Use "juice" to understand how DNA is packaged in the nucleus

If you stretch the DNA found in one of your cells from head to tail, it stretches about 2 meters or 6.
5 feet
.
Every cell in your body can pack so much DNA
by wrapping it around a protein called histone.
DNA is turned on and off when cells need to enter normal processes such as cell division
.
However, many cancer cells are particularly sensitive to packing and unpacking DNA because they divide much faster than our healthy, normal cells
.
Understanding which proteins specifically package and break down DNA could help us more accurately target these cancer cells
with inhibitors.

The South Carolina Medical University (MUSC) research team, led by Dr.
David Long, reports in the Journal of Biochemistry that a protein called HDAC1 plays a larger
role in the DNA packaging surrounding the histone than previously thought.

"Cells need to carefully take apart and read their DNA to create different proteins
found in your body," Long said.

To explain how DNA packaging works, Dr.
Colleen Quaas, the first author of the paper, offers an analogy
.

"Histones are like a scroll, and DNA is like a hose
wrapped around a scroll," she said.
Quaas was a graduate student
doing the research in Lang's lab.
She is now a postdoctoral researcher
in the lab of Dr.
Tim Barnoud at MUSC.
Quaas' new research goals include developing new therapies
to treat pancreatic cancer.

Prior to this study, HDAC1 and HDAC2 were thought to play a similar role by winding DNA around histone "scrolls," providing some built-in redundancy
.
Using a new technique developed in Long's lab, the two researchers set out to explore and compare the functions of HDAC1 and HDAC2 proteins
.
They found that the truth was far more complicated
than that.

"Things are a lot more complicated than you think, so all these very simple early explanations are open to further digging and exploring
," Long said.

All the information necessary to make proteins is written in
your DNA.
To extend Quas's analogy, imagine the process of using DNA to make proteins, like watering a garden
.
You need to loosen the hose from the reel to water all the plants, and when you are done watering, wrap the hose back onto the
reel.

To better understand which proteins play a role in winding DNA, Lang developed a system
using extracts extracted from African claw frog eggs.
The extraction system includes all proteins within the nucleus, but removes the DNA
.

"This extract is basically like a cellular juice, and if you think of the nucleus as an orange, the extract is the juice
that has been squeezed out.
We are looking at all the proteins
'squeezed' out of oranges.
”

This extraction system is unique in that it does not rely on cell culture or animal models to answer scientific questions
.
Researchers can simply add the DNA of interest to an extraction system that concentrates the protein and analyze how the DNA is packaged or unpacked
.
In addition, they can determine which specific proteins interact
with the DNA they add to the extraction system.

"We can observe DNA in real time outside the cell, which makes it easier to study the mechanisms of DNA
," Quaas said.

"We can do a lot of things in extracts that you can't do in cells because you have to keep the cells alive
," Long said.
"We can take things out and put things back in, so it's very easy
to manipulate the system.
"

Long and Quaas wanted to see what happened
when they used inhibitors that targeted different groups of HDAC proteins.
Currently, multiple HDAC inhibitors have been approved by the U.
S.
Food and Drug Administration and used in clinical trials
for cancer treatment.
The researchers decided to test several of these inhibitors and found that romidepsin (Istodax, Bristol-Meyers Squibb) specifically prevented the accumulation of DNA
.

Romidepsin targets both HDAC1 and HDAC2, but it was not known which of the two HDACs was responsible for DNA packaging
.
In their study, the researchers developed tools
specifically for HDAC1 or HDAC2.
Given the popular view, they believe that the effect on DNA packaging is the same
regardless of the protein they target.
Instead, the packaging of DNA is delayed
only when HDAC1 is inhibited.
This surprised the researchers, prompting them to further explore how HDAC1 interacts with proteins other than HDAC2 to do its work
.

"We found that HDAC1 and HDAC2 have different roles in our system, and they are also present in
different protein complexes," Quaas said.

The study's findings are important for several
reasons.
First, the extraction system used in Long's lab is novel and can be used to answer questions
that are difficult to solve in traditional cell or animal models.
Second, future cancer treatments could focus on developing inhibitors
that specifically target a single HDAC protein.
The researchers found that HDAC1, not HDAC2, was the main driver of DNA packaging, so targeting only HDAC1 may be more effective and have fewer
side effects during treatment.

"These selective inhibitors are a great way
to target cancer cells," Long said.
"Cancer cells grow quickly, so if we can disrupt the way they pack and break down DNA, it makes them more sensitive
to cell death.
"