Biology subjects

Navarro, P.

Publications and source records attributed to Navarro, P..

At least 19 recordsLinked to original sources

bioRxiv2026

Transposable Element insertions Repurpose Immune Endonucleases as Drivers of Reproductive Isolation in Mice

The emergence of reproductive barriers between closely related populations is a fundamental step in speciation, yet the underlying genetic mechanisms remain poorly understood in mammals. Here we resolve the DDK syndrome, a long-standing model of hybrid incompatibility in mice, by showing that two independent retrotransposon insertions rewire immune Schlafen endoribonuclease genes expression, causing hybrid embryo death. A DDK-private MERVL element drives ectopic oocyte expression of Slfn1, while an intragenic ETn/MusD insertion in incompatible strains is associated with zygotic Slfn15 expression. SLFN1-SLFN15 heterodimerization constitutively activates tRNA ribonuclease activity, leading to global translation inhibition, and integrated stress response activation. Abolishing SLFN1 catalytic activity or SLFN15 expression rescues syndromic embryo development. Our findings uncover a previously unrecognized speciation mechanism in which transposable elements repurpose immune effectors as drivers of postzygotic reproductive isolation.

developmental biology↗

bioRxiv2026

Topological Regulation of the Mammalian Genome by Positive DNA Supercoiling

DNA supercoiling is a fundamental aspect of genome topology characterizing all DNA transactions. While negative supercoiling has been extensively characterized, positive supercoiling remains poorly understood. Using a quantitative GapR profiling system, we establish comprehensive maps of positive supercoiling across interphase and mitosis. We show that positive super-coils accumulate not only at gene ends but prominently at promoters, enhancers, insulators and loop anchors, where they are resolved by Topoisomerases. Biochemical and functional assays reveal the main sources of positive torsion: transcription generates genic supercoils, while R-loops and Cohesin drive accumulation at regulatory elements, topologically associating domains and their boundaries. During mitotic chromosomal compaction, Condensins establish a global wave of positive supercoiling that largely homogenizes the genome, yet promoters with rapid post-mitotic reactivation retain elevated torsion and R-loops. These findings establish positive DNA supercoiling as a form of topological memory that links DNA mechanics to transcriptional control, genome architecture and epigenetic inheritance.

molecular biology↗

bioRxiv2025

The RUMIGEN EpiChip: a versatile, medium density DNA methylation Beadchip for large scale population studies in cattle

BackgroundDNA methylation contributes to the elaboration of phenotypes and is hypothesized to account for interindividual variations in farm animals. Currently, methodologies available to investigate DNA methylation in cattle rely on high throughput sequencing, which cannot be applied to large cohorts. To enable large scale DNA methylation analysis, we developed the RUMIGEN EpiChip, the first DNA methylation array specifically designed for cattle. ResultsManufactured by Illumina, the EpiChip contains 43,317 CpG markers allowing analysis of phenotypes of agronomical interest as well as the study of regulatory processes. The assay design drew on data from numerous studies achieved by the scientific community, and includes CpGs where methylation varies with health status, physiological stage, fertility, and environmental challenges, as well as CpGs located in functional genomic elements (promoters, CTCF binding sites, expression quantitative trait loci). The technical performances of the EpiChip were tested on several semen and blood DNA samples and in two laboratories, showing excellent repeatability, accuracy and interoperability. Methylation values were also concordant with those obtained by reduced representation bisulfite sequencing. The EpiChip has demonstrated a good ability to explore biological processes such as genomic imprinting and differences between cell types, opening the possibility of inferring blood cell composition. Finally, analysis of longitudinal ear biopsies allowed accurate age prediction, suggesting the potential of the array to refine epigenetic clocks. ConclusionsThe RUMIGEN EpiChip is a cost-effective and versatile resource that opens new opportunities for the study of regulatory mechanisms underlying phenotypic variation and for large-scale association analyses in cattle.

