Biology subjects

Uzel, K.

Publications and source records attributed to Uzel, K..

3 recordsLinked to original sources

bioRxiv2026

Paternal diet shapes paternal and maternal transcriptomes in the early embryo through parallel sperm-associated mechanisms

Life experiences in fathers can influence phenotypes in the offspring. While it is known that acquired paternal information can be transferred to descendants via the germline, how such transfer operates between sperm and embryo remains unclear. We examined the effects of low protein diet (LPD) on males of different genotypes and their hybrid offspring generated by reciprocal outcross and on their genome. We found that LPD induces genotype-specific effects in fathers and different phenotypes in their male and female offspring. Allele-specific analyses revealed that paternal LPD modifies paternal and maternal transcriptomes differently in early two-cell embryos. Changes in the paternal transcriptome overlap with the sperm transcriptome and are associated with sperm chromatin features, suggesting that sperm-inherited transcripts and chromatin states may shape the paternal transcriptome in the embryo. The maternal transcriptome, by contrast, is linked to sperm-derived small RNAs, consistent with a possible role of sperm-derived small RNAs in modulating maternal transcript levels in the embryo. Analyses of undifferentiated spermatogonia populations suggest that LPD-induced sperm states can originate from early stages of germ cells. These findings provide evidence that paternal experiences can influence the early embryo via processes involving each parental allele differently.

molecular biology↗

bioRxiv2026

Early life stress affects the transcription and chromatin accessibility of spermatogonial cells

Adversity in early life has lasting effects on the physiology and behavior of exposed individuals and their descendants. In mice, early-life stress alters the RNA content of adult sperm, and this RNA is sufficient to transmit some of the effects to the offspring who were never exposed. However, sperm cells are not yet formed during the early postnatal window in which the exposure occurs. Spermatogonial cells (SPGs), which give rise to them, are present at that time, but whether they respond to the exposure and maintain a molecular signature of it into adulthood is unknown. Here we show that early-life stress alters both the transcriptome and the chromatin accessibility of mouse SPGs, and that a molecular signature of the exposure remains detectable in adulthood. One day after exposure ended, the transcriptional response was extensive, with proliferation and nucleosome-organization programs coordinately up-regulated. In adulthood, the transcriptional response was modest and dominated by coordinately down-regulated gene programs. Single-cell profiling of the whole testis localized the adult response to spermatogonial stem cells (SSCs) and to genes involved in spermatogenesis. At the chromatin level, accessibility shifted one day after exposure at binding motifs for signal-responsive transcription factor families, and in adulthood at a different set of families, in both cases at primed enhancers. These data demonstrate that SPGs respond to an early postnatal environmental exposure and identify them as a candidate origin of the molecular changes later found in adult sperm.

genomics↗

bioRxiv2024

Genotype likelihoods incorporated in non-linear dimensionality reduction techniques infer fine-scale population genetic structure

O_LIUnderstanding population structure is essential for conservation genetics, as it provides insights into population connectivity and supports the development of targeted strategies to preserve genetic diversity and adaptability. C_LIO_LIT-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP) have proven effective for revealing population genetic structures in human and model organisms using hard-called genotypes, but their application in wild species using genotype likelihoods from low coverage sequencing (as a cost-saving measure) remains underexplored. C_LIO_LIHere, we present a Jupyter Notebook-based workflow that facilitates the use of UMAP and t-SNE on genotype likelihood-derived principal components. C_LIO_LIThis workflow is demonstrated using medium to low-coverage whole-genome sequencing data from scimitar-horned oryx, which has been reintroduced into the wild and faces multiple conservation challenges. C_LIO_LIDetailed guidance on hyperparameter tuning and practical implementation is also provided, enhancing the application of these methods in wildlife genetics to potentially support biodiversity conservation. C_LI

bioinformatics↗