Biology subjects

El-Sherif, E.

Publications and source records attributed to El-Sherif, E..

10 recordsLinked to original sources

bioRxiv2026

Temporal-to-spatial patterning of embryonic structures can involve active transformation of temporal information rather than direct mapping

How spatial patterns arise during embryonic development is classically explained by the French Flag model, in which cells acquire positional identities by interpreting morphogen concentration thresholds. However, in many developmental systems, spatial patterns instead emerge progressively through temporal programs of gene expression that are transformed into spatial organization. For example, in the short-germ insect Tribolium castaneum, both periodic pair-rule gene expressions that generate body segments and non-periodic gap gene expressions that establish regional identities arise sequentially at the posterior and propagate anteriorly in waves across the developing embryo. Understanding how such temporal gene expression programs are translated into spatial patterns remains a major challenge. To address this problem, we developed a sequential multiplexed imaging strategy based on hybridization chain reaction (HCR), enabling visualization of up to ten anterior-posterior (AP) patterning genes within the same Tribolium embryo. By combining this approach with intronic-exonic labeling, we established a framework to infer gene expression dynamics and propagatory behavior during AP patterning. Using this framework, we show that gap gene expression domains remain dynamic and continue to propagate during tissue elongation, indicating that spatial patterns are actively remodeled throughout development. We then directly compared temporal gene activation at the posterior with the resulting spatial organization of pair-rule and gap genes. Surprisingly, while primary pair-rule genes preserve their temporal phase relationships in space, gap genes do not. Instead, the relative positioning of gap gene domains progressively changes as they move anteriorly, indicating that the final spatial organization of gap genes is actively reshaped during propagation rather than being directly inherited from the initial temporal sequence. The continued propagatory behavior of gap gene domains suggests that such reshaping could arise through differential propagation dynamics between genes and/or through progressive reconfiguration of underlying gene regulatory interactions during pattern formation. Together, these findings reveal that temporal-to-spatial patterning can involve active transformation of temporal information rather than a simple mapping from time into space.

developmental biology↗

bioRxiv2026

Enhancer RNA Transcription Near Segmentation Gene Enhancers Can Be Analyzed In Situ Using FISH

Enhancer RNAs (eRNAs) are non-coding transcripts produced at enhancer regions, which appear to be involved in transcriptional regulation. Up to date, these have been primarily investigated using labor-and cost-intensive genomic techniques. However, the precise mechanisms by which eRNA transcription or the eRNA transcripts themselves mediate transcriptional regulation remain unclear. Here, we present a novel experimental approach that allows us to analyze the characteristics of eRNA transcription in fixed and live whole Drosophila melanogaster embryos. We employ the anterior-posterior patterning genes as a model system to investigate the dynamics of eRNA expression, utilizing an imaging-based approach. We combined high-sensitivity fluorescence in situ hybridization (FISH) chain reaction (HCR) with high-resolution confocal microscopy to detect eRNA and mRNA molecules. Through this experimental assay, we identified foci of elevated transcriptional activity that generate eRNA transcripts correlated with mRNA production at the same gene locus. We could show that this eRNA transcription is independent of promoter activity. Additionally, we demonstrate that insulators can influence eRNA transcription, resulting in loss of eRNA transcription. Moreover, we observe that eRNAs can originate both within classical enhancer regions and outside of them, including from foreign bacterial sequences when these are placed near enhancer sequences, underscoring the strong influence of local regulatory context on eRNA initiation. In live embryos using MS2-MCP live imaging, our analysis of insulators showed a modest reduction in mRNA burst intensity accompanied by a slight increase in burst frequency. Overall, our imaging-based approach offers a novel platform for dissecting enhancer-eRNA interactions and could be adapted for wider applications.

developmental biology↗

bioRxiv2025

Gene network switching provides a mechanistic basis for time-to-space translation in insect embryonic patterning

The French Flag model has long served as the prevailing framework for explaining how morphogen gradients generate spatial domains during embryonic development. More recently, however, evidence has shown that many tissues instead establish patterns by translating the sequential activation of genes (organized into genetic cascades) into spatial domains. This translation is thought to occur through modulation of the speed or timing of cascade progression, but the mechanisms underlying such temporal control remain unclear. Two models have been proposed: the general kinetic modulation model, in which morphogens influence global kinetic factors such as transcription and decay rates, and the gene regulatory network (GRN) switching model, in which morphogens reconfigure regulatory interactions so that genes initially function within a genetic cascade driving sequential activation, but are later integrated into a stabilizing network that locks their expression into mutually reinforcing domains. This transition is hypothesized to occur through a shift from a dynamic GRN (a genetic cascade that drives sequential activations) to a static GRN (a stabilizing network that maintains gene expression domains). Using gap genes in Tribolium castaneum as a model, we combined HCR in situ hybridization, parental RNA interference, and computational modeling to test these hypotheses. We show that gap genes initially act in a genetic cascade producing sequential activations, followed by a morphogen-dependent reconfiguration that stabilizes spatial domains. In particular, we identify the Mlpt-Svb complex as a key stabilizing factor that maintains svb expression anteriorly after its initial activation in the posterior. Computational simulations reproduce experimental phenotypes and support GRN switching as the underlying mechanism. Together, these findings demonstrate how morphogen-driven rewiring of network interactions converts temporal cascades into stable spatial patterns, providing a mechanistic basis for robust anterior- posterior patterning in insect embryos and beyond.

