Description of Research Expertise

The Cotney Lab is interested in determining how gene regulatory elements, also known as enahancers, control gene expression during mammalian development. We aim to understand how new gene regulatory functions evolve, to identify mechanisms of enhancer function over large genomic distances, and globally identify variants of enhancer sequences that are associated with human disease.

We use a variety of functional genomics techniques including ChIP-Seq, RNA-Seq, ATAC-Seq, and HiC at both bulk and single cell levels to identify gene regulatory networks active during human organogenesis. We integrate this data with a variety of public datasets including transcriptomic (GTEx), epigenomic (Roadmap Epigenome, ENCODE), and genetic resources (UKBB, All Of Us, DECIPHER, GMKF).

We model our findings in culture models of human development including Neural Crest and cardiac organoids as well as mice and zebrafish (collaboration with Dr. Eric Liao's lab).

We aim to provide a better understanding of rare variation in noncoding regions and identify additional disease causing genes related to craniofacial and cardiac development.