individual molecules to macroscopic properties of their condensates, really for the first time,” Rosen says. “I'm certain that we're only at the tip of the iceberg – that we and others will come up with even better ways of developing those structure-function relationships at the meso (intermediate) scale.”

A Blueprint for Studying Condensates

Beyond chromatin, the new work provides a blueprint for studying and understanding the organization and function of many types of biomolecular condensates. These membrane-less blobs carry out many important functions all over the cell — from regulating gene expression to responding to stress.  

Understanding how these droplet-like structures form and function can help researchers understand what happens when condensation goes awry, a potential contributing factor for different diseases — from neurodegenerative conditions to cancer.

“By doing this research, we will better understand how abnormal condensation could lead to different diseases and, potentially, that could help us develop a new generation of therapeutics,” says Huabin Zhou, a postdoctoral scientist in the Rosen Lab and the lead author of the new research.