KANAZAWA, Japan, April 24, 2024 /PRNewswire/ -- Researchers
at Nano Life Science Institute (WPI-NanoLSI), Kanazawa
University report in Nano
Letters how the use of high-speed atomic force
microscopy helps to understand the crucial role played by certain
biomolecules in DNA wrapping dynamics.
In plants and animals, the basic packaging units of DNA, which
carry genetic information, are the so-called nucleosomes.
A nucleosome consists of a segment of DNA wound around eight
proteins known as histones. During gene expression (the process
lying at the basis of protein production), nucleosomes are
involved in various dynamical structural changes, such as
nucleosome sliding, DNA unwrapping and other DNA–histone
interactions. Of particular importance in these processes are the
end structures, or tails, of the histones. Histone tails
undergo chemical modifications, changing the histone's
functionality as needed. Detailed studies, and especially
visualizations, of nucleosome dynamics are crucial for better
understanding the role of histone tails. Mikihiro Shibata from Kanazawa University and
colleagues have now succeeded in making video recordings of
tail-less nucleosomes, showing that the absence of histone tails
significantly increases a nucleosome's dynamic activity.
The scientists used high-speed atomic force microscopy (HS-AFM),
a powerful nanoimaging tool for visualizing molecular structures
and their dynamics at high spatial and temporal resolution. For
this, the nucleosomes needed to be put onto a substrate. Shibata
and colleagues used a film of so-called pillar[5]arenes (molecules
with a pentagonal tubular structure) as the substrate, forming an
ideal surface as the nucleosomes are easily adsorbed to it without
dynamical processes getting suppressed.
The researchers first looked at nucleosomes for which all eight
histones lacked tails. Based on their HS-AFM observations,
they concluded that nucleosome sliding and DNA
unwrapping/rewrapping occurred more often than for normal
(canonical) nucleosomes. This suggests that without tails,
the histone–DNA interaction is weakened, leading to a
situation in which DNA can more easily detach from the
histones.
To better understand the roles of specific histone tails,
Shibata and colleagues prepared nucleosomes where one type of
histone was tailless. There are four different types
of histones, called H2A, H2B, H3 and H4. HS-AFM experiments on
the nucleosomes revealed that H2B and H3 tail-less nucleosomes
showed an increased frequency of dynamics. Conversely, this means
that canonical H2B and H3 histones are essential for
nucleosome stability.
The scientists point out that they could not observe any actual
motion of histone tails — most likely the temporal resolution of
the study, 0.3 seconds, was much slower than the rate of the
wrapping/unwrapping dynamics of the tails. Despite this limitation,
the work of Shibata and colleagues clearly proves that the tails of
H2B and H3 histones are the main contributors to nucleosome
dynamics. Regarding future work, quoting the researchers, "a
technique for tagging histone tail tips might enable HS-AFM to
capture the movements of the histone tails themselves."
Background
High-speed atomic force microscopy
The general principle of atomic force microscopy (AFM) is to
make a very small tip scan the surface of a sample. During this
horizontal (xy) scan, the tip, which is attached to a small
cantilever, follows the sample's vertical (z) profile,
inducing a force on the cantilever that can be measured. The
magnitude of the force at the xy position can be
related to the z value; the xyz data generated during
a scan then result in a height map providing structural information
about the investigated sample. In high-speed-AFM (HS-AFM), the
working principle is slightly more involved: the cantilever is made
to oscillate near its resonance frequency. When the tip is moved
around a surface, the variations in the amplitude (or the
frequency) of the cantilever's oscillation — resulting from the
tip's interaction with the sample's surface — are recorded, as
these provide a measure for the local z value. AFM does not involve
lenses, so its resolution is not restricted by the so-called
diffraction limit as in X-ray diffraction, for example.
HS-AFM results in a video, where the time interval between
frames depends on the speed with which a single image can be
generated (by xy-scanning the sample). Researchers at Nano
Life Science Institute (WPI-NanoLSI), Kanazawa University have in
recent years developed HS-AFM further, so that it can be applied to
study biochemical molecules and biomolecular processes in
real-time. Mikihiro Shibata and
colleagues have now applied the method to study nucleosome dynamics
in detail, and in particular the role of the molecular endings of
histones — proteins that play a crucial role in DNA
accessibility.
Reference
Shin Morioka, Takumi Oishi, Suguru
Hatazawa, Takahiro Kakuta,
Tomoki Ogoshi, Kenichi Umeda, Noriyuki
Kodera, Hitoshi Kurumizaka, and Mikihiro Shibata. High-Speed Atomic Force
Microscopy Reveals the Nucleosome Sliding and DNA
Unwrapping/Wrapping Dynamics of Tail-less Nucleosomes,
Nano Letters ,2024.
DOI: 10.1021/acs.nanolett.4c00801
https://pubs.acs.org/doi/10.1021/acs.nanolett.4c00801
https://nanolsi.kanazawa-u.ac.jp/wp/wp-content/uploads/Figure-1-12.png
Figure 1.
High-speed atomic force microscopy visualization of nucleosome
dynamics with canonical (top) and tail-less (bottom) histones.
© 2024 American Chemical Society
Contact
Hiroe
Yoneda
Senior Specialist in Project Planning and Outreach
NanoLSI Administration Office, Nano Life Science Institute
(WPI-NanoLSI)
Kanazawa University
Kakuma-machi, Kanazawa 920-1192, Japan
Email: nanolsi-office@adm.kanazawa-u.ac.jp
Tel: +81 (76) 234-4555
About Nano Life Science Institute (WPI-NanoLSI), Kanazawa
University
Understanding nanoscale mechanisms of life phenomena by
exploring "uncharted nano-realms"
Cells are the basic units of almost all life forms. We are
developing nanoprobe technologies that allow direct imaging,
analysis, and manipulation of the behavior and dynamics of
important macromolecules in living organisms, such as proteins and
nucleic acids, at the surface and interior of cells. We aim at
acquiring a fundamental understanding of the various life phenomena
at the nanoscale.
https://nanolsi.kanazawa-u.ac.jp/en/
About the World Premier International Research Center
Initiative (WPI)
The WPI program was launched in 2007 by Japan's Ministry of Education, Culture,
Sports, Science and Technology (MEXT) to foster globally visible
research centers boasting the highest standards and outstanding
research environments. Numbering more than a dozen and operating at
institutions throughout the country, these centers are given a high
degree of autonomy, allowing them to engage in innovative modes of
management and research. The program is administered by the Japan
Society for the Promotion of Science (JSPS).
See the latest research news from the centers at the WPI News
Portal:
https://www.eurekalert.org/newsportal/WPI
Main WPI program site:
www.jsps.go.jp/english/e-toplevel
About Kanazawa University
As the leading comprehensive university on the Sea of
Japan coast, Kanazawa University
has contributed greatly to higher education and academic research
in Japan since it was founded in
1949. The University has three colleges and 17 schools offering
courses in subjects that include medicine, computer engineering,
and humanities.
The University is located on the coast of the Sea of
Japan in Kanazawa – a city rich in
history and culture. The city of Kanazawa has a highly respected
intellectual profile since the time of the fiefdom (1598-1867).
Kanazawa University is divided into two main campuses: Kakuma and
Takaramachi for its approximately 10,200 students including 600
from overseas.
http://www.kanazawa-u.ac.jp/e/
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