Biology subjects

Dima, S. S.

Publications and source records attributed to Dima, S. S..

5 recordsLinked to original sources

bioRxiv2026

Enhancer Activity-informed Gap GEne Regulatory Network (EAGER) to model Drosophila gap gene expression on the entire anterior-posterior (A-P) axis

Across metazoa, morphogen gradients differentially regulate gene expression and activate a spatially distinct program to specify body axis development. The Drosophila gap gene network, initiated by maternal morphogen Bicoid, is one of the most well-studied systems. Several regulatory interactions act synergistically to produce distinct gap gene expression patterns along the anterior-posterior (AP) axis of the blastoderm stage Drosophila embryo to ensure the proper segmentation of the larval and, eventually, adult stage fly. Several mathematical models have been proposed to summarize the interconnectivity of gap gene regulatory elements and predict expression in mutant systems. However, these models have not successfully predicted the gap gene expression profile over the entire AP axis. Here, we present an Enhancer Activity-informed Gap GEne Regulatory network (EAGER) model that incorporates enhancer activity-driven differential regulation along the AP axis, which successfully summarizes gap gene expression patterns over the entire AP axis. We validated the predictions of EAGER on Kr mutants and performed a comprehensive parametric sensitivity and identifiability analysis to evaluate the robustness of the EAGER model fits and predictions. We also propose a reduced version of the model, rEAGER, which identifies a minimal set of regulatory interactions and successfully summarizes the gap gene interactions over the entire AP axis. Our results suggest that the expression driven by individual enhancers must be accounted for in models of developmental pattern formation.

developmental biology↗

bioRxiv2026

Genome-wide mapping of Bicoid/DNA interactions reveals quantitative constraints on transcriptional regulation

During Drosophila embryogenesis, Bicoid (Bcd) forms a gradient that provides positional information to regulate target genes along the anteroposterior axis. To understand how the information provided by the Bcd gradient drives gene expression in a concentration-dependent manner, the subpopulations of Bcd participating in gene regulation need to be characterized. Therefore, to understand the mechanism of Bcd-mediated gene regulation, we quantified the absolute concentration of the nuclear subpopulations of Bcd, such as freely diffusing and DNA bound Bcd. These subpopulations have distinct diffusivities and DNA-binding properties and are crucial for gene regulation. This quantification allowed us to construct a global dose/response relationship between the free and DNA-bound concentration of Bcd. Our data show that Bcd/DNA binding is strongly correlated with the free concentration of Bcd, indicated by the dose/response relationship being in the linear regime, despite the barrier presented by nucleosomes. Our data are quantitatively consistent with a Monod-Wyman-Changeux model in which transcription factors passively compete with nucleosomes for DNA binding. We further apply this model to Bcd/DNA interactions at the enhancer/promoter for hunchback (hb), a Bcd target gene which has a steep posterior boundary, despite being driven primarily by the graded Bcd concentration, a conundrum which has been under scrutiny for decades. We show that, using parameters determined from the global dose/response relationship, a reversible multistate promoter model, in which the promoter activation rate is determined by Bcd binding to the hb enhancer, can successfully recapitulate features of hb transcriptional dynamics, including the sharp posterior boundary. Therefore, this work sheds light on mechanism of hb regulation by Bcd and provides a potential experimental/computational pipeline that bridges the input of global properties of transcription factors to the transcriptional output of specific target genes.

developmental biology↗

bioRxiv2025

Novel Fluorescent and Photoconvertible Fusions Reveal Dorsal Activator Dynamics

Over the last two decades, new in vivo and in cellulo imaging technologies have uncovered the inherently dynamic nature of transcriptional regulation in embryonic development and, in particular, in the fruit fly D. melanogaster. These technologies have made it possible to characterize the subnuclear and single-molecule dynamics of transcription factors. However, a lack of appropriate fluorescent protein fusions has, until now, limited these studies to only a few of the dozens of important transcription factors in the fruit fly gene regulatory network dictating early development. Here, we report the creation of four new fluorescent protein fusions to Dorsal, a member of the NF-{kappa}B/Rel family that initiates dorsal-ventral patterning. We generated and characterized two bright fluorescent protein fusions for Dorsal, meGFP and mNeonGreen, and two photoconvertible fluorescent protein fusions, mEos4a and Dendra2. We show that removal of the DsRed2 cassette commonly used to mark the CRISPR integration restores endogenous Dorsal mRNA and protein levels and enables the fusion allele to rescue a dorsal null allele, meeting the gold standard for endogenous function of a tagged protein in a fruit fly. We then demonstrate that our bright fluorescent protein fusions can be used to dissect the spatiotemporal dynamics of stable Dorsal clusters that traverse the nucleoplasm and uncovered that these clusters preferentially interact with active sites of Dorsal-modulated transcription. We further demonstrate that our photoconvertible fluorescent protein fusions make it possible to detect individual molecules of Dorsal in the nuclei of developing embryos. These new fluorescent protein fusions constitute a valuable resource for the community to elucidate the role of Dorsal activator dynamics in dictating fruit fly early embryonic development.

developmental biology↗

bioRxiv2025

Global maps of transcription factor properties reveal threshold-based formation of DNA-bound and mobile clusters

The relationship between bulk transcription factor concentration and DNA binding has been a central question in gene regulation for decades. Recent studies propose that DNA-bound transcription factor hubs, or clusters, aid in fast and precise transcriptional interpretation. Using live imaging techniques, we quantify the concentration, binding, and mobility of the morphogen Dorsal (Dl), both in bulk and in clusters, in Drosophila blastoderm embryo. Our experiments encompass multiple length and time scales, allowing us to obtain a nucleus-wide view of the mechanism connecting hub formation to bulk Dl concentration. Our results show that previously unobserved, slowly-moving clusters of Dl are present, in addition to the expected populations of freely mobile and DNA-bound Dl. Furthermore, both mobile clusters and DNA-bound Dl appear only once a threshold concentration in the nucleus is surpassed, a behavior consistent with liquid-liquid phase separation. Thus, our work elucidates how bulk transcription factor concentration dictates the formation and spatiotemporal changes of different populations needed for gene regulation.

developmental biology↗

bioRxiv2024

Bulk-level maps of pioneer factor binding dynamics during Drosophila maternal-to-zygotic transition

Gene regulation by transcription factors (TFs) binding cognate sequences is of paramount importance. For example, the TFs Zelda (Zld) and GAGA factor (GAF) are widely acknowledged for pioneering gene activation during zygotic genome activation (ZGA) in Drosophila. However, quantitative dose/response relationships between bulk TF concentration and DNA binding, an event tied to transcriptional activity, remain elusive. Here, we map these relationships during ZGA: a crucial step in metazoan development. To map the dose/response relationship between nuclear concentration and DNA binding, we performed raster image correlation spectroscopy, a method that can measure biophysical parameters of fluorescent molecules. We found that, although Zld concentration increases during nuclear cycles (ncs) 10 to 14, its binding in the transcriptionally active regions decreases, consistent with its function as an activator for early genes. In contrast, GAF-DNA binding is nearly linear with its concentration, which sharply increases during the major wave, implicating it in the major wave. This study provides key insights into the properties of the two factors and puts forward a quantitative approach that can be used for other TFs to study transcriptional regulation.

systems biology↗