Periodic Reporting for period 1 - OGRE (The spatial organization of gene regulation in embryonic development.)
Periodo di rendicontazione: 2023-02-01 al 2025-07-31
The project aims to investigate the spatial organization of gene regulation in embryonic development and stress response, focusing on transcriptional condensates - dense, sub-micrometre clusters of transcription factors and other regulatory proteins. The research uses the nematode Caenorhabditis elegans as a model organism and combines in vivo studies with novel in vitro assays. The project has three main objectives: (1) understand the physiological relevance of transcriptional condensates in animal development and stress response; (2) determine the molecular composition and regulators of transcriptional condensates; (3) dissect the mechanism of transcriptional condensate formation using a novel chromatin carpet assay.
In the last decade, the field of transcription has focused heavily on studying various types of clusters and condensates formed by components of transcriptional machinery. The main model systems used are yeast, mamalian cell culture, Drosophila embryo and to a lesser extent Zebrafish embryos. We have made the first steps in establishing C. elegans embryo as a powerfull system to study transcriptional condensates during normal development and in face of environmental stress. We have made progress in studying several types of nuclear condensates. First, we characterized the formation of condensates by a master regulator of heat shock response. Importantly, we identified the genomic locations of condensate formation within the non-coding, transposon-derived repetitive parts of the genome, which are believed to be non-functional. We began investigating their role in gene expression during stress and development. Second, we described and characterized dynamic nuclear clusters formed by RNA Polymerase II in early C. elegans embryos. We were able to pinpoint the genomic location of some of these clusters and observed cell-specific differences in clustering patterns. Lastly, we created transgenic lines to study a key muscle fate transcription factor's role in differentiation and investigated the effects of protein domain modifications on function and condensate formation. The team has also conducted screens to identify regulators of these condensates identifying putative regulators for all studied nuclear bodies. Lastly, we performed in vitro studies to investigate the phase separation properties of purified proteins identifying the domain regions which promote phase transition.
While the project is still in its early stages, two potentially significant breakthroughs have been made:
1. The discovery that specific transposable elements can serve as nucleation sites for stress response condensates, challenging the notion of "junk DNA" and opening up new avenues for understanding stress response mechanisms.
2. The characterization and identification of genomic regions associated with large transcriptional condensates in C. elegans embryos, establishing a new area of study in this model organism.
Identifying these specific genomic regions provides a unique opportunity to study condensate function by engineering or modifying these regions. This approach could lead to unprecedented insights into the role of condensates in gene regulation.
These findings have the potential to significantly advance our understanding of gene regulation in development and stress response. The project's interdisciplinary approach, combining in vivo and in vitro techniques, is expected to provide novel insights into the composition, assembly, and physiological relevance of biomolecular condensates in transcriptional regulation. This could have far-reaching implications for developmental biology, stress biology, and potentially for understanding and treating diseases related to transcriptional dysregulation.
1. The discovery that specific transposable elements can serve as nucleation sites for stress response condensates, challenging the notion of "junk DNA" and opening up new avenues for understanding stress response mechanisms.
2. The characterization and identification of genomic regions associated with large transcriptional condensates in C. elegans embryos, establishing a new area of study in this model organism.
Identifying these specific genomic regions provides a unique opportunity to study condensate function by engineering or modifying these regions. This approach could lead to unprecedented insights into the role of condensates in gene regulation.
These findings have the potential to significantly advance our understanding of gene regulation in development and stress response. The project's interdisciplinary approach, combining in vivo and in vitro techniques, is expected to provide novel insights into the composition, assembly, and physiological relevance of biomolecular condensates in transcriptional regulation. This could have far-reaching implications for developmental biology, stress biology, and potentially for understanding and treating diseases related to transcriptional dysregulation.