genomics↗

bioRxiv2025

The Vaginal Microbiome in Women Recently Experiencing BV and UTI

The vaginal microbiome (VMB) influences susceptibility to urogenital infections, yet large-scale, population-based species-level metagenomic studies are rare. We analyzed cross-sectional shotgun metagenomic profiles and linked clinical metadata from 10,003 women across the United States who self-reported recent bacterial vaginosis (BV), urinary tract infection (UTI), both, or neither. Women reporting recent BV or UTI displayed distinct community structures, including higher prevalence of VALENCIA CST-IV subtypes and significantly elevated alpha diversity compared with women who reported no prior diagnosis. Species-level Gardnerella profiling revealed that multiple Gardnerella species were enriched in the recent BV group but did not differ significantly between UTI and non-UTI groups, refining prior mechanistic hypotheses. Uropathogens such as E. coli, E. faecalis, and S. saprophyticus were detectable at higher prevalence and relative abundance in women who recently experienced UTI, including among participants who reported recent antibiotic use, consistent with the possibility of residual or recurrent vaginal colonization. These findings demonstrate that microbial signatures associated with recent BV and UTI remain detectable at population scale, provide a high-resolution reference for human vaginal metagenomics, and offer new directions for prevention strategies that consider the vaginal reservoir in recurrent urogenital infections.

microbiology↗

bioRxiv2025

Epitope Effect Prevalence in Affinity-based pQTL studies

Affinity-based proteomics platforms Olink and SomaScan have enabled population-wide human proteogenomic studies, linking genetic variants to protein abundances. However, sequence alterations in the binding site of the detection reagent may introduce platform-specific measurement bias unrelated to protein levels, referred to as the epitope effect. In this study, we investigated the prevalence of epitope effects using cis protein quantitative trait loci (pQTL) discovered in three of the largest proteogenomic studies: UK Biobank, deCODE, and Fenland. Across 5,817 protein targets assayed in these studies, cis-pQTL were identified for 914 proteins by both platforms, 301 (33%) of which were linked to a missense variant. We identified 37 proteins with opposing effect directions in two platforms for the same missense pQTL, and 85 proteins where a missense pQTL was significant in only one platform. We present examples where such discrepancies reflect differences in isoform or proteoform targeting, as well as examples where the discordance appears to result from true platform-specific detection bias. Further structural analyses reveal that missense cis-pQTL are more likely to be detected when they alter residues located on accessible protein surfaces - regions most likely to interfere with reagent binding in affinity-based assays. Overall, our findings suggest that missense-mediated epitope effects influence only a minority (12% or less) of cis-pQTL results. We also highlight the need for detailed assay annotations and structural context to improve result interpretation in proteogenomic studies.

genomics↗

bioRxiv2025

Meta plasticity and Continual Learning: Mechanisms sub serving Brain Computer Interface Proficiency

ObjectiveBrain Computer Interfaces (BCIs) require substantial cognitive flexibility to optimize control performance across diverse settings. Remarkably, learning this control is rapid, suggesting it might be mediated by neuroplasticity mechanisms operating on very short time scales. However, these mechanisms remain far from understood. Here, we propose a meta plasticity model of BCI learning and skill consolidation at the single cell and population levels comprised of three elements: a) behavioral time scale synaptic plasticity (BTSP), b) intrinsic plasticity (IP) and c) synaptic scaling (SS) operating at time scales from seconds to minutes to hours and days. Notably, the model is able to explain representational drift - a frequent and widespread phenomenon observed in multiple brain areas that adversely affects BCI control and continued use. ApproachWe developed a closed loop, all optical approach to characterize IP, BTSP and SS with single cell resolution in cortical L2/3 of awake mice using fluorescent two photon (2P) GCaMP7s imaging and optogenetic stimulation of the soma targeted ChRmineKv2.1. We further trained mice on a one-dimensional (1D) BCI control task and systematically characterized within session (seconds to minutes) learning as well as across sessions (days and weeks) with different neural ensembles. Main resultsWe found that on the time scale of seconds, substantial BTSP could be induced and was associated with significant IP over minutes. Over the time scale of days and weeks, these changes could predict BCI control proficiency, suggesting that BTSP and IP might be complemented by SS to stabilize and consolidate BCI control. SignificanceOur results provide theoretical and early experimental support for an integrated meta plasticity model of continual BCI learning and skill consolidation. The model predictions may be used to design and calibrate neural decoders with complete autonomy while considering the temporal and spatial scales of plasticity mechanisms and their anticipated order of occurrence. With the power of modern-day machine learning (ML) and artificial Intelligence (AI), fully autonomous neural decoding and adaptation in BCIs might be achieved with minimal to no human intervention.