developmental biology↗

bioRxiv2024

From Genes to Patterns: A Framework for Modeling the Emergence of Embryonic Development from Transcriptional Regulation

Understanding embryonic patterning, the process by which groups of cells are partitioned into distinct identities defined by gene expression, is a central challenge in developmental biology. This complex phenomenon is driven by precise spatial and temporal regulation of gene expression across many cells, resulting in the emergence of highly organized tissue structures. While similar emergent behavior is well understood in other fields, such as statistical mechanics, the regulation of gene expression in development remains less clear, particularly regarding how molecular-level gene interactions lead to the large-scale patterns observed in embryos. In this study, we present a modeling framework that bridges the gap between molecular gene regulation and tissue-level embryonic patterning. Beginning with basic chemical reaction models of transcription at the single-gene level, we progress to model gene regulatory networks (GRNs) that mediate specific cellular functions. We then introduce phenomenological models of pattern formation, including the French Flag and Temporal Patterning/Speed Regulation models, and integrate them with molecular/GRN realizations. To facilitate understanding and application of our models, we accompany our mathematical framework with computer simulations, providing intuitive and simple code for each model. A key feature of our framework is the explicit articulation of underlying assumptions at each level of the model, from transcriptional regulation to tissue patterning. By making these assumptions clear, we provide a foundation for future experimental and theoretical work to critically examine and challenge them, thereby improving the accuracy and relevance of gene regulatory models in developmental biology. As a case study, we explore how different strategies for integrating enhancer activity affect the robustness and evolvability of gene expression patterns in embryonic development. Our simulations suggest that a two-step regulation strategy, enhancer activation followed by competitive integration at the promoter, ensures more standardized integration of new enhancers into developmental GRNs, highlighting the adaptability of eukaryotic transcription. These findings provide new insights into the transcriptional mechanisms underlying embryonic patterning, offering a framework for future experimental and theoretical investigations.

developmental biology↗

bioRxiv2022

How enhancers regulate wavelike gene expression patterns: A novel enhancer prediction and live reporter system identifies an enhancer associated with the arrest of pair-rule waves in Tribolium

A key problem in development is to understand how genes turn on or off at the right place and right time during embryogenesis. Such decisions are made by non-coding sequences called enhancers. Much of our models of how enhancers work rely on the assumption that genes are activated de novo as stable domains across embryonic tissues. Such view has been strengthened by the intensive landmark studies of the early patterning of the anterior-posterior (AP) axis of the Drosophila embryo, where indeed gene expression domains seem to arise more or less stably. However, careful analysis of gene expressions in other model systems (including the AP patterning in vertebrates and short-germ insects like the beetle Tribolium castaneum) painted a different, very dynamic view of gene regulation, where genes are oftentimes expressed in a wavelike fashion. How such gene expression waves are mediated at the enhancer level is so far unclear. Here we establish the AP patterning of the short-germ beetle Tribolium as a model system to study dynamic and temporal pattern formation at the enhancer level. To that end, we established an enhancer prediction system in Tribolium based on time- and tissue-specific ATAC-seq and an enhancer live reporter system based on MS2 tagging. Using this experimental framework, we discovered several Tribolium enhancers, and assessed the spatiotemporal activities of some of them in live embryos. We found our data consistent with a model in which the timing of gene expression during embryonic pattern formation is mediated by a balancing act between enhancers that induce rapid changes in gene expressions (that we call dynamic enhancers) and enhancers that stabilizes gene expressions (that we call static enhancers).

developmental biology↗

bioRxiv2020

Geometric models for robust encoding of dynamical information into embryonic patterns

During development, cells gradually assume specialized fates via changes of transcriptional dynamics, sometimes even within the same developmental stage. For anterior-posterior (AP) patterning in metazoans, it has been suggested that the gradual transition from a dynamic genetic regime to a static one is encoded by different transcriptional modules. In that case, the static regime has an essential role in pattern formation in addition to its maintenance function. In this work, we introduce a geometric approach to study such transition. We exhibit two types of genetic regime transitions, respectively arising through local or global bifurcations. We find that the global bifurcation type is more generic, more robust, and better preserves dynamical information. This could parsimoniously explain common features of metazoan segmentation, such as changes of periods leading to waves of gene expressions, "speed/frequency-gradient" dynamics, and changes of wave patterns. Geometric approaches appear as possible alternatives to gene regulatory networks to understand development.

