Biology subjects

El-Sherif, E.

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

3 recordsLinked to original sources

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↗