neuroscience↗

bioRxiv2024

CRISPR targeting of FOXL2 c.402C>G mutation reduces malignant phenotype in granulosa tumor cells and identifies anti-tumoral compounds

FOXL2 is a transcription factor essential for sex determination and ovary development and maintenance. Mutations in this gene are implicated in syndromes involving premature ovarian failure and granulosa cell tumors (GCTs). This rare cancer accounts for less than 5% of diagnosed ovarian cancers and is causally associated with the FOXL2 c.402C>G, p.C134W mutation in 97% of the adult cases (AGCTs). In this study, we employed CRISPR technology to specifically eliminate the FOXL2 c.402C>G mutation in granulosa tumor cells. Our results show that this Cas9-mediated strategy selectively targets the mutation without affecting the wild-type allele. Granulosa cells lacking the FOXL2 c.402C>G exhibit a reduced malignant phenotype, with significant changes in cell proliferation, invasion, and cell death. Furthermore, these modified cells are more susceptible to Dasatinib and Ketoconazole. Transcriptomic and proteomic analyses reveal that CRISPR-modified granulosa tumor cells shift their expression profiles towards a wild-type like phenotype. Additionally, this altered expression signature has led to the identification of new compounds with antiproliferative and pro-apoptotic effects on granulosa tumor cells. Our findings demonstrate the potential of CRISPR technology for the specific targeting and elimination of a mutation causing granulosa cell tumors, highlighting its therapeutic promise for treating this rare ovarian cancer. Simple SummaryAdult granulosa cell tumors (AGCTs), characterized by a specific point mutation (C134W) in the gene FOXL2, are less than 5% of all the diagnosed ovarian cancers. Surgery is the cornerstone treatment for AGCT even at relapse, with systemic therapy showing poor results. The aim of our study is to explore the potential therapeutic effect of the elimination of the C134W mutation. To achieve our goal, we have eliminated the mutant allele using CRISPR technology. Our results demonstrate that CRISPR-mediated elimination of FOXL2-C134W reduces the malignant phenotype of granulosa tumor cells, which change their transcriptional, proteomic, and cellular phenotype to a wild type like, granulosa type. Moreover, the induced changes allowed us to find new compounds with antitumoral activity. This work highlights the therapeutic potential of CRISPR mediated technology for the treatment of AGCT.

cancer biology↗

bioRxiv2024

Evaluating regional heritability mapping methods for identifying QTLs in a wild population of Soay sheep

Regional heritability mapping (RHM) is a method that estimates the heritability of genomic segments that may contain both common and rare variants affecting a complex trait. We compared three RHM methods: SNP-RHM, which uses genomic relationship matrices (GRMs) based on SNP genotypes; Hap-RHM, which uses GRMs based on haplotypes; and SNHap-RHM, which uses both SNP-based and haplotype-based GRMs jointly. We applied these methods to data from a wild population of sheep, analysed eleven polygenic morphometric traits and compared the results with previous genome wide association analyses (GWAS). We found that whilst the inclusion of the regional matrix did not explain significant variation for all regions that were associated with trait variation using GWAS, it did for several regions that were not previously associated with trait variation.

genomics↗

bioRxiv2024

Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation

Pioneer transcription factors (TF) bind nucleosome-embedded DNA motifs to activate new regulatory elements and promote differentiation. However, the complexity, binding dependencies and temporal effects of their action remain unclear. Here, we dissect how the pioneer TF GATA6 triggers Primitive Endoderm (PrE) differentiation from pluripotent cells. We show that transient GATA6 binding exploits accessible regions to decommission active enhancers and promote pluripotency gene silencing. Simultaneously, GATA6 targets closed chromatin and initiates an extensive remodeling culminating in the establishment of fragile nucleosomes flanked by ordered nucleosome arrays and increased accessibility. This is directly enhanced by rapidly expressed PrE TFs (SOX17) and by pluripotency TFs repurposed for differentiation (OCT4/SOX2). Furthermore, GATA6 mediates the replacement of essential nuclear receptors for PrE differentiation, from ESRRB to ESRRA. Therefore, pioneer TFs orchestrate a complex gene regulatory network involving many if not all available pioneer TFs, including those required to support the original identity of differentiating cells.

