Scientists discover a role for 'junk' DNA

April 11, 2018

ANN ARBOR -- Researchers at the University of Michigan Life Sciences Institute and the Howard Hughes Medical Institute have determined how satellite DNA, considered to be "junk DNA," plays a crucial role in holding the genome together.

Their findings, published recently in the journal eLife, indicate that this genetic "junk" performs the vital function of ensuring that chromosomes bundle correctly inside the cell's nucleus, which is necessary for cell survival. And this function appears to be conserved across many species.

This pericentromeric satellite DNA consists of a very simple, highly repetitive sequence of genetic code. Although it accounts for a substantial portion of our genome, satellite DNA does not contain instructions for making any specific proteins. What's more, its repetitive nature is thought to make the genome less stable and more susceptible to damage or disease. Until fairly recently, scientists believed this so-called "junk" or "selfish" DNA did not serve any real purpose.

"But we were not quite convinced by the idea that this is just genomic junk," said Yukiko Yamashita, research professor at the LSI and lead author on the study. "If we don't actively need it, and if not having it would give us an advantage, then evolution probably would have gotten rid of it. But that hasn't happened."

Yamashita and her colleagues decided to see what would happen if cells could not use this pericentromeric satellite DNA. Because it exists in long, repetitive sequences, the researchers could not simply mutate or cut the entire satellite DNA out of the genome. Instead, they approached the question through D1, a protein known to bind to satellite DNA.

The researchers removed D1 from the cells of a commonly used model organism, Drosophila melanogaster (fruit flies). And the team quickly noticed that germ cells--the cells that ultimately develop into sperm or eggs--were dying.

Further analysis revealed that the dying cells were forming micro-nuclei, or tiny buds, outside the nucleus that included pieces of the genome. Without the entire genome encapsulated in the nucleus, the cells could not survive.

The researchers believe that the D1 protein binds onto the satellite DNA to pull all of the chromosomes together in the nucleus. If the D1 protein cannot grab the satellite DNA, the cell loses its ability to form a complete nucleus and ultimately dies.

"It's like forming a bouquet," said Yamashita, who is also a professor of cell and developmental biology at the U-M Medical School and an HHMI investigator. "The protein has multiple binding sites, so it can bind onto multiple chromosomes and package them together in one place, preventing individual chromosomes from floating out of the nucleus."

The team conducted similar experiments using mouse cells and found the same results: When they removed a protein that normally binds to mouse satellite DNA, the cells again formed micro-nuclei and did not survive.

The similar findings from both fruit fly and mouse cells lead Yamashita and her colleagues to believe that satellite DNA is essential for cellular survival, not just in model organisms, but across species that embed DNA into the nucleus--including humans.
-end-
The research was supported by the Howard Hughes Medical Institute, the National Institutes of Health and the American Heart Association.

In addition to Yamashita, other authors of the study are Madhav Jagannathan and Ryan Cummings, also of U-M. The title is "A conserved function for pericentromeric satellite DNA," DOI: 10.7554/eLife.34122

The paper published online March 26 in eLife.

University of Michigan

Related DNA Articles from Brightsurf:

A new twist on DNA origami
A team* of scientists from ASU and Shanghai Jiao Tong University (SJTU) led by Hao Yan, ASU's Milton Glick Professor in the School of Molecular Sciences, and director of the ASU Biodesign Institute's Center for Molecular Design and Biomimetics, has just announced the creation of a new type of meta-DNA structures that will open up the fields of optoelectronics (including information storage and encryption) as well as synthetic biology.

Solving a DNA mystery
''A watched pot never boils,'' as the saying goes, but that was not the case for UC Santa Barbara researchers watching a ''pot'' of liquids formed from DNA.

Junk DNA might be really, really useful for biocomputing
When you don't understand how things work, it's not unusual to think of them as just plain old junk.

Designing DNA from scratch: Engineering the functions of micrometer-sized DNA droplets
Scientists at Tokyo Institute of Technology (Tokyo Tech) have constructed ''DNA droplets'' comprising designed DNA nanostructures.

Does DNA in the water tell us how many fish are there?
Researchers have developed a new non-invasive method to count individual fish by measuring the concentration of environmental DNA in the water, which could be applied for quantitative monitoring of aquatic ecosystems.

Zigzag DNA
How the cell organizes DNA into tightly packed chromosomes. Nature publication by Delft University of Technology and EMBL Heidelberg.

Scientists now know what DNA's chaperone looks like
Researchers have discovered the structure of the FACT protein -- a mysterious protein central to the functioning of DNA.

DNA is like everything else: it's not what you have, but how you use it
A new paradigm for reading out genetic information in DNA is described by Dr.

A new spin on DNA
For decades, researchers have chased ways to study biological machines.

From face to DNA: New method aims to improve match between DNA sample and face database
Predicting what someone's face looks like based on a DNA sample remains a hard nut to crack for science.

Read More: DNA News and DNA Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.