Biology subjects

Vincent, S.

Publications and source records attributed to Vincent, S..

8 recordsLinked to original sources

bioRxiv2025

Promoter-proximal gatekeepers restrict pleiotropic enhancer inputs to achieve tissue specificity

The spatiotemporal expression of developmental genes is regulated by the interplay of two key regulatory elements: core promoters, generally assumed to support only basal transcription, and enhancers, which enable their tissue- and stage-specific activation. Here, we show that spatiotemporal specificity can also be encoded within the core promoter. Using the Drosophila twist E3 enhancer as a model, we found that E3 is pleiotropic and activates four functionally unrelated genes. Despite receiving the same enhancer input, each target gene displays distinct and non-overlapping expression patterns. We demonstrate that the selective activation of each target gene is encoded within their promoter regions. Core promoters act as "gatekeepers" that restrict enhancer input into precise tissue- and stage-specific transcription, while proximal-promoter elements facilitate enhancer responsiveness. We propose that promoters function as active interpreters rather than passive recipients of enhancer signals, providing a critical but under-appreciated layer of regulatory specificity within complex gene expression programs.

genetics↗

bioRxiv2024

High-Throughput Epigenetic Profiling Immunoassays for Accelerated Disease Research and Clinical Development

Epigenetics, which examines the regulation of genes without modification of the DNA sequence, plays a crucial role in various biological processes and disease mechanisms. Among the different forms of epigenetic modifications, histone post-translational modifications (PTMs) are important for modulating chromatin structure and gene expression. Aberrant levels of histone PTMs are implicated in a wide range of diseases, including cancer, making them promising targets for biomarker discovery and therapeutic intervention. In this context, blood, tissues, or cells serve as valuable resources for epigenetic research and analysis. Traditional methods such as mass spectrometry and western blotting are widely used to study histone PTMs, providing qualitative and (semi)quantitative information. However, these techniques often face limitations that could include throughput and scalability, particularly when applied to clinical samples. To overcome these challenges, we developed and validated 13 Nu.Q(R) immunoassays to detect and quantify specific histone PTM-nucleosomes from K2EDTA plasma samples. Then, we tested these assays on other types of samples, including chromatin extracts from frozen tissues, as well as cell lines and white blood cells Our findings demonstrate that the Nu.Q(R) assays offer high specificity, sensitivity, precision and linearity, making them effective tools for epigenetic profiling. A comparative analysis of HeLa cells using mass spectrometry, Western blot, and Nu.Q(R) immunoassays revealed a consistent histone PTMs signature, further validating the effectiveness of these assays. Additionally, we successfully applied Nu.Q(R) assays across various biological samples, including human tissues from different organs and specific white blood cell subtypes, highlighting their versatility and applicability in diverse biological contexts.

molecular biology↗

bioRxiv2024

Spatial reconstruction of single-cell enhancer activity in a multicellular organism

Enhancers play an essential role in developmental processes by orchestrating the spatial and temporal regulation of gene expression. However, mapping the location of these regulatory elements in the genome and precisely characterizing their spatial and temporal activity remain important challenges. Here we introduce a novel in vivo and in silico method for spatial single-cell enhancer-reporter assays (spatial-scERA) designed to reconstruct the spatial activity of multiple candidate enhancer regions in parallel in a multicellular organism. Spatial-scERA integrates massively parallel reporter assays coupled with single-cell RNA sequencing (scRNA-seq) and spatial reconstruction using optimal transport, to map cell-type-specific enhancer activity at the single-cell level on a 3D virtual representation of the sample. We evaluated spatial-scERA in stage 6 Drosophila embryos using 25 candidate enhancers (including 19 uncharacterized regions), and validated the robustness of our predicted reconstructions by comparing them to microscopy images generated by in situ hybridization. Remarkably, spatial-scERA faithfully reconstructed the spatial activity of these enhancers, even when the enhancer-reporter construct was expressed in as few as 10 cells. Our results demonstrate the importance of integrating transcriptomic and spatial data for the accurate prediction of enhancer activity patterns in complex multicellular samples. Indeed, we found that chromatin modifications and open chromatin regions are often poor predictors of enhancer activity. Moreover, spatial data can often be essential for the accurate annotation of scRNA-seq clusters. Finally, we showed that spatial-scERA could be a powerful tool to link enhancers with their potential target genes. Overall, spatial-scERA provides a scalable approach to map spatio-temporal enhancer activity at single-cell resolution without the need for imaging or a priori knowledge of embryology and can be applied to any multicellular organism amenable to transgenesis.

genomics↗

bioRxiv2023

Novel method for collecting hippocampal interstitial fluid extracellular vesicles (EV-ISF) reveals sex-dependent changes in microglial EV proteome in response to Aβ pathology

