Nav: Home

New genomic tool for salamander biology could spur deeper understanding of tissue regeneration

January 17, 2017

A research team led by scientists at Brigham and Women's Hospital has assembled a catalogue of every active gene in a variety of tissues in the axolotl, a type of salamander known for its striking ability to fully regenerate limbs following amputation. The catalogue, known as a "transcriptome," provides a important resource for the community of researchers who study axolotls -- a model organism that promises to shed light not only on the molecular mechanisms that underlie limb regeneration but also how on potential ways to repair and replace human tissues that are damaged or lost as a result of injury, illness, or even congenital disorders.

Despite the promise of axolotl research for human regenerative medicine, the genomic resources currently available for axolotls remain quite limited. This is due in part to the large size and highly repetitive nature of the organism's genome -- indeed, it is roughly 10 times the size of the human genome. Propelled by recent advances in genomic sequencing and bioinformatics, researchers have found an alternative for identifying and studying axolotl genes: transcriptomes.

"Our hope is that this new resource will help make axolotls accessible not only to researchers who already work on the organism, but also to those in other fields who wish to explore it," said Jessica Whited, PhD, a senior author of the study and an assistant professor in the Department of Orthopedic Surgery at BWH. "Unfortunately, the axolotl has been largely impenetrable for the majority of scientists." To help accomplish this goal, Whited and her collaborators, led by Brian Haas, Senior Computational Biologist at the Broad Institute, are making their data available through an easily navigable web portal, https://portals.broadinstitute.org/axolotlomics/.

In the last few years, a handful of axolotl transcriptome studies have been published. What distinguishes the latest study is its near-completeness, in terms of represented genes, and its coverage of diverse tissues involved in limb regeneration, including bone and cartilage, skeletal muscle, heart, and blood vessels. The researchers also included different portions of the blastema, a cluster of cells that forms shortly after limb amputation and directs the formation of a complete new limb.

In addition to developing this valuable resource, Whited and her colleagues also mined it to uncover important axolotl genes and investigate the genes' potential functions. One interesting gene is kazald1, which is very highly enriched in blastema cells. Although it has been identified in mammals and has even been found in certain types of tumors, virtually nothing is known about kazald1's function.

Because of the axolotl's relatively long generation time -- it takes 9 months for a newly-fertilized embryo to develop, grow, and become sexually mature-- traditional methods for deleting genes to understand their effects are labor-intensive and daunting at large scale. Therefore, the study's first author, graduate student Donald Bryant, developed an innovative approach to modify, or "edit" genes solely in the axolotl limb. Although the efficiency of the method needs to be improved, future work in this area could help accelerate efforts to elucidate the functions of scores of axolotl genes and, in turn, help reveal the molecular steps required for limb regeneration.
-end-
Paper cited: Bryant DM et al. "A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors." Cell Reports.

Brigham and Women's Hospital

Related Genes Articles:

Insomnia genes found
An international team of researchers has found, for the first time, seven risk genes for insomnia.
Genes affecting our communication skills relate to genes for psychiatric disorder
By screening thousands of individuals, an international team led by researchers of the Max Planck Institute for Psycholinguistics, the University of Bristol, the Broad Institute and the iPSYCH consortium has provided new insights into the relationship between genes that confer risk for autism or schizophrenia and genes that influence our ability to communicate during the course of development.
The fate of Neanderthal genes
The Neanderthals disappeared about 30,000 years ago, but little pieces of them live on in the form of DNA sequences scattered through the modern human genome.
Face shape is in the genes
Many of the characteristics that make up a person's face, such as nose size and face width, stem from specific genetic variations, reports John Shaffer of the University of Pittsburgh in Pennsylvania, and colleagues, in a study published on Aug.
Study finds hundreds of genes and genetic codes that regulate genes tied to alcoholism
Using rats carefully bred to either drink large amounts of alcohol or to spurn it, researchers at Indiana and Purdue universities have identified hundreds of genes that appear to play a role in increasing the desire to drink alcohol.
Reading between the genes
For a long time dismissed as 'junk DNA,' we now know that also the regions between the genes fulfill vital functions.
The silence of the genes
Research led by Dr. Keiji Tanimoto from the University of Tsukuba, Japan, has brought us closer to understanding the mechanisms underlying the phenomenon of genomic imprinting.
Why some genes are highly expressed
The DNA in our cells is folded into millions of small packets, like beads on a string, allowing our two-meter linear DNA genomes to fit into a nucleus of only about 0.01 mm in diameter.
Activating genes on demand
A new approach developed by Harvard geneticist George Church, Ph.D., can help uncover how tandem gene circuits dictate life processes, such as the healthy development of tissue or the triggering of a particular disease, and can also be used for directing precision stem cell differentiation for regenerative medicine and growing organ transplants.
Controlling genes with light
Researchers at Duke University have demonstrated a new way to activate genes with light, allowing precisely controlled and targeted genetic studies and applications.

Related Genes Reading:

Best Science Podcasts 2019

We have hand picked the best science podcasts for 2019. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Moving Forward
When the life you've built slips out of your grasp, you're often told it's best to move on. But is that true? Instead of forgetting the past, TED speakers describe how we can move forward with it. Guests include writers Nora McInerny and Suleika Jaouad, and human rights advocate Lindy Lou Isonhood.
Now Playing: Science for the People

#527 Honey I CRISPR'd the Kids
This week we're coming to you from Awesome Con in Washington, D.C. There, host Bethany Brookshire led a panel of three amazing guests to talk about the promise and perils of CRISPR, and what happens now that CRISPR babies have (maybe?) been born. Featuring science writer Tina Saey, molecular biologist Anne Simon, and bioethicist Alan Regenberg. A Nobel Prize winner argues banning CRISPR babies won’t work Geneticists push for a 5-year global ban on gene-edited babies A CRISPR spin-off causes unintended typos in DNA News of the first gene-edited babies ignited a firestorm The researcher who created CRISPR twins defends...