Genetic perturbation screens have  generated large collections of morphological phenotypes, playing a fundamental role in our understanding of gene function in development and disease. The observed morphological changes are the manifestation of molecular phenotypes such as altered genomic sequence and transcriptional variation. Changes in transcription levels can be due to gene regulatory events, genomic variation and other non-genetic factors. Untangling the different contributions is critical for understanding the relationship between molecular and morphological phenotype.

We explore these molecular phenotypes through the transcript sequencing of whole vertebrate embryos and tissues either by traditional RNA-seq or 3' end transcript counting. Taking advantage of the high quality reference genomes of the zebrafish and mouse, we are able to capture the full complement of polyadenylated transcripts, establishing a baseline of gene expression across the development of unperturbed organisms.

Foremost, we are exploring the level of gene expression variation that can be tolerated by a particular biological system and when this variation leads to phenotypic changes. We are able to manipulate these systems through specific genome engineering or gene knockout, exposure to chemical compounds or infection challenges. Following perturbations we are then able to measure the changes in transcript abundance across the entire organism and simultaneously link them to genotype information.