DEC 06, 2020 7:11 AM PST

New Epigenetic Signature Discovered in Zebrafish

WRITTEN BY: Carmen Leitch

Zebrafish are an excellent model organism for biomedical research studies. They generate large numbers of embryos that develop rapidly, and are transparent for the first few hours of life and even longer with chemical treatments. We also know a lot about their genome, and they have enough in common, from a genetic standpoint, with humans to act as a biological parallel. Scientists have now identified a new characteristic of the zebrafish genome.

Zebrafish in an aquatics facility / Credit: Carmen Leitch

Reporting in Nucleic Acids Research, the researchers determined that unusually high levels of repeats of the DNA sequence 'TGCT' in the zebrafish genome are tagged with an epigenetic marker known as a methyl group. Epigenetics refers to biochemical changes in the genomic sequence that are not permanent, but they are heritable and can affect gene expression. Methylation is one of the more common epigenetic features of the genome, and happens in plants and animals.

"We've revealed a new form of DNA methylation in zebrafish at TGCT repeats, and crucially, the enzyme that makes the modification," said Dr. Ozren Bogdanovic, head of the Developmental Epigenomics Lab at Garvan and Senior Research Fellow at the School of Biotechnology and Biomolecular Sciences, UNSW Sydney. "These findings open the field to new possibilities in studying the epigenome - the additional layer of instructions on DNA that change how genes are read - and understand how it may be clinically relevant."

"DNA methylation is vital to cellular function, as it controls which genes are turned on and off," noted first study author and graduate candidate Sam Ross.

It's been thought that methylation usually tends to happen in the genome where 'CG' sequences occur, but there are other places that are methylated. In Rett syndrome, for example, methylation occurs at places other than CG in the genome of brain cells.

This study showed that when TGCT was appearing multiple times together in zebrafish, there was also methylation. Additional work revealed that an enzyme called Dnmt3ba is crucial to the methylation of TGCT repeats in zebrafish.

"We were fascinated to see that methylation levels at TGCT repeats were higher than any non-CG methylation previously observed in the majority of adult vertebrate tissues," said Bogdanovic. "Further, this methylation was present at high levels in the sperm and egg, absent in the fertilized egg, and then appeared again in the growing embryo, reaching its highest levels in adult tissues such as the brain and gonads. While we are yet to reveal how this modification changes gene expression, we believe TGCT methylation to be linked to the 'awakening' of the embryonic genome in zebrafish."

More work will have to be done to determine whether this is happening in other species including humans.

"While it's unclear if a similar modification occurs in animals more broadly, our discovery in zebrafish is significant, because it means we can start to selectively manipulate this atypical form of methylation in a model organism. It means we can change the levels of Dnmt3ba to see what happens when we remove just one form of methylation, but not another," added Bogdanovic.

"This could greatly facilitate our understanding of how changes in atypical methylation patterns affect specific tissues such as the brain, to gain further insights into the molecular mechanisms of neurodevelopmental disorders," Bogdanovic concluded.

Sources: AAAS/Eurekalert! via Garvan Institute of Medical Research, Nucleic Acid Research

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
JAN 10, 2021
Microbiology
Some Bacteria Know the Time
JAN 10, 2021
Some Bacteria Know the Time
People, animals, and even plants are known to have biological clocks, and new work has revealed that free-living bacteri ...
JAN 11, 2021
Genetics & Genomics
Treating Progeria With a CRISPR Technique
JAN 11, 2021
Treating Progeria With a CRISPR Technique
Hutchinson-Gilford progeria syndrome is a rare disorder that impacts around 400 people in the world. Many people have he ...
FEB 08, 2021
Genetics & Genomics
Human Epigenome Map Reveals Genetic Circuitry
FEB 08, 2021
Human Epigenome Map Reveals Genetic Circuitry
While the human genome was sequenced many years ago, there was so much to learn about it beyond just its sequence, like ...
FEB 10, 2021
Genetics & Genomics
The Evolution of Snake Venom From Predation to Protection
FEB 10, 2021
The Evolution of Snake Venom From Predation to Protection
The venom of some spitting snakes has evolved to cause more pain to mammals, a defense mechanism likely meant to fend of ...
APR 05, 2021
Health & Medicine
April is Autism Awareness Month
APR 05, 2021
April is Autism Awareness Month
April is autism awareness month (April 2 was autism awareness day), during which people are encouraged to learn more abo ...
APR 13, 2021
Genetics & Genomics
Skull Fossil Yields One of the Oldest Modern Human Genomes
APR 13, 2021
Skull Fossil Yields One of the Oldest Modern Human Genomes
DNA from a very old skull is changing what we know about when and where early humans lived.
Loading Comments...