MAY 30, 2021 10:19 AM PDT

Creating a 'Periodic Table' of Cells

WRITTEN BY: Carmen Leitch

You've heard of the periodic table of the elements, but do you know of a periodic table for cells? Researchers have now created a system for classifying cell nuclei, and this work also revealed a method for reprogramming a nucleus from one kind of cell into another. This research has been reported in Science by a team of investigators including a consortium called the DNA Zoo. In the DNA Zoo project, the investigators are classifying how chromosomes are compacted to fit inside of cell nuclei from different species.

Image credit: Cropped from Pixabay

The effort revealed consistencies - there seemed to be two types of nuclear designs. "Whether we were looking at worms or urchins, sea squirts or coral, we kept seeing the same folding patterns coming up," said co-first study author Dr. Olga Dudchenko, a member of the Center for Genome Architecture at Baylor University among other appointments. "In some species, chromosomes are organized like the pages of a printed newspaper, with the outer margins on one side and the folded middle at the other, and then in other species, each chromosome is crumpled into a little ball."

"So we had a puzzle," added senior study author Dr. Erez Lieberman Aiden, an associate professor of molecular and human genetics and Emeritus McNair Scholar at Baylor College of Medicine. "The data implied that over the course of evolution, species can switch back and forth from one type to the other. We wondered: What is the controlling mechanism? Might it be possible to change one type of nucleus into another in the lab?"

A different group of researchers had recently made a surprising observation that was relevant to this work.

"I was doing experiments on a protein called condensin II, which we knew plays a role in how cells divide," said co-first study author Claire Hoencamp, who works in the laboratory of Dr. Benjamin Rowland at the Netherlands Cancer Institute. "But we observed the strangest thing: When we mutated the protein in human cells, the chromosomes would totally rearrange. It was baffling!"

When the team met to discuss these findings, they determined that Hoencamp had found something that would convert the nuclei of one type of human cell to another.

"When we looked at the genomes being studied at the DNA Zoo, we discovered that evolution had already done our experiment many, many times! When mutations in a species break condensin II, they usually flip the whole architecture of the nucleus," said senior study author Rowland. "It's always a little disappointing to get scooped on an experiment, but evolution had a very long head start."

During this research project, the pandemic hit. "Without access to our laboratories, we were left with only one way to establish what condensin II was doing," Hoencamp said. "We needed to create a computer program that could simulate the effects of condensin II on the chain of hundreds of millions of genetic letters that comprise each human chromosome."

The team looked to Dr. José Onuchic, the Harry C. and Olga K. Wiess Chair of Physics at Rice for assistance. "Our simulations showed that by destroying condensin II, you could make a human nucleus reorganize to resemble a fly nucleus," said Onuchic.

"We began with an incredibly broad survey of 2 billion years of nuclear evolution," Brahmachari said. "And we found that so much boils down to one simple mechanism, that we can simulate as well as recapitulate, on our own, in a test tube. It's an exciting step on the road to a new kind of genome engineering in 3D!"

Sources: AAAS/Eurekalert! via Baylor College of Medicine, Science

About the Author
  • Experienced research scientist and technical expert with authorships on over 30 peer-reviewed publications, traveler to over 70 countries, published photographer and internationally-exhibited painter, volunteer trained in disaster-response, CPR and DV counseling.
You May Also Like
JUN 07, 2021
Cardiology
Researchers Find a Way to Improve Outcomes After a Heart Attack
JUN 07, 2021
Researchers Find a Way to Improve Outcomes After a Heart Attack
It's thought that in the United States, there is a heart attack once every 40 seconds, or that each year, about 80,0 ...
JUN 28, 2021
Earth & The Environment
Yeast Engineered to Produce Biofuel from Previously Unusable Biomass
JUN 28, 2021
Yeast Engineered to Produce Biofuel from Previously Unusable Biomass
Researchers from the Massachusetts Institute of Technology have found a way to expand biofuel production with geneticall ...
JUL 05, 2021
Cell & Molecular Biology
A Step Toward Artificial Chromosomes - Manufacturing a Kinetochore
JUL 05, 2021
A Step Toward Artificial Chromosomes - Manufacturing a Kinetochore
In human cells, lengthy strands of DNA have to be carefully organized and compacted so they'll fit into the nucleus; our ...
JUL 06, 2021
Cell & Molecular Biology
Can Some Brain Plasticity Be Restored with Ketamine or Light?
JUL 06, 2021
Can Some Brain Plasticity Be Restored with Ketamine or Light?
The perineuronal net is known to play a crucial role in memory. This structure surrounds certain neurons, encasing their ...
JUL 12, 2021
Genetics & Genomics
Vision of Retinitis Pigmentosa Patient Partially Restored by New Therapy
JUL 12, 2021
Vision of Retinitis Pigmentosa Patient Partially Restored by New Therapy
Scientists have been developing gene therapies that can help restore vision that's lost due to a problem with a gene ...
JUL 18, 2021
Genetics & Genomics
Researchers Find Strange 'Borg' DNA - It's Assimilating
JUL 18, 2021
Researchers Find Strange 'Borg' DNA - It's Assimilating
Our environment is full of DNA molecules. While researchers have become concerned about DNA waste material that's ac ...
Loading Comments...