This application proposes to develop fundamental genomic and bioinformatic resources that will better enable studies of a model amphibian, the Mexican axolotl (Ambystoma mexicanum). The axolotl is used in several areas of biomedical research including regenerative medicine and stem cell biology. Axolotls show a remarkable ability to regenerate damaged body parts, including whole limbs, spinal cord, and brain. Understanding how axolotls regenerate complex tissues may reveal mechanisms to achieve endogenous regeneration in humans.
Specific Aim 1 will continue efforts to sequence the large axolotl genome, which is 10x larger than the human genome. An innovative chromatin capture approach (Hi-C) will be used to develop DNA libraries that contain information for scaffolding unordered genomic fragments. Accomplishment of this aim will yield a highly contiguous and annotated genome assembly, an essential resource for any model organism.
Specific Aim 2 will perform the first epigenetic studies of the axolotl genome. These studies will characterize changes in histone modifications, whole genome methylation patterns, and local chromatin interactions during limb regeneration, leveraging an existing transcriptional dataset that provides robust temporal resolution of gene expression. These studies will identify chromatin modifications and interactions that arise or are remodeled during critical phases of limb regeneration.
Specific Aim 3 will develop genomic sequence for a second salamander model, the red-spotted newt (Notophthalamus viridescens). The newt is a logical choice for sequencing because it too serves as a model organism in tissue regeneration research, and its phylogenetic distance from axolotl is ideal for identifying conserved and lineage-specific non-coding sequences that may function to regulate transcription during regeneration. Thus, the proposed newt genomic sequence will broaden the salamander toolkit, increasing the likelihood for future clinical applications in biomedicine. Broad impact will be achieved by sharing genomic and epigenetic data from all three Specific Aims through an existing public website (Sal-Site). Overall, the project will greatly enhance salamander models for biomedical research.

Public Health Relevance

The project will develop critical genomic resources to enhance research efforts using the Mexican axolotl. Studies using the axolotl may reveal strategies to achieve endogenous tissue regeneration in humans.

Agency
National Institute of Health (NIH)
Institute
Office of The Director, National Institutes of Health (OD)
Type
Resource-Related Research Projects (R24)
Project #
2R24OD010435-16
Application #
9149749
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Contreras, Miguel A
Project Start
2001-10-01
Project End
2020-06-30
Budget Start
2016-07-01
Budget End
2017-06-30
Support Year
16
Fiscal Year
2016
Total Cost
Indirect Cost
Name
University of Kentucky
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
939017877
City
Lexington
State
KY
Country
United States
Zip Code
40506
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Randal Voss, S; Murrugarra, David; Jensen, Tyler B et al. (2018) Transcriptional correlates of proximal-distal identify and regeneration timing in axolotl limbs. Comp Biochem Physiol C Toxicol Pharmacol 208:53-63
Keinath, Melissa C; Voss, S Randal; Tsonis, Panagiotis A et al. (2017) A linkage map for the Newt Notophthalmus viridescens: Insights in vertebrate genome and chromosome evolution. Dev Biol 426:211-218
Woodcock, M Ryan; Vaughn-Wolfe, Jennifer; Elias, Alexandra et al. (2017) Identification of Mutant Genes and Introgressed Tiger Salamander DNA in the Laboratory Axolotl, Ambystoma mexicanum. Sci Rep 7:6
Amamoto, Ryoji; Huerta, Violeta Gisselle Lopez; Takahashi, Emi et al. (2016) Adult axolotls can regenerate original neuronal diversity in response to brain injury. Elife 5:
Keinath, Melissa C; Timoshevskiy, Vladimir A; Timoshevskaya, Nataliya Y et al. (2015) Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing. Sci Rep 5:16413
McCusker, Catherine D; Athippozhy, Antony; Diaz-Castillo, Carlos et al. (2015) Positional plasticity in regenerating Amybstoma mexicanum limbs is associated with cell proliferation and pathways of cellular differentiation. BMC Dev Biol 15:45
Ponomareva, Larissa V; Athippozhy, Antony; Thorson, Jon S et al. (2015) Using Ambystoma mexicanum (Mexican axolotl) embryos, chemical genetics, and microarray analysis to identify signaling pathways associated with tissue regeneration. Comp Biochem Physiol C Toxicol Pharmacol 178:128-35
Voss, S Randal; Palumbo, Alex; Nagarajan, Radha et al. (2015) Gene expression during the first 28 days of axolotl limb regeneration I: Experimental design and global analysis of gene expression. Regeneration (Oxf) 2:120-136
Sommer, Lauren M; Cho, Hyuk; Choudhary, Madhusudan et al. (2015) Evolutionary Analysis of the B56 Gene Family of PP2A Regulatory Subunits. Int J Mol Sci 16:10134-57

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