The reorganization of genetic material that
takes place when a stem cell matures into a nerve cell have been mapped by scientists. Detailed 3-D
visualizations show an unexpected connectivity in the genetic material
in a cell's nucleus, and provide a new understanding of a cell's
These unique 3-D reconstructions of mouse olfactory cells, which
govern the sense of smell, were obtained using X-ray imaging tools at
the Department of Energy's Lawrence Berkeley National Laboratory
(Berkeley Lab). The results could help us understand how patterning and
reorganization of DNA-containing material called chromatin in a cell's
nucleus relate to a cell's specialized function as specific genes are
activated or silenced.
‘A powerful X-ray microscope was used to capture images of nerve cell samples at different stages of maturity as they became more specialized in their function.’
Chromatin is compacted to form chromosomes, which pass along an
organism's genetic fingerprint to newly formed cells during cell
The results were published in a special edition of Cell Reports
that highlights epigenetics, a field of study focused on a layer of
biochemistry that affects gene expression and that is closely coupled to
DNA but does not alter the genetic code.
Researchers used a powerful X-ray microscope at Berkeley Lab's
Advanced Light Source (ALS) to capture images of nerve cell samples at
different stages of maturity as they became more specialized in their
function - this process is known as "differentiation." Cells at each
stage were imaged from dozens of different angles using X-rays. Each
set of 2-D images was used to calculate a 3-D reconstruction of a cell
detailing the changing chromatin formations in the nuclei.
They also were able to measure the dense packing in a form of
chromatin called heterochromatin, and they learned about the importance
of a specific protein in controlling the compaction of heterochromatin
and its confinement to the nucleus.
"It's a new way of looking at the nucleus where we don't have to
chemically treat the cell," said Carolyn Larabell, director of the
National Center for X-ray Tomography (NCXT), a joint program of Berkeley
Lab and UC San Francisco (UCSF). "Being able to directly image and
quantify changes in the nucleus is enormously important and has been on
cell biologists' wish list for many years."
Chromatin is "notoriously sensitive," she said, to chemical stains
and other chemical additives that are often used in biological imaging
to highlight regions of interest in a given sample. "Until now, it has
only been possible to image the nucleus indirectly by staining it, in
which case the researcher has to take a leap of faith that the stain was
Larabell, a faculty scientist at Berkeley Lab and a UCSF professor,
said it was previously thought that chromatin existed as a series of
disconnected islands, though the latest study showed how the chromatin
is compartmentalized into two distinct regions of "crowding" that form a
continuous network throughout the nucleus.
"We were really surprised: There are no islands, it's all
connected," she said, adding, "We could see how chromatins pack through
the nucleus and how molecules move through the nucleus, and we found
that heterochromatin is 30% more crowded than the region where
active genes are. That cannot be done with any other imaging
techniques." Two-dimensional images would have shown the nucleus as a
"flat, confusing mess," she said.
One aim of the latest study was to gain new insight into gene
expression in mice specific to olfactory genes. Mice have about 1,500
genes related to smell. Each olfactory nerve cell expresses just one of
these olfactory genes to produce a receptor that recognizes a related
set of odors. The many receptors in a mouse's nasal cavity allow it to
detect a wide range of smells.
"We're trying to understand how the reorganization of chromatin
affects gene expression," Larabell said. "No one's been able to study
this at the human level yet." This research will hopefully lead to new
insights about diseases and disorders that relate to gene expression.
Already, the study's results are being incorporated into models of cell
One of the precursors to Alzheimer's disease, which attacks the
brain's nerve cells, is a loss of smell, so understanding this
connection to olfactory nerve cells could perhaps serve as a diagnostic
tool and perhaps unlock a deeper understanding of the degenerative
The latest study used a microscopy technique known as soft X-ray
tomography to record a series of images from small groups of dozens of
frozen olfactory nerve cells in three separate stages of development.
The technique, which is unique to Berkeley Lab's ALS, captured details
as small as tens of nanometers, or tens of billionths of a meter.
Researchers visually distinguished regions of highly compacted
heterochromatin from other chromatin types.
With the proven success of the imaging technique, Larabell said it's
possible to perform statistical analyses based on large collections of
cell nuclei images sorted by different stages of development. Coupled
with other types of imaging techniques, researchers hope to isolate
individual gene-selection processes in upcoming work.
"This work highlights the power of multidisciplinary research," said
Mark Le Gros, associate director of the NCXT and a physicist who was
responsible for the design and construction of the X-ray microscope. Le
Gros, the lead author in this research, added, "This is an example of
work that required a combination of molecular biologists and cell
biologists with physicists and computer scientists."