molecular biology↗

bioRxiv2024

Gill regeneration in the mayfly Cloeon uncovers new molecular pathways in insect regeneration

The capacity to regenerate lost or damaged organs is widespread among animals, and yet, the species in which regeneration has been experimentally probed using molecular and functional assays is very small. This is also the case for insects, for which we still lack a complete picture of their regeneration mechanisms and the extent of conservation of these mechanisms. Here we contribute to filling this gap by investigating regeneration in the mayfly Cloeon dipterum. Mayflies, or Ephemeroptera, appeared early in the evolution of insects. We focus on the abdominal gills of Cloeon nymphs, which are critical for osmoregulation and gas exchange. After amputation, gills re-grow faster than they do during normal development. Direct cell count and EdU proliferation assays indicate that growth acceleration involves an uniform increase in cell proliferation throughout the gill, rather than a localized growth zone. Transcriptomic analysis reveals an early enrichment in cell cycle-related genes, in agreement with fast proliferation. Several other gene classes are also enriched in regenerating gills, including protein neddylation and other proteostatic processes. We then showed that protein neddylation, the activin signaling pathway or the mRNA-binding protein Lin28, among other genes and processes, are required for Drosophila larval/pupal wing regeneration, and that some of these genes may have a regeneration-specific function in the wing. Globally, our results contribute to elucidating regeneration mechanisms in mayflies and suggest a conservation of regeneration mechanisms across insects, as evidenced by the regenerative role of candidate genes identified in Cloeon in the distant Drosophila.

developmental biology↗

bioRxiv2023

Mitotic chromosomes harbor cell type and species-specific structural features within a universal looping architecture

The architecture of mammalian mitotic chromosomes is considered to be universal across species and cell types. However, some studies suggest that features of mitotic chromosomes might be cell type or species specific. We previously reported that CTCF binding in human differentiated cell lines is lost in mitosis, whereas mouse embryonic stem cells (mESC) display prominent binding at a subset of CTCF sites in mitosis. Here, we perform parallel footprint ATAC-seq data analyses of mESCs and somatic mouse and human cells to further explore these differences. We then investigate roles of mitotically bound (bookmarked) CTCF in prometaphase chromosome organization by Hi-C. We do not find any remaining interphase structures such as TADs or CTCF loops at mitotically bookmarked CTCF sites in mESCs. This suggests that mitotic loop extruders condensin I and II are not blocked by bound CTCF, and thus that any remaining CTCF binding does not alter mitotic chromosome folding. Lastly, we compare mitotic Hi-C data generated in this study in mouse with publicly available data from human and chicken cell lines. We do not find any cell type specific differences; however, we do find a difference between species. The average genomic size of mitotic loops is much smaller in chicken (200-350 kb), compared to human (500-750 kb) and mouse (1-2 mb). Interestingly, we find that this difference in loop size is correlated with the average genomic length of the q-arm in these species, a finding we confirm by microscopy measurements of chromosome compaction. This suggests that the dimensions of mitotic chromosomes can be modulated through control of sizes of loops generated by condensins to facilitate species-appropriate shortening of chromosome arms.

genomics↗

bioRxiv2023

High-throughput in vivo synaptic connectivity mapping of neuronal micro-circuits using two-photon holographic optogenetics and compressive sensing

Understanding the intricate synaptic connectivity in living neural circuits is crucial for unraveling the relationship between network structure and function, as well as its evolution during development, learning, and recovery from injury. However, current methodologies for identifying connected neurons in vivo suffer from limitations, particularly with regards to their throughput. In this study, we introduce a groundbreaking framework for in vivo connectivity mapping that combines two-photon holographic optogenetics for activating single or multiple potential presynaptic neurons, whole-cell recording of postsynaptic responses, and a compressive sensing strategy for efficiently retrieving individual postsynaptic neurons responses when multiple potential presynaptic neurons are simultaneously activated. The approach was validated in the layer 2/3 of the visual cortex in anesthetized mice, enabling rapid probing of up to 100 cells in approximately 5 minutes. By identifying tens of synaptic pairs, including their connection strength, kinetics, and spatial distribution, this method showcases its potential to significantly advance circuit reconstruction in large neuronal networks with minimal invasiveness. Moreover, through simultaneous multi-cell stimulation and compressive sensing, we demonstrate up to a three-fold reduction in the number of required measurements to infer connectivity with limited loss in accuracy, thereby enabling high-throughput connectivity mapping in vivo. These results pave the way for a more efficient and rapid investigation of neuronal circuits, leading to deeper insights into brain function and plasticity.

