Transcriptional regulation is an extremely complex process that allows for appropriate readout of genetic information in every living organism. This process is particularly important during development and disease, and controlled by intricate mechanisms of DNA regulatory elements. These regulatory elements, including gene promoters and distal enhancers, compile regulatory signals received through transcription factor binding. The three-dimensional architecture of the genome brings enhancers, often located at large linear distance along the genome, into spatial proximity to the target genes.
On a larger scale, the genome is partitioned into Topologically Associated Domains (TADs), characterized by having internal contacts more frequent than contacts to the outside regions. TAD boundaries are thought to insulate regulatory environments between adjacent TADs, preventing gene promoters from being inadvertently activated by enhancers located in other TADs. Several studies showed that disruption of a TAD boundary could affect expression of genes on the other side of the boundary through enhancer hijacking. This is also the case for naturally occurring structural variants that disrupt TAD boundaries, and this mechanism has been shown to have a role in driving certain developmental disorders and cancers.
This project used chromosome conformation capture techniques, Hi-C and Capture-C, to measure chromatin topology at a genome-wide scale in the context of embryonic development of Drosophila melanogaster. We performed Hi-C experiments during multiple stages of development spanning the entire embryonic timespan to determine if the chromatin interaction landscape observed during the early stages of development is maintained to the end of embryogenesis. For this purpose, we identified topologically associated domains (TADs) and annotated long-range looping interactions.
To investigate the relationship between genome topology and gene expression, we utilized highly rearranged balancer chromosomes, which contained eight large nested inversions, thousands of smaller structural variants, and hundreds of thousands of single nucleotide variants. We then assessed the impact of these genomic rearrangements on genome topology and gene expression in cis, using a heterozygous cross (balancer over wild-type), which minimizes the contribution of trans effects. For this purpose, we performed allele-specific Hi-C and RNA-seq experiments on F1 embryos.
