Team creates online database to compare regenerative tissue capabilities among animals

June 14, 2018 by Margaret Nagle, University of Maine
Credit: University of Maine

Comparing regenerative tissue capabilities among animals is the focus of a new database created by a team of researchers at the University of Maine and MDI Biological Laboratory.

Benjamin King, an assistant professor of bioinformatics at UMaine, and Viravuth Yin from the MDI Biological Laboratory in Bar Harbor, led a team to create RegenDbase, the Comparative Models of Regeneration Database.

While regenerative capacity in mammals is limited to select tissues, lower vertebrates such as and salamanders have the ability to regenerate entire limbs and most adult tissues, including heart muscle, according to the researchers.

The online resource allows researchers to compare patterns across animals with different regenerative capacities to look for shared and unique patterns of gene expression. It incorporates sets for protein-coding and regulatory RNA molecules from zebrafish, axolotl salamanders and mice.

The researchers used the new database to conduct a comprehensive gene expression study to find RNAs common to heart regeneration in both neonatal mice and zebrafish using an extensive new zebrafish data set. Twenty-eight new zebrafish regulatory RNA molecules were identified using those data, according to King.

"The new zebrafish data set allowed us to identify putative novel genes expressed during early stages of cardiac regeneration," King says. "These long noncoding RNAs are promising candidate genes that could regulate protein-coding genes. The bioinformatics database provides systems-level analysis of to understand how networks of genes regulate tissue regeneration."

Future incorporation of data sets from other organisms and human tissues will enable broader cross-species comparisons of regenerative biology, the researchers hypothesize.

King is the lead author of "RegenDbase: a comparative database of noncoding RNA regulation of tissue regeneration circuits across multiple taxa," which was recently published in the journal npj Regenerative Medicine.

Explore further: Scientists describe the mechanism of heart regeneration in the zebrafish

More information: Benjamin L. King et al. RegenDbase: a comparative database of noncoding RNA regulation of tissue regeneration circuits across multiple taxa, npj Regenerative Medicine (2018). DOI: 10.1038/s41536-018-0049-0

Related Stories

Scientists describe the mechanism of heart regeneration in the zebrafish

February 12, 2018
Some animals, including the zebrafish, have a high capacity to regenerate tissues, allowing them to recovery fully after cardiac injury. During this process, the heart muscle cells divide to replace the damaged tissue. However, ...

Novel gene in red blood cells may help adult newts regenerate limbs

June 5, 2018
Newts are the only four-legged vertebrates that can regenerate their body parts, even as adults. When a newt loses a limb, a mass of cells called a blastema is generated at the stump, from which a new, fully functional limb ...

Stem Cell discovery refreshes the heart

August 7, 2017
Some people are better than others at recovering from a wounded heart, according to a new USC Stem Cell study published in Nature Genetics.

Study uncovers genetic elements that drive regeneration

April 6, 2016
If you trace our evolutionary tree way back to its roots—long before the shedding of gills or the development of opposable thumbs—you will likely find a common ancestor with the amazing ability to regenerate lost body ...

Inflammation in regeneration: A friend or foe?

March 7, 2017
Regeneration is an inherent property of life. However, the potential to regenerate differs across species: while fish and amphibians can re-grow appendages such as limbs, tails, and fins, mammals, including humans, cannot ...

Conserved microRNAs may regulate limb regeneration in evolutionarily distant species

June 29, 2016
Several conserved microRNAs, or short, highly conserved noncoding RNAs that are targeted to and inhibit expression of specific genes, may be involved in the regulation of limb regeneration across evolutionarily distant species, ...

Recommended for you

Researchers identify new genetic disorder

September 21, 2018
Researchers from Michigan State University College of Human Medicine and physicians from Spectrum Health have identified for the first time in a human patient a genetic disorder only previously described in animal models.

Test could detect patients at risk from lethal fungal spores

September 20, 2018
Scientists at The University of Manchester have discovered a genetic mutation in humans linked to a 17-fold increase in the amount of dangerous fungal spores in the lungs.

Researchers identify a new cause of childhood mitochondrial disease

September 20, 2018
A rapid genetic test developed by Newcastle researchers has identified the first patients with inherited mutations in a new disease gene.

Why some human genes are more popular with researchers than others

September 18, 2018
Historical bias is a key reason why biomedical researchers continue to study the same 10 percent of all human genes while ignoring many genes known to play roles in disease, according to a study publishing September 18 in ...

Class of neurological disorders share 3-D genome folding pattern, study finds

September 18, 2018
In a class of roughly 30 neurological disorders that includes ALS, Huntington's Disease and Fragile X Syndrome, the relevant mutant gene features sections of repeating base pair sequences known as short tandem repeats, or ...

Researchers resolve decades-old mystery about the most commonly mutated gene in cancer

September 18, 2018
The most commonly mutated gene in cancer has tantalized scientists for decades about the message of its mutations. Although mutations can occur at more than 1,100 sites within the TP53 gene, they arise with greatest frequency ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.