Scientists at the University of California San Diego School of Medicine and the Salk Institute for Biological Studies report the development and application of new electron microscopic imaging tools and a special stain for DNA to visualize the 3D structure of chromatin. They published their study (“ChromEMT: Visualizing 3D Chromatin Structure and Compaction in Interphase and Mitotic Cells”) in Science.

“We show that chromatin is a disordered 5- to 24-nanometer-diameter curvilinear chain that is packed together at different 3D concentration distributions in interphase and mitosis,” write the investigators. “Chromatin chains have many different particle arrangements and bend at various lengths to achieve structural compaction and high packing densities.”

“The primary functions of chromatin are fundamental,” said study co-lead Mark Ellisman, Ph.D., distinguished professor of neurosciences and bioengineering and director of the National Center for Microscopy and Imaging Research (NCMIR) at UC San Diego. “It efficiently packages DNA to fit inside the cell nucleus, making it possible for chromosomes and cells to divide and replicate safely and correctly. It's a basic, working element of life.”

He explained that the team’s work allow them to help resolve an on-going, persistent debate about the actual structure of chromatin, long poorly understood. DNA wraps around nucleosomes and this chain of disks was thought “to organize into increasingly thicker fibers that progressively form what are seen as condensed chromosomes in dividing cells.”

Dr. Ellisman, with co-senior author Clodagh O'Shea, Ph.D., an associate professor at Salk and Howard Hughes Medical Institute Faculty Scholar, and colleagues show that that this hierarchical packing model is not correct. They developed a novel imaging approach called ChromEMT, which combines an advanced form of electron microscopy tomography with a new labeling technique to selectively enhance electron scattering and thus the specific contrast associated with DNA to directly image within cells the threads of this important core element of the genome.

Dr. Ellisman said that it is now clear that the biological functions and activity of our genomes in the nucleus are not determined by linear DNA sequence information alone. Instead, it is the local nucleosome structure combined with its global 3D organization in the nucleus that determines gene expression and cell fate. ChromEMT enables DNA and chromatin to be visualized across this critical set of biological and structural scales in single cells for the first time, he added.

“In contrast to ordered and rigid fibers, chromatin is a flexible chain that can collapse and pack together into 3D domains that have a wide range of different concentration densities,” pointed out Dr. O’Shea. “This provides exciting new insights into how different gene sequences, interactions, and epigenetic modifications can be integrated at the level of chromatin structure to regulate gene expression and inherited and maintained through cell division.”

The team’s goal is to use ChromEMT to crack the cell nucleus and decipher how a cell's nucleus or control center oversees cell growth, metabolism, and reproduction. They are now developing additional labels that can be combined with ChromEMT to visualize the structural basis of gene silencing and how viral and cancer proteins remodel DNA to drive pathological replication.