Biology subjects

Wexler, Y.

Publications and source records attributed to Wexler, Y..

4 recordsLinked to original sources

bioRxiv2026

Integration of zebrafish pineal transcriptomes reveals cell type-specific timing

The teleost pineal gland is an eye-like photoreceptive organ with a central role in the circadian clock system, primarily through its melatonin-producing photoreceptor cells. However, the functional molecular interactions between pineal photoreceptors, accessory cells predicted to support photoreceptor function, and projecting neurons remain incompletely understood. Here, we integrated single-cell zebrafish pineal transcriptomes with bulk circadian and light-response pineal transcriptomes. Combined analysis of two single-cell datasets identified novel photoreceptor and neuronal subtypes, including parietopsin-expressing cone-like cells and neurons expressing markers of neuronal maturation. Integration with the light-response dataset revealed light inhibition of photoreceptor opsin genes. Integration with circadian transcriptomes from wildtype fish and fish expressing the clock-disrupting dominant-negative CLOCK ({Delta}CLK) in pineal photoreceptors revealed cell-type-specific rhythmicity. Despite comparable expression of {Delta}CLK, photoreceptor subtypes differed in sensitivity to rhythm disruption, with rod-like cells (rods) most severely affected. In neurons, despite the absence of {Delta}CLK expression, rhythm disruption was comparable to that of rods. Moreover, rhythmic neuronal markers and rhythmic photoreceptor markers exhibited a similar circadian pattern, peaking mainly during the early night. These observations suggest that clock function in neurons depend on photoreceptor output. In contrast, accessory cell rhythmic markers were relatively resistant to {Delta}CLK disruption and peaked predominantly around subjective dawn, consistent with partially autonomous clock function. To facilitate comparative analysis of gene expression, rhythmicity and light responsiveness across pineal cell types, we developed the Zebrafish Pineal Transcriptomics Viewer. Our findings reveal a temporally structured and functionally heterogeneous organization of the zebrafish pineal gland.

neuroscience↗

bioRxiv2026

A Calcium-mediated signaling pathway modulates ion homeostasis via HKT1;1 during Arabidopsis seed germination under salt stress

Soil salinization severely constrains seedling establishment by disrupting cellular Na/K homeostasis. Calcium (Ca{superscript 2}) signaling contributes to the re-establishment of ion balance during early growth, yet the mechanisms linking Ca{superscript 2} perception to ion transport regulation remain unclear. Here, we identify a Ca{superscript 2}-responsive regulatory module in Arabidopsis thaliana comprising CALMODULIN-BINDING TRANSCRIPTION ACTIVATOR 6 (CAMTA6), the TYPE 2C PROTEIN PHOSPHATASE PP2C49, and the HIGH-AFFINITY K TRANSPORTER HKT1;1, and define their coordinated roles during germination under salt stress. Spatial promoter analyses revealed that NaCl induces CAMTA6 expression at cotyledon margins, while CaCl2 stimulates HKT1;1 transcription in the radicle, consistent with CAMTA6-mediated repression of HKT1;1. In camta6 mutants, PP2C49 expression expanded beyond its normal radicle-restricted domain, indicating CAMTA6-dependent spatial control. Promoter activation assays in planta demonstrated CAMTA6-dependent transactivation of the HKT1;1 and PP2C49 promoters. Treatment with the PP2C inhibitor sanguinarine enhanced germination under salinity in the wild type, but not in hkt1 nor in the salt-tolerant camta6 and pp2c49 mutants. Sanguinarine restricted CAMTA6 promoter activity to cotyledon margins, suppressed PP2C49 expression, and enhanced HKT1;1 accumulation in the radicle, collectively supporting improved Na/K balance. Transcriptome profiling further revealed additional Ca{superscript 2}-responsive PP2C genes under CAMTA6-dependent regulation. Together, these findings establish a Ca{superscript 2}-regulated transcriptional network coordinating ion homeostasis during germination and suggest strategies to support seedling performance in saline environments. Significance statementSalinity impairs germination largely by disrupting Na/K homeostasis, yet the signaling pathways that protect seedlings at this stage remain poorly defined. We identify a calcium-responsive regulatory mechanism that spatially coordinates transcriptional control of genes involved in ion transport during early development, providing a mechanistic basis for improving seedling establishment in saline soils.

plant biology↗

bioRxiv2026

RBOHC-Generated ROS Tune GNOM-Dependent Root Halotropism in Arabidopsis

Halotropism--the directional growth of roots away from saline environments--requires coordinated integration of tropic cues. We show that halotropic bending in Arabidopsis thaliana roots is fine-tuned by a spatially confined, symmetric reactive oxygen species (ROS) domain generated by the NADPH oxidase RBOHC in elongation-zone epidermal cells. This domain, visualized by dihydrorhodamine-123 staining and confocal microscopy, emerges during the first hours of halostimulation and limits excessive curvature. Reducing ROS, either chemically with ascorbate or diphenyleneiodonium, or genetically in rbohC mutants, enhances halotropic bending, whereas miz2, defective in the ARF-GEF GNOM, exhibits negative halotropism due to an expanded and mislocalized ROS domain that disrupts spatial restriction. The miz2 rbohC double mutant shows a much weaker halotropic response than rbohC alone and similarly lacks the halotropic ROS signals in the elongation zone, indicating that GNOM acts upstream of RBOHC-mediated ROS production. Comparisons with hydrotropism--a moisture-seeking response also involving defined ROS distribution--suggest that GNOM-dependent regulation of RBOHC constitutes a shared module for adjusting root orientation to environmental gradients. Understanding these molecular mechanisms is essential for enhancing crop resilience to soil salinity, particularly in the context of increasing soil salinization driven by climate change.

plant biology↗

bioRxiv2024

Transcriptome analysis of atad3-null zebrafish embryos elucidates possible disease mechanisms

ATAD3A, a nuclear gene encoding the ATAD3A protein, has diverse roles in mitochondrial processes, encompassing mitochondrial dynamics, mitochondrial DNA maintenance, metabolic pathways and inter-organellar interactions. Pathogenic variants in this gene cause neurological diseases in humans with recognizable genotype-phenotype correlations. To further investigate the gene function and its implication in health and disease, we utilized CRISPR/Cas9 genome editing to generate a knockout (KO) model of the zebrafish ortholog gene, atad3. Analysis of atad3-null zebrafish embryos revealed microcephaly, small eyes, pericardial edema and musculature thinning, closely mirroring with the human rare disease phenotype. Larvae exhibited delayed hatching and embryonic lethality by 13 days post-fertilization (dpf). Locomotor activity, ATP content, mitochondrial content, and mitochondrial activity were all reduced in the mutant embryos. Transcriptome analysis at 3 dpf via RNA-sequencing indicated decline in most mitochondrial pathways, accompanied by a global upregulation of cytosolic tRNA synthetases, presumably secondary to mitochondrial stress and possibly endoplasmic reticulum (ER)-stress. Differential expression of select genes was corroborated in fibroblasts from an affected individual. The atad3-null zebrafish model emerges as a reliable representation of human ATAD3A-associated disorders, with similarities in differentially expressed pathways and processes. Furthermore, our study underscores mitochondrial dysfunction as the primary underlying pathogenic mechanism in ATAD3A-associated disorders and identifies potential readouts for therapeutic studies.

genetics↗