Eskut, K. I. | Search bioRxiv

bioRxiv2026

Dissecting functional elements in giant genomes using the first generation of high quality salamander assemblies

Salamanders are an enduring and historically significant group that helped originate multiple scientific fields of study, including regeneration, cytogenetics, experimental embryology, cloning, evolutionary developmental biology and evolution of extreme genome size. We generated a high-quality, single haplotype assembly for the 32 Gb axolotl (Ambystoma mexicanum) genome using an F1 hybrid between axolotl and a divergent relative the tiger salamander (A. tigrinum). Using multi-genome alignments to other salamanders that meet VGP metrics, we leveraged strong conservation of karyotypic structure to identify >523,000 highly conserved non-coding elements within massively expanded intronic and intergenic regions, the vast majority of which are unique to the salamander lineage. Orthogonal measures of chromatin state and enhancer activity confirmed that many conserved elements correspond to cis-regulatory sequences and identified several thousand that are utilized during regeneration. The conserved elements identified here will enable robust functional genomic analyses of tissue regeneration and other traits that uniquely empower salamander models in biological research.

genomics↗

bioRxiv2025

Glutamine-Dependent Slc25a39-Nrf2 Axis Couples Mitochondrial Dynamics with Metabolic Reprogramming to Establish Myogenic Commitment

Myogenic commitment is a decisive and irreversible step in skeletal muscle regeneration, necessitating proliferating myoblasts to integrate metabolic cues with nuclear transcriptional programs. Among amino acids, glutamine is uniquely positioned to influence this transition by coupling energy production to macromolecule biosynthesis and epigenetic regulation. We reasoned that myoblasts must sense glutamine availability to ensure orderly progression toward commitment, and we tested this by examining the molecular consequences of acute glutamine withdrawal. We find that continued glutamine oxidation is required to sustain glycolysis, maintain mitochondrial fission, and preserve a redox balance that supports progression towards myogenic commitment. In its absence, myoblasts undergo a reductive shift, characterized by mitochondrial elongation, membrane depolarization, and suppression of glycolysis, ultimately leading to growth arrest. Transcriptomic profiling reveals reduced MyoD and MKi67, accompanied by increased Sprouty1 levels, defining a reversible non-proliferative state that resembles but is distinct from quiescent and reserve cells. We term this state Poised Metabolic Arrest (PMA), a cellular response to glutamine limitation during myogenic progression. Mechanistically, PMA is driven by Nrf2-dependent increased glutathione (GSH) biosynthesis and upregulation of mitochondrial GSH carrier Slc25a39 when glutamine is limited. Depleting mitochondrial glutathione or silencing Slc25a39 forces exit from PMA. However, this premature exit compromises subsequent differentiation potential, indicating PMA serves to preserve differentiation competence when glutamine is limited. Consistent with this, both loss and overexpression of Slc25a39 impair myoblast differentiation in vitro and disrupt regeneration in vivo. Together, these data suggest that a reciprocal Slc25a39-Nrf2 redox axis functions as a nutrient-dependent checkpoint, coupling glutamine availability to mitochondrial remodeling and metabolic reprogramming, necessary to establish irreversible myogenic commitment.

biochemistry↗