Structures considered key to gene expression are surprisingly fleeting


Date:
April 14, 2022
Source:
Massachusetts Institute of Technology
Summary:
Scientists find that loops in the genome may be much rarer and
shorter- lived than previously thought, lasting only tens of
minutes, which suggests current theories of how loops influence
gene expression may need to be revised.



FULL STORY ==========================================================================
In human chromosomes, DNA is coated by proteins to form an exceedingly
long beaded string. This "string" is folded into numerous loops, which
are believed to help cells control gene expression and facilitate DNA
repair, among other functions. A new study from MIT suggests that these
loops are very dynamic and shorter-lived than previously thought.


==========================================================================
In the new study, the researchers were able to monitor the movement of
one stretch of the genome in a living cell for about two hours. They saw
that this stretch was fully looped for only 3 to 6 percent of the time,
with the loop lasting for only about 10 to 30 minutes. The findings
suggest that scientists' current understanding of how loops influence
gene expression may need to be revised, the researchers say.

"Many models in the field have been these pictures of static loops
regulating these processes. What our new paper shows is that this picture
is not really correct," says Anders Sejr Hansen, the Underwood-Prescott
Career Development Assistant Professor of Biological Engineering at
MIT. "We suggest that the functional state of these domains is much
more dynamic." Hansen is one of the senior authors of the new study,
along with Leonid Mirny, a professor in MIT's Institute for Medical
Engineering and Science and the Department of Physics, and Christoph
Zechner, a group leader at the Max Planck Institute of Molecular Cell
Biology and Genetics in Dresden, Germany, and the Center for Systems
Biology Dresden. MIT postdoc Michele Gabriele, recent Harvard University
PhD recipient Hugo Branda~o, and MIT graduate student Simon Grosse-Holz
are the lead authors of the paper, which appears today in Science.

Out of the loop Using computer simulations and experimental data,
scientists including Mirny's group at MIT have shown that loops in the
genome are formed by a process called extrusion, in which a molecular
motor promotes the growth of progressively larger loops. The motor stops
each time it encounters a "stop sign" on DNA. The motor that extrudes such loops is a protein complex called cohesin, while the DNA-bound protein
CTCF serves as the stop sign. These cohesin-mediated loops between CTCF
sites were seen in previous experiments.



========================================================================== However, those experiments only offered a snapshot of a moment in time,
with no information on how the loops change over time. In their new study,
the researchers developed techniques that allowed them to fluorescently
label CTCF DNA sites so they could image the DNA loops over several
hours. They also created a new computational method that can infer the
looping events from the imaging data.

"This method was crucial for us to distinguish signal from noise in
our experimental data and quantify looping," Zechner says. "We believe
that such approaches will become increasingly important for biology
as we continue to push the limits of detection with experiments."
The researchers used their method to image a stretch of the genome in
mouse embryonic stem cells. "If we put our data in the context of one
cell division cycle, which lasts about 12 hours, the fully formed loop
only actually exists for about 20 to 45 minutes, or about 3 to 6 percent
of the time," Grosse-Holz says.

"If the loop is only present for such a tiny period of the cell cycle
and very short-lived, we shouldn't think of this fully looped state as
being the primary regulator of gene expression," Hansen says. "We think
we need new models for how the 3D structure of the genome regulates
gene expression, DNA repair, and other functional downstream processes."
While fully formed loops were rare, the researchers found that partially extruded loops were present about 92 percent of the time. These smaller
loops have been difficult to observe with the previous methods of
detecting loops in the genome.



==========================================================================
"In this study, by integrating our experimental data with polymer
simulations, we have now been able to quantify the relative extents of
the unlooped, partially extruded, and fully looped states," Branda~o says.

"Since these interactions are very short, but very frequent, the
previous methodologies were not able to fully capture their dynamics,"
Gabriele adds.

"With our new technique, we can start to resolve transitions between
fully looped and unlooped states." The researchers hypothesize that
these partial loops may play more important roles in gene regulation than
fully formed loops. Strands of DNA run along each other as loops begin
to form and then fall apart, and these interactions may help regulatory elements such as enhancers and gene promoters find each other.

"More than 90 percent of the time, there are some transient loops,
and presumably what's important is having those loops that are being perpetually extruded," Mirny says. "The process of extrusion itself
may be more important than the fully looped state that only occurs for
a short period of time." More loops to study Since most of the other
loops in the genome are weaker than the one the researchers studied in
this paper, they suspect that many other loops will also prove to be
highly transient. They now plan to use their new technique study some
of those other loops, in a variety of cell types.

"There are about 10,000 of these loops, and we've looked at one,"
Hansen says.

"We have a lot of indirect evidence to suggest that the results
would be generalizable, but we haven't demonstrated that. Using the
technology platform we've set up, which combines new experimental and computational methods, we can begin to approach other loops in the
genome." The researchers also plan to investigate the role of specific
loops in disease.

Many diseases, including a neurodevelopmental disorder called FOXG1
syndrome, could be linked to faulty loop dynamics. The researchers are now studying how both the normal and mutated form of the FOXG1 gene, as well
as the cancer- causing gene MYC, are affected by genome loop formation.

The research was funded by the National Institutes of Health, the National Science Foundation, the Mathers Foundation, a Pew-Stewart Cancer Research Scholar grant, the Chaires d'excellence Internationale Blaise Pascal,
an American-Italian Cancer Foundation research scholarship, and the Max
Planck Institute for Molecular Cell Biology and Genetics.


========================================================================== Story Source: Materials provided by
Massachusetts_Institute_of_Technology. Original written by Anne
Trafton. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Michele Gabriele, Hugo B. Branda~o, Simon Grosse-Holz, Asmita
Jha, Gina
M. Dailey, Claudia Cattoglio, Tsung-Han S. Hsieh, Leonid
Mirny, Christoph Zechner, Anders S. Hansen. Dynamics of CTCF-
and cohesin-mediated chromatin looping revealed by live-cell
imaging. Science, 2022; DOI: 10.1126/science.abn6583 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/04/220414143929.htm

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