3D Genome Organization and Gene Expression in Drosophila

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Project Summary/Abstract Topologically associating domains (TADs) are three-dimensional organizational units that bring distant genetic loci into close proximity with their regulatory elements and demarcate regions of highly-interacting chromatin. Early studies suggested that TADs play a critical role in gene regulation since they were found to be highly conserved in verte- brates and Drosophila. However, more recent research suggests that TADs are frequently reorganized and that re- structuring does not affect gene expression. The lack of clarity surrounding both TAD conservation and the role of TADs in regulating gene expression represents a critical barrier to understanding genetic regulatory evolution. The long-term goal within the field of 3D genome evolution is to elucidate the relationship between 3D genome organiza- tion and gene expression. The objective of this proposal is to describe the relationship between 3D genome evolu- tion and gene expression by characterizing the conservation and divergence of TAD structures and gene expression across 11 species of Drosophila. My preliminary data show that the rate of TAD and gene expression evolution may vary by TAD subtype based on chromatin enrichment. Therefore, my central hypothesis is that rate of TAD evolu- tion and the associated divergence in gene expression varies by TAD subtype. I will test this hypothesis through the following specific aims: I will 1) implement a phylogenetic comparative analysis to evaluate the conservation of TAD architecture and accompanying gene expression profiles across 11 Drosophila species and 2) use CRISPR to test the effects of lineage-specific TAD disruptions on 3D genome organization and gene expression directly. The proposed research represents an innovative approach because it will take advantage of natural variation between species of Drosophila to describe the relationship between TADs and gene expression. Disruption of TAD boundaries has been associated with aberrant enhancer-promoter contacts and gene misregulation, leading to developmental abnormalities and cancer . These results will assist in future research identifying genetic factors causing species-specific genetic ex- pression patterns and disease states, and improve overall understanding of the evolution of gene regulation. The training plan focuses on formal education of the applicant in computational genomic and molecular genetic approaches through courses, workshops, and completion of the proposed research in the Sponsor's laboratory setting. The training outlined in this proposal will prepare the applicant to accomplish her career goal of leading a research team studying basic evolutionary processes in wild and model organisms as a multifaceted approach to discover the genetic underpinning of health and disease. The Co-Sponsors for this proposal have the expertise in evolutionary genomics and genetic structural variation, and Rutgers University has the resources, facilities, and intellectual environment to support the applicant through the training period and ensure a successful transition to independence and attainment of her goal.