Brain-derived extracellular vesicles (EVs) play an active role in Alzheimers disease (AD), relaying important physiological information about their host tissues. Circulating EVs are protected from degradation, making them attractive AD biomarkers. However, it is unclear how circulating EVs relate to EVs isolated from disease-vulnerable brain regions. We developed a novel method for collecting EVs from the hippocampal interstitial fluid (ISF) of live mice. EVs (EVISF) were isolated via ultracentrifugation and characterized by nanoparticle tracking analysis, immunogold labeling, and flow cytometry. Mass spectrometry and proteomic analyses were performed on EVISF cargo. EVISF were 40-150 nm in size and expressed CD63, CD9, and CD81. Using a model of cerebral amyloidosis (e.g. APPswe,PSEN1dE9 mice), we found protein concentration increased but protein diversity decreased with A{beta} deposition. Genotype, age, and A{beta} deposition modulated proteostasis- and immunometabolic-related pathways. Changes in the microglial EVISF proteome were sexually dimorphic and associated with a differential response of plaque associated microglia. We found that female APP/PS1 mice have more amyloid plaques, less plaque associated microglia, and a less robust- and diverse-EVISF microglial proteome. Thus, in vivo microdialysis is a novel technique for collecting EVISF and offers a unique opportunity to explore the role of EVs in AD. Graphical AbstractHippocampal EVISF response to amyloid beta (A{beta}) is sexually dimorphic and related to the microglial EVISF proteome. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/532133v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1a275d6org.highwire.dtl.DTLVardef@e63da5org.highwire.dtl.DTLVardef@1d93cecorg.highwire.dtl.DTLVardef@12ed0db_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2022

Enhancer-promoter interactions form independently of genomic distance and are functional across TAD boundaries

Developmental enhancers are essential regulatory elements that drive precise spatio-temporal gene expression patterns. They do so by interacting with the promoter of their target genes, often across large genomic distances, in a highly specific manner. However, it is unclear how such specificity can be achieved. While several studies have suggested that Topologically Associating Domains (TADs)1-3 facilitate and constrain enhancer-promoter interactions, the role of TAD boundaries in effectively restricting enhancer-promoter interactions is heavily debated. Here we show that enhancers can establish long-range interactions across TAD boundaries and even between different chromosomes. Moreover, some of these interactions are functional in vivo, illustrating their functional importance. Using the twist locus in Drosophila embryos, we systematically relocated one of its enhancers to different regulatory contexts and distances from the twist promoter. We found that the twist promoter can engage in functional enhancer-promoter interactions across a TAD boundary and that distal interactions are sometimes favored over proximal ones. Our results demonstrate that TAD boundaries are not sufficient to constrain enhancer-promoter interactions and that the formation of long-range interactions is not solely driven by distance. These observations suggest that other general mechanisms must exist to establish and maintain specific enhancer-promoter interactions across large distances.

genomics↗

bioRxiv2021

The transcription factor Zic4 acts as a transdifferentiation switch

The molecular mechanisms that maintain cell identities and prevent transdifferentiation remain mysterious. Interestingly, both dedifferentiation and transdifferentiation are transiently reshuffled during regeneration. Therefore, organisms that regenerate readily offer a fruitful paradigm to investigate the regulation of cell fate stability. Here, we used Hydra as a model system and show that Zic4 silencing is sufficient to induce transdifferentiation of tentacle into foot cells. We identified a Wnt-controlled Gene Regulatory Network that controls a transcriptional switch of cell identity. Furthermore, we show that this switch also controls the re-entry into the cell cycle. Our data indicate that maintenance of cell fate by a Wnt-controlled GRN is a key mechanism during both homeostasis and regeneration. One-Sentence SummaryA Wnt-controlled GRN controls fate maintenance in Hydra.

developmental biology↗

bioRxiv2021

Evidence for a selective link between cooperation and individual recognition

The ability to recognize and discriminate among others is a frequent assumption of models of the evolution of cooperative behavior. At the same time, cooperative behavior has been proposed as a selective agent favoring the evolution of individual recognition abilities. While theory predicts that recognition and cooperation may co-evolve, data linking recognition abilities and cooperative behavior with fitness or evidence of selection are elusive. Here, we provide evidence of a fitness link between individual recognition and cooperation in the paper wasp Polistes fuscatus. Nest founding females in northern populations frequently form cooperative multiple foundress nests and possess highly variable facial patterns that mediate individual recognition. We describe a dearth of cooperative nesting, low phenotypic diversity, and a lack of individual recognition in southern populations. In a common garden experiment, northern co-foundress associations successfully reared offspring while all cooperative southern groups failed to rear any offspring, suggesting a fitness link between individual recognition and successful cooperation. Consistent with a selective link between individual recognition and cooperation, we find that rates of cooperative co-nesting correlate with identity-signaling color pattern diversity across the species range. Moreover, genomic evidence of recent positive selection on cognition loci likely to mediate individual recognition is substantially stronger in northern compared to southern P. fuscatus populations. Collectively, these data suggest that individual recognition and cooperative nesting behavior have co-evolved in P. fuscatus because recognition helps mediate conflict among co-nesting foundresses. This work provides evidence of a specific cognitive phenotype under selection because of social interactions, supporting the idea that social behavior can be a key driver of cognitive evolution.

animal behavior and cognition↗

bioRxiv2017

In silico and in vitro screening of FDA-approved drugs for potential repurposing against tuberculosis

MotivationRepurposing of known drugs to newer clinical conditions is a promising avenue for finding novel therapeutic applications for tuberculosis.\n\nMethodsWe performed docking-based virtual screening for 1554 known drugs against two of the potential drug targets, namely trpD and coaA of M. tuberculosis. In the first round of in silico screening we used rigid docking using Glide and AutoDock Vina. We subjected the consistently ranked drugs for induced-fit docking by these tools against the same target proteins. We performed luciferase reporter phage (LRP) assay to determine the biological activity of five selected drugs against M. tuberculosis.\n\nResultsWe observed lymecycline and cefpodoxime to be active against drug susceptible and drug resistant strains of M. tuberculosis. In addition, lymecycline and cefpodoxime showed synergistic activity with rifampin and isoniazid against M. tuberculosis.\n\nConclusionOur results suggest that lymecycline and cefpodoxime have potential to be repurposed for the treatment of tuberculosis.

bioinformatics↗