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March 02, 2013

Genetic level map of the newt regeneration process

Scientists at the University of Dayton have mapped out the process at the genetic level newts use to regenerate lenses, limbs and other tissue.

The research, published this week in BioMed Central's open access journal Genome Biology, identifies the protein families expressed during tissue regeneration in the common North American newt, laying the groundwork for research into what particular sets of genes are used for this purpose. This is the first comprehensive map of all RNA molecules — called the transcriptome — expressed in regeneration.

For 250 years, scientists have believed old age and repeated amputation weaken a newt's ability to regenerate. They were wrong. And that's good news for humans.

Panagiotis Tsonis, director of the University of Dayton's Center for Tissue Regeneration and Engineering at Dayton (TREND), said his discovery will benefit the entire field of regeneration research and brings us one step closer to a complete understanding of how newts regenerate, which could one day enable humans to replicate the process.

Nature Communications published Tsonis' research July 12, 2011. The study shows even after surgically removing the lens from a newt 18 times over 16 years, the newt was still able to regenerate a perfect lens. Tsonis' findings overturn long-accepted theories proposed by regeneration scientists, including Charles Darwin.

"When would a person benefit from regeneration most? It's when they are older," Tsonis said. "This shows the newt is an excellent source for finding answers to regeneration, particularly as it relates to old age. It has the ability to protect and preserve regeneration."



Genome Biology - A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration



Background
Notophthalmus viridescens, an urodelian amphibian, represents an excellent model organism to study regenerative processes, but mechanistic insights into molecular processes driving regeneration have been hindered by paucity and poor annotation of coding nucleotide sequences. The enormous genome size and the lack of a closely related reference genome have so far prevented assembly of the urodelian genome.

Results
We describe the de novo assembly of the transcriptome of the newt Notophthalmus viridescens and its experimental validation. RNA pools covering embryonic and larval development, different stages of heart, appendage and lens regeneration, as well as a collection of different undamaged tissues were used to generate sequencing datasets on Sanger, Illumina and 454 platforms. Through a sequential de novo assembly strategy, hybrid datasets were converged into one comprehensive transcriptome comprising 120,922 non-redundant transcripts with a N50 of 975. 38,384 putative transcripts were annotated and around 15,000 transcripts were experimentally validated as protein coding by mass spectrometry based proteomics. Bioinformatical analysis of coding transcripts identified 826 proteins specific for urodeles. Several newly identified proteins establish novel protein families based on the presence of new sequence motifs without counterparts in public databases, while others containing known protein domains extend already existing families and also constitute new ones.

Conclusions
We demonstrate that our multistep assembly approach allows de novo assembly of the newt transcriptome with an annotation grade comparable to well characterized organisms. Our data provide the groundwork for mechanistic experiments to answer the question whether urodeles utilize proprietary sets of genes for tissue regeneration.


SOURCES- University of Dayton, Youtube, Genome Biology

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