Die physikalischen und dynamischen Eigenschaften transkriptioneller Mikroumgebungen während der Embryonalentwicklung
Biophysik
Zusammenfassung der Projektergebnisse
During embryo development, the animal must undergo a series of changes in order to develop the various body segments and appendages necessary for the functioning and survival of the organism. This process begins with a uniformly shaped embryo; as development progresses, the shape of the body becomes progressively refined, eventually forming specific tissues, organs, and body parts. Protein molecules inside cells called transcription factors control this process by turning on (expressing) genes that control embryo development at the right place and time. Inside the nucleus of cells, transcription factors must bind to DNA regions near the genes they control (regulatory regions). However, recent research has found that transcription factors stay for only a few seconds at any specific location on the DNA and that regulatory regions use interaction (binding) sites that are very weak in their ability to interact with transcription factors. Replacing these sites with stronger ones disrupted their function, leading to a conundrum in developmental biology of how such weak interactions between transcription factors and the genes they regulate could precisely and robustly control embryo development. I have previously found, in the embryos of the common fruit fly (Drosophila melanogaster), that, by having multiple binding sites for the same transcription factor in clusters, they could create a local trap for the transcription factor around the genes that need it. This local trapping near genes creates microscopic environments spanning less than a tenth of the length of the nucleus (a few hundred nanometers). These microenvironments have high concentrations of the correct transcription factors that allow them to drive gene expression, even with weak binding sites. In fact, multiple genes can share the same environment when they are close by, mutually strengthening the microenvironment. This improves the embryo’s ability to develop normally when faced with challenging conditions, such as increased temperatures and genetic mutations. While the importance of these local environments in the nucleus around key genes for development is becoming clear, we still do not know much about the properties, behaviors, and consequences of these environments during embryo development. For example, when do these environments form? What are the components inside the nucleus that guide transcription factors to specific locations? What happens to the animal when we disrupt some of those components? In this project, we addressed these questions by looking at the where different transcription factors, genes, and the underlying organized DNA (chromatins) are at across development using advanced light microscopes that can acquire images at and beyond the resolution limit of conventional light microscopy (high- and super-resolution imaging). We found that, at the beginning of embryo development, transcription factors are spread uniformly across the nucleus. As development progresses, transcription factors went progressively into specific locations inside the nucleus. The structure of the DNA where the transcription factors interact with also became progressively complex, with chemical (epigenetic) marks being deposited onto the chromatin to mark regions with specific functions. Interestingly, this microscopic process inside the nucleus parallels the macroscopic development of the animal body from uniform to complex. Inside an older embryo, where the nucleus is organized into distinct compartments, the specific location of a gene could greatly alter the environment it sees. As we observed dynamic changes in how the chromatin is marked that is correlated to the location of transcription factors, especially at specific developmental genes, we reduced the amount of a specific mark (H3K4me1) to investigate how it affects the integrity of microenvironments and, thus, development of the embryo. We found that while flies with reduced H3K4me1 looked normal under optimal conditions, they have weakened microenvironments around developmental genes, leading to significant defects in their body development when subjected to increased temperatures and genetic mutations. They also produce more fat and behave differently on non-standard fruitbased foods than normal flies. Surprisingly, they sometimes survive better, leading to interesting questions of how variations in such marks could help populations adapt and evolve. These results highlight how nuclear organization could ensure robust embryo development. A deeper understanding of how these organized environments in the nucleus interact with their genes would provide insights into why normal embryos develop robustly under a variety of external challenges without developmental defects and how to treat problems when they arise.
Projektbezogene Publikationen (Auswahl)
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Robust and efficient gene regulation through localized nuclear microenvironments. Development, 147(19).
Tsai, Albert; Galupa, Rafael & Crocker, Justin
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Developmental phenomics suggests that H3K4 monomethylation confers multi-level phenotypic robustness. Cell Reports, 41(11), 111832.
Gandara, Lautaro; Tsai, Albert; Ekelöf, Måns; Galupa, Rafael; Preger-Ben, Noon Ella; Alexandrov, Theodore & Crocker, Justin
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Nuclear morphogenesis: forming a heterogeneous nucleus during embryogenesis. Development, 149(4).
Tsai, Albert & Crocker, Justin