neuroscience↗

bioRxiv2023

MYC and MAX drive the reactivation of the genome after mitosis

Shortly after cell division, a robust wave of hyper-transcription reactivates the genome1-3. This phenomenon is particularly pronounced in pluripotent cells4, which necessitate rapid transcrip-tome reactivation to maintain their undifferentiated state and prevent premature differentiation. While recent work has illuminated how specific groups of genes are reactivated4-8, the mechanisms enabling the global, efficient and accurate post-mitotic reactivation of the genome remain unknown. Here we elucidate the direct involvement of the MYC/MAX transcription factors in the post-mitotic reactivation of pluripotent mouse embryonic stem cells. While MYC undergoes extensive phosphorylation and largely dissociates from its DNA binding sites during mitosis, we report that MAX remains bound to its targets, preferentially at promoters, and facilitates early recruitment of MYC following mitosis. Through the application of MYC/MAX heterodimerization inhibitors, we demonstrate their indispensable role in sustaining hyper-transcription in ES cells, including during the critical transition from mitosis to G1 phase. Our findings uncover a novel role for MAX in mitotic book-marking, highlighting its pivotal role in post-mitotic MYC recruitment and the re-establishment of high global transcription levels. These findings hold significant implications for medically relevant contexts, particularly when cell proliferation is of paramount importance9. We anticipate that the study of mitotic bookmarking by MYC and MAX and of the effects of anticancer drugs targeting MYC/MAX interactions in such process10-12 will be relevant for our understanding of cancer and its potential treatments.

molecular biology↗

bioRxiv2023

PI3K/AKT signalling orchestrates ICM maturation and proper epiblast and primitive endoderm specification

The inner cell mass (ICM) of early mouse embryos is specified into Epiblast (Epi) and primitive endoderm (PrE) lineages during blastocyst formation. The antagonistic transcription factors (TFs) NANOG and GATA6 in combination with FGF/ERK signalling are central actors in ICM fate choice. However, what initiates the specification of ICM progenitors and whether other factors are involved in this process is not fully understood yet. Here, we show that PI3K/AKT is constitutively active during preimplantation development. Using pharmacological inhibition, we demonstrate that PI3K/AKT enables the formation of a functional ICM capable of giving rise to both the EPI and the PrE: it maintains the expression of the TF NANOG, which specifies the EPI, and confers responsiveness to FGF4, which is essential for PrE specification. Our observations thus identify PI3K/AKT signalling as an upstream regulator orchestrating the molecular events required for both EPI and PrE specification.

developmental biology↗

bioRxiv2023

Investigating pedigree- and SNP-associated components of heritability in a wild population of Soay sheep

Estimates of narrow sense heritability derived from genomic data that contain related individuals may be biased due to the within-family effects such as dominance, epistasis and common environmental factors. However, for many wild populations, removal of related individuals from the data would result in small sample sizes. In 2013, Zaitlen et al. proposed a method to estimate heritability in populations that include close relatives by simultaneously fitting an identity-by-state genomic relatedness matrix (GRM) and an identity-by-descent GRM. The IBD GRM is identical to the IBS GRM, except relatedness estimates below a specified threshold are set to 0. We applied this method to a sample of 8557 wild Soay sheep from St. Kilda, with genotypic information for 419,281 single nucleotide polymorphisms to investigate polygenic and monogenic traits. We also implemented a variant of the model in which the IBD GRM was replaced by a GRM constructed from SNPs with low minor allele frequency to examine whether any additive genetic variance is captured by rare alleles. Each model was compared to an animal model with a single GRM based on all genotyped markers (the IBS GRM) using a log likelihood ratio test. Whilst the inclusion of the IBD GRM did not significantly improve the fit of the model for the monogenic traits, it improved the fit for some of the polygenic traits, suggesting that dominance, epistasis and/or common environment not already captured by the non-genetic random effects fitted in our models may influence these traits.

