RegulatoryTEmbryo: Dissecting the role of regulatory transposable elements in shaping embryonic gene networks

Objective

The precise regulation of gene expression is essential for embryogenesis. Transposable elements (TEs), often considered genomic parasites, are hypothesised to function as regulatory hubs coordinating gene networks during this critical window, but evidence remains largely correlational. The RegulatoryTEmbryo project will bridge this gap by dissecting the causal impact of regulatory TEs on Arabidopsis thaliana development. This project moves beyond correlation to establish causation through an integrated experimental strategy. First, I will use a dedicated bioinformatic pipeline and in vivo reporter assays to identify and validate the regulatory function of specific TE families. Second, I will employ multiplexed CRISPR-Cas9 to perform targeted deletions of these families, allowing for a definitive assessment of their impact on embryonic transcription and phenotype. Finally, I will use biochemical assays (EMSA) to mechanistically confirm the underlying transcription factor-TE interactions, and evolutionary approaches to uncover the general principles governing TE-encoded gene regulation in plant embryo patterning. This research will deliver a new model for the role of TEs as key drivers of developmental gene regulation. Ultimately, it will provide a mechanistic framework for understanding how TE-encoded gene regulatory activity fuels morphological diversity in nature. By integrating advanced cell biology and biochemistry with my expertise in epigenomics, this fellowship will provide the crucial interdisciplinary skills required to launch my career as an independent research leader.