Analysis of Drosophila Virilis Chromatin Structure and its Formation During Early Embryogenesis

Abstract

The 3-dimensional organization of the Drosophila virilis genome and the mechanism of its development are poorly understood. A series of technological advancements over the past decade have revolutionized the ability to study chromatin structure in the cell. In this thesis, I analyze D. virilis Micro-C and ATAC-seq data during embryogenesis to better understand the patterns of chromatin architecture and the genetic elements involved in its formation. By comparing ATAC-seq chromatin accessibility data between nc14 and later mixed-stage D. virilis embryos, I identified a number of potentially regulated genes during embryogenesis. I propose that these putative cis-regulatory regions can be useful targets for investigation on changes in chromatin structure during early embryogenesis. Additionally, I identified a pattern of heightened chromatin accessibility at topologically associating domain (TAD) borders, especially during nc14, implicating the possibility of genetic elements involved in TAD formation. Separately, I helped optimize the RD-SPRITE protocol for Drosophila virilis embryos, setting up future research to understand the role of DNA-RNA interactions in establishing 3D genomic structure during early embryogenesis.