genetics↗

bioRxiv2023

Phenome-wide analysis identifies parent-of-origin effects on the human methylome associated with changes in the rate of aging

Variation in the rate at which humans age may be rooted in early life events acting through genomic regions that are influenced by such events and subsequently are related to health phenotypes in later life. The parent-of-origin-effect (POE)-regulated methylome includes regions either enriched for genetically controlled imprinting effects (the typical type of POE) or atypical POE introduced by environmental effects associated with parents. This part of the methylome is heavily influenced by early life events, making it a potential route connecting early environmental exposures, the epigenome and the rate of aging. Here, we aim to test the association of POE-influenced methylation of CpG dinucleotides (POE-CpG sites) with early and later environmental exposures and subsequently with health-related phenotypes and adult aging phenotypes. We do this by performing phenome-wide association analyses of the POE-influenced methylome using a large family-based population cohort (GS:SFHS, Ndiscovery=5,087, Nreplication=4,450). At the single CpG level, 92 associations of POE-CpGs with phenotypic variation were identified and replicated. Most of the associations were contributed by POE-CpGs belonging to the atypical class and the most strongly enriched associations were with aging (DNAmTL acceleration), intelligence and parental (maternal) smoking exposure phenotypes. We further found that a proportion of the atypical-POE-CpGs formed co-methylation networks (modules) which are associated with these phenotypes, with one of the aging-associated modules displaying increased internal module connectivity (strength of methylation correlation across constituent CpGs) with age. Atypical POE-CpGs also displayed high levels of methylation heterogeneity and epigenetic drift (i.e. information loss with age) and a strong correlation with CpGs contained within epigenetic clocks. These results identified associations between the atypical-POE-influenced methylome and aging and provided new evidence for the "early development of origin" hypothesis for aging in humans.

genetics↗

bioRxiv2023

Nr5a2 is essential for morula development

Early embryogenesis is driven by transcription factors (TFs) that first activate the zygotic genome and then specify the lineages constituting the blastocyst. While the TFs specifying the blastocysts lineages are well characterised, those playing earlier roles are ill-defined. Using mouse models of the TF Nr5a2, we show that Nr5a2-/- embryos arrest at the early morula stage and exhibit overt phenotypical problems such as altered lineage specification, frequent mitotic failure and substantial chromosome segregation defects. Transcriptomic profiling shows that NR5A2 is a master regulator required for appropriate expression of thousands of genes at the 8-cells stage, including lineage-specifying TFs and genes involved in mitosis, telomere maintenance and DNA repair. We conclude that NR5A2 coordinates proliferation, genome stability and lineage specification to ensure proper morula development.

developmental biology↗

bioRxiv2022

Impact of mixing between parallel year groups on genomic prediction in Atlantic salmon breeding programmes under random selection

A commercial breeding programme in Atlantic salmon utilises a four-year generation interval with four parallel breeding populations. In this study, we develop a computer simulation of a salmon breeding programme and explore the impact of gene flow between the parallel year groups on the accuracy of genomic prediction within and between breeding lines. We simulated four parallel lines for 10 discrete generations with random selection and different mixing rates between parallel year groups. The genetic distance between fish (as a measure of diversity) and the accuracy of estimated genomic breeding values were used as criteria of comparison. With no mixing the genetic distance increased between populations, the genetic variation within populations decreased and there was no increase in accuracy when combining data across populations. Even a low percentage of mixing decreased the genetic distance between populations and increased the genetic variation within populations. The higher the percentage of mixing the faster the lines became more similar. The accuracy of prediction climbed as the percentage of mixing increased. The increase in accuracy from the combined evaluation approach compared to the within evaluation approach was greater with an increased percentage of mixing. In conclusion, if there is no gene flow between populations the lines drift apart and there is no value in combining information across populations for genomic breeding value prediction. Only a low amount of mixing between lines brings the lines closer together and facilitates the use of information across lines to improve breeding value prediction. Optimising gene flow between lines should be an integral part of salmon breeding programme design.

genetics↗