Long-Range Regulatory Interactions in the Drosophila Brain.

This research proposal is dedicated to unraveling the intricate regulatory mechanisms governing chromatin organization and gene transcription during neural development in the model organism Drosophila. The primary focus is on understanding how 3D genome architecture, specifically chromatin loops, contributes to the spatial and temporal control of gene expression, particularly in the context of cell adhesion molecule (CAM) genes. This comprehensive investigation involves a multi-faceted approach, combining cutting-edge experimental techniques, advanced computational analyses, and genetic manipulations. The first aim involves the identification of focal contact anchors using Micro-C maps, high-resolution chromatin contacts maps. These maps will be generated for various developmental stages, including the wing imaginal disc, larval brain, and adult brain. The analysis will also include CAM genes, a significant group of genes with critical roles in neural development. This aim will provide insight into the specific chromatin regions involved in gene regulation and spatial organization. The second aim delves into the functional role of identified focal contact anchors in regulating gene transcription. By employing precise deletions and insertions of these anchors, the study aims to decipher their contribution to gene expression. The investigation will focus on CAM genes, aiming to distinguish between essential anchors that disrupt transcription upon deletion and assisting anchors that do not significantly impact gene expression. This analysis will provide a nuanced understanding of the functional significance of these anchors in gene regulation. The third aim focuses on dissecting the involvement of transcription factors in the formation of chromatin loops. Through motif enrichment analysis and depletion experiments using RNA interference, the study aims to identify critical transcription factors that contribute to loop formation. This aim will provide insights into the intricate interplay between transcription factors and chromatin architecture, shedding light on the complex regulatory mechanisms governing gene expression. The proposed research holds potential for transformative contributions to our understanding of neural development and gene regulation. By dissecting the role of 3D genome organization in gene expression, this study bridges the gap between chromatin architecture and functional gene networks. This research not only contributes to fundamental insights into neural circuit assembly but also has broader implications for our understanding of gene regulation in diverse biological contexts.