Gebelein Lab

Assessing How Transcription Factor Specificity Impacts Development and Disease

The development of specific cells, tissues, and organs throughout the body requires master control genes, which typically encode transcription factors (TFs) that regulate the expression of many target genes. Paradoxically, most master control genes are members of common TF families that bind the same DNA sequences in vitro, and yet these factors regulate very distinct outcomes in vivo.

As an example, the human genome encodes over 200 homeodomain TFs that largely bind similar AT-rich DNA sequences, but studies in model organisms revealed that most of these TFs regulate very different developmental processes. Moreover, recent human genetic studies revealed that variants in homeodomain TFs are associated with a large number of rare human diseases. These findings raise the fundamental question: How do TFs with highly similar DNA binding activities achieve sufficient specificity to ensure the accurate regulation of distinct genetic programs in different cell types during development? Defining how these TFs recognize the appropriate target genes required for development is a fundamental problem of study in biomedical research.

The Gebelein Lab is focused on identifying the mechanisms underlying homeodomain specificity at the genomic and molecular levels. Our current hypothesis is that homeodomain TFs achieve target and regulatory specificity by forming larger TF complexes that bind distinct combinations of DNA sites. To test this hypothesis, we are using a multi-disciplinary approach that incorporates a combination of molecular, cellular, biochemical, and structural approaches with cutting edge genomics and bioinformatics.

The Gebelein Lab has expertise in Drosophila genetics, reporter assays, TF biochemistry, mammalian and human cell cultures, and genomic binding approaches. Using this interdisciplinary expertise, we have created and validated a computational pipeline that assesses the likelihood of TF complex formation using data from a widely available in vitro binding assay. With these predictions, we are now assessing the functional impacts of this type of regulation in vivo using genomic studies and cell/animal models through the help of collaborations Matthew Weirauch, PhD, Hee Woong Lim, PhD, and Jason Tchieu, PhD at Cincinnati Children's and Rhett Kovall, PhD at the University of Cincinnati College of Medicine. Drs. Weirauch and Lim have expertise in applying bioinformatics to analyze complex datasets from in vivo assays (CUT&RUN, ChIP-seq, RNAseq, etc). Dr. Tchieu provides expertise in using human embryonic stem cells and directed differentiation cultures, and Dr. Kovall provides protein purification, biophysics, and structural biology expertise.