The Zeitlinger Lab focuses on how DNA sequence information in the genome controls gene regulation in Drosophila and mice to gain insight that can be applied to the human genome in development and disease.

Gene regulation is the process by which a cell determines which genes to turn on and off and when to create specific cells in the body. The Zeitlinger Lab analyzes whole genomes to predict the fate of cells.

Zeitlinger discovered that paused RNA polymerase II is found genome-wide. RNA polymerase II starts the transcription process - producing RNA messages from DNA - but then pauses, as if waiting for a signal to proceed. If paused polymerase is present, the gene is more likely to be activated in the future.

The Zeitlinger Lab develops genomic techniques, including ChIP-nexus, that allow researchers to collect information from vast amounts of cells — sometimes numbering in the millions — to provide an accurate picture of how genes are regulated. They also apply deep learning to ChIP-nexus data from different cell types and stages to better understand the cis-regulatory code (how regulatory DNA sequences affect neighboring genes) and how this code changes during development. Additional technology developed is ChIP-next that allows deciphering of cis-regulatory information, stretches of non-coding DNA that regulate gene expression, from many fewer cells.