Comparative Functional Genomic Analyses of Development

The identification of human-specific changes in gene expression, epigenetic modifications, trans-factor binding, and overall chromatin state is an essential complement to the study of cis-regulatory elements with human-specific activities. We are using functional genomics methods to directly study enhancer activity and gene expression in human and nonhuman embryonic tissues. Our current efforts focus on two structures that are highly specialized in humans compared to other species: the limb and the cortex.

Comparative gene expression profiling of human and primate corticogenesis.

We are collaborating with the Rakic lab in the Department of Neurobiology at Yale to compare gene expression profiles in the early developing cortex of human, rhesus and mouse using RNA sequencing. The goal of this effort is to identify primate and human-specific differences in gene expression that may contribute to species-specific aspects of early cortical development and function.

Comparative expression analysis of limb development in humans and model species.

We are carrying out RNA-seq analyses of early human, rhesus and mouse limb development to characterize conserved and human-specific patterns of gene expression. The long-term goal of this study is to identify genes underlying the evolutionary specialization of the human hand and foot.

Identifying enhancers with human-specific functions using ChIP-seq in early human embryonic tissues.

To directly detect active regulatory elements in human and nonhuman embryonic limb and cortex, we are generating comparative maps of enhancer-associated histone modifications and other factors. These studies have identified HACNSs specifically marked in human embryonic tissues relative to other species. We are integrating these data with the expression studies described above to identify human-specific regulatory changes that altered gene expression during human evolution.

Large-scale identification of developmental regulatory domains in the genome.

The gene targets of most enhancers are unknown. In order to develop a comprehensive understanding of the human developmental regulatory program, we are employing circular chromatin conformation capture-based methods to characterize long-range enhancer interactions. Active enhancers recruit chromatin remodeling factors and transcription factors, which are hypothesized to bind both the enhancer and target promoter. These complexes can be stabilized by crosslinking and ligating the crosslinked enhancer and target fragments together, and the interacting elements identified by massively parallel sequencing. We are applying this technique to mouse and primate embryonic tissue samples to gain an understanding of in vivo developmental enhancer activity.