biophysics↗

bioRxiv2018

Speeding up anterior-posterior patterning of insects by differential initialization of the gap gene cascade

Recently, it was shown that anterior-posterior patterning genes in the red flour beetle Tribolium castaneum are expressed sequentially in waves. However, in the fruit fly Drosophila melanogaster, an insect with a derived mode of embryogenesis compared to Tribolium, anterior-posterior patterning genes quickly and simultaneously arise as mature gene expression domains that, afterwards, undergo slight posterior-to-anterior shifts. This raises the question of how a fast and simultaneous mode of patterning, like that of Drosophila, could have evolved from a rather slow sequential mode of patterning, like that of Tribolium. In this paper, we elucidate a mechanism for this evolutionary transition based on a switch from a uniform to a gradient-mediated initialization of the gap gene cascade by maternal Hb. The model is supported by computational analyses and experiments.

developmental biology↗

bioRxiv2018

A re-inducible genetic cascade patterns the anterior-posterior axis of insects in a threshold-free fashion

Gap genes mediate the division of the anterior-posterior axis of insects into different fates through regulating downstream hox genes. Decades of tinkering the segmentation gene network of the long-germ fruit fly Drosophila melanogaster led to the conclusion that gap genes are regulated (at least initially) through a threshold-based French Flag model, guided by both anteriorly- and posteriorly-localized morphogen gradients. In this paper, we show that the expression patterns of gap genes in the intermediate-germ beetle Tribolium castaneum are mediated by a threshold-free Speed Regulation mechanism, in which the speed of a genetic cascade of gap genes is regulated by a posterior gradient of the transcription factor Caudal. We show this by re-inducing the leading gap gene (namely, hunchback) resulting in the re-induction of the gap gene cascade at arbitrary points in time. This demonstrates that the gap gene network is self-regulatory and is primarily under the control of a posterior speed regulator in Tribolium and possibly all insects.

developmental biology↗

bioRxiv2018

Speed Regulation and Gradual Enhancer Switching Models as Flexible and Evolvable Patterning Mechanisms

Short AbstractUsing simple animations, mathematical formulations, and computational implementation in Matlab, we present a newly devised embryonic patterning mechanism: the Speed Regulation model, and its molecular realization: the Gradual Enhancer Switching model. We show how our models shed light on the phenomenology of insect development and evolution.\n\nLong AbstractPartitioning an initially homogeneous group of cells into different fates is a common problem in development. A curious case is the anterior-posterior (AP) fate specification during early embryogenesis in insects. The AP fates of most insects are specified in two different phases: (i) the blastoderm, where the AP axis does not undergo any axial elongation, and (ii) the germband, where the AP axis undergoes gradual axis elongation. Throughout evolution, insects show remarkable flexibility in the number of fates specified in the blastoderm vs germband. This hints that AP specification in insects relies on a flexible mechanism that can pattern both non-elongating embryonic structures (like the blastoderm) and elongating tissues (like the germband). Here we describe the Speed Regulation model, a recently suggested patterning mechanism, that can pattern both elongating and non-elongating tissues and ensures the evolvability between them. The model is successful in reproducing the phenomenology of AP axis specification and evolution in insects. In addition, it explains the temporal-based patterning of other embryonic structures like the AP axis of vertebrates and the dorsoventral axis of vertebrate neural tube. The Speed Regulation model is phenomenological in its formulation, in the sense that it does not specify a particular molecular realization. We then present the Gradual Enhancer Switching model, in which we describe a specific molecular implementation of the Speed Gradient model that incorporates a novel scheme of cis-regulation within gene regulatory networks. The paper is linked to two videos on YouTube referred to below.\n\nLinked VideosVideo I: https://youtu.be/YcGotl8OdYw\n\nVideo II: https://youtu.be/f-JnjF2aNLw

developmental biology↗

bioRxiv2017

Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum

Evolution of cis-properties (such as enhancers) often plays an important role in the production of diverse morphology. However, a mechanistic understanding is often limited by the absence of methods to study enhancers in species outside of established model systems. Here, we sought to establish methods to identify and test enhancer activity in the red flour beetle, Tribolium castaneum. To identify possible enhancer regions, we first obtained genome-wide chromatin profiles from various tissues and stages of Tribolium via FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)-sequencing. Comparison of these profiles revealed a distinct set of open chromatin regions in each tissue and stage. Second, we established the first reporter assay system that works in both Drosophila and Tribolium, using nubbin in the wing and hunchback in the embryo as case studies. Together, these advances will be useful to study the evolution of cis-language and morphological diversity in Tribolium and other insects.

developmental biology↗