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Hox proteins are one of the best studied sets of transcription factors in developmental biology. They are major determinants for establishing morphological differences along the anterior-posterior axis of animals and are generally regarded…
The Hox gene collinearity enigma has often been approached using models based on biomolecular mechanisms. The biophysical model, is an alternative approach, speculating that collinearity is caused by physical forces pulling the Hox clusters…
The X chromosome is present as a single copy in the heterogametic sex, and this hemizygosity is expected to drive unusual patterns of evolution on the X relative to the autosomes. For example, the hemizgosity of the X may lead to a lower…
A number of studies have indicated a potential association between prenatal exposure to radiation and late mental disabilities. This is believed to be due to long-term developmental changes and functional impairment of the central nervous…
Embryonic development is driven by spatial patterns of gene expression that determine the fate of each cell in the embryo. While gene expression is often highly erratic, embryonic development is usually exceedingly precise. In particular,…
Embryonic development relies on the formation of sharp, precise gene expression boundaries. In the fruit fly Drosophila melanogaster, boundary formation has been proposed to occur at a dynamical critical point. Yet, in the paradigmatic case…
Genes are frequently regulated in complex manners, necessitating modelling approaches which go beyond simple (linear) gene-to-gene interactions and address the modularity of cis-regulatory regions and alternate transcription initiation…
Spatial transcriptomics offers spatially resolved gene expression profiling within tissue sections, but its cost and limited throughput hinder large-scale deployment. To extend this capability to routine practice, recent computational…
Here we use Drosophila melanogaster to create a genetic model of human permanent neonatal diabetes mellitus and present experimental results describing dimensions of this complexity. The approach involves the transgenic expression of a…
The simultaneous expression of the hunchback gene in the numerous nuclei of the developing fly embryo gives us a unique opportunity to study how transcription is regulated in living organisms. A recently developed MS2-MCP technique for…
During development, morphogen gradients precisely determine the position of gene expression boundaries despite the inevitable presence of fluctuations. Recent experiments suggest that some morphogen gradients may be interpreted prior to…
The mammalian cortex is divided into architectonic and functionally distinct areas. There is growing experimental evidence that their emergence and development is controlled by both epigenetic and genetic factors. The latter were recently…
Two cliques of genes identified computationally for their high co-expression in the mouse brain according to the Allen Brain Atlas, and for their enrichment in genes related to autism spectrum disorder, have recently been shown to be highly…
A model is proposed to study the process of hypoxia-induced angiogenesis in cancer cells. The model accounts for the role played by the vascular endothelial growth factor (VEGF)-A in regulating the oxygen intake. VEGF-A is dynamically…
Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on…
Much of the genome is expressed in the vertebrate brain, with individual genes exhibiting different spatially-varying patterns of expression. These variations are not independent, with pairs of genes exhibiting complex patterns of…
For long it has been known that specific patterns of folding are necessary for an optimally functioning brain. For instance, lissencephaly and polymicrogyria can lead to severe mental retardation, short life expectancy, epileptic seizures,…
Numerous transcription factors self-assemble into different order oligomeric species in a way that is actively regulated by the cell. Until now, no general functional role has been identified for this widespread process. Here we capture the…
The precise layout of gene expression patterns is a crucial step in development. Formation of a sharp boundary between high and low expression domains requires a genetic mechanism which is both sensitive and robust to fluctuations, a demand…
Transcriptional repressor CTCF is an important regulator of chromatin 3D structure, facilitating the formation of topologically associating domains (TADs). However, its direct effects on gene regulation is less well understood. Here, we…