Leveraging genetic divergence to uncover mechanisms of genomic organization

The National Institute of General Medical Sciences awarded the University of Wisconsin - Madison $152,600 on September 30, 2026, under the Biomedical Research and Research Training program (CFDA 93.859) to investigate mechanisms of genomic organization by leveraging genetic divergence in Drosophila embryos.

The research will determine how the nucleus partitions active and inactive chromatin compartments during early embryogenesis, focusing on the transcription factor GAGA factor (GAF). The project will modulate the ratio of GAF to GA-rich satellite repeats in hybrid Drosophila embryos to measure effects on nuclear organization and gene expression, and will use proximity ligation assays to identify cofactors that function with GAF in distinct subnuclear compartments.

Work is performed in Madison, Wisconsin. The award period runs through August 31, 2028. This is a Project Grant, the assistance type supporting investigator-initiated research.

Abstract

As all the cells in an organism share the same DNA, IT is how the genome is structured and interpreted that gives rise to the diversity of cell types. To allow for proper gene expression, the genome must be organized into active and inactive nuclear compartments. Active regions are gene rich and accessible to transcription-factor binding. By contrast, repetitive DNA must be localized to inactive nuclear compartments, as failure to permanently silence repetitive loci leads to developmental defects and cancer. Because nuclear organization is essential for proper development, IT is established during the earliest stages of embryogenesis. The embryo is initially transcriptionally quiescent and must establish chromatin architecture DE novo during the maternal-to-zygotic transition (MZT). This project will leverage the rapidity of drosophila embryogenesis to determine how the nucleus is partitioned. We demonstrated that the transcription factor gaga factor (GAF) is non-uniformly distributed in the nucleus and is required for establishing both the active and inactive nuclear compartments. In active compartments, GAF is essential for promoting accessible chromatin and activating gene expression. Simultaneously, GAF is concentrated in foci at GA-rich satellite repeats to promote establishment of constitutive heterochromatin and silence expression of repetitive loci. By determining the features that allow GAF to perform two contradictory functions in the same nucleus at the same time, we will elucidate the fundamental molecular mechanisms that partition the genome. We will modulate the ratio of GAF to the GA-rich regions IT binds by generating hybrid drosophila embryos and determine the effects on nuclear organization and gene expression. In a complementary aim, we will use proximity ligation to identify cofactors that function with GAF in distinct subnuclear compartments. Together, our work will use evolutionary, biochemical, and genetic approaches to determine how the interactions between fast-evolving repeats and the factors that bind them segregate the nucleus into active and silenced regions. Our proposed research is significant because IT will investigate how repetitive elements can affect the genome in trans by redistributing regulatory factors with implications for normal development and cancer.