Our lab operates at the interface of biology and technology to investigate important questions in biomedical sciences. We develop new tools using a variety of strategies, including molecular engineering, CRISPR-based manipulation, and computational approaches. We apply these tools to problems in mammalian development, neurobiology, and synthetic biology.

Molecular devices for in vivo barcoding

Engineering cells to label their genomes with unique barcodes is an effective way of tracking cellular identity, behavior, and history. We are interested in developing molecular devices that accomplish this in vivo barcoding with both high efficiency and minimal negative side-effects. For instance, we have developed the homing CRISPR system as a versatile platform for in vivo barcoding. In this platform, homing guide RNAs (hgRNAs) target their own loci to create highly diverse and unique random mutations. Among other topics, we are applying these molecular devices in brain connectome mapping and the deep lineage tracing of embryonic develpoment.

Further reading: Rapidly evolving homing CRISPR barcodes.

Developmental barcoding and lineage mapping

The development of an organism from single totipotent zygote is a subject of foundational interest for our lab. The path of orchestrated zygotic divisions and differentiation events during development creates cell lineages, much like a tree. This tree has been entirely mapped in C. elegans, an organism of ~1000 cells, and led to broad-ranging genetic insights. Our work aims to create a similar mapping system in higher eukaryotes, enabling characterization of deep, single-cell resolution lineage trees in mammals using molecular recording devices.

To this end, we have established a unique mouse model, dubbed MARC1 (Mouse for Actively Recording Cells!), which carries multiple hgRNA loci distributed across its genome. Activating these hgRNAs in the zygote results in their mutagenesis throughout gestation, creating developmentally barcoded mice in which lineage information is recorded in hgRNA barcodes. We use this strategy to study early and extraembryonic development, as well as the development of the central nervous system.

Further reading: Developmental barcoding of whole mouse via homing CRISPR.

In situ readout of nucleic acids

The ability to extract transcriptomic, genomic, and epigenetic information from individual cells in high throughput while preserving detailed information about their spatial position enhances our understanding of biological behavior, especially in heterogenous mixtures such as tissues. We work on technologies that allow for high throughput readout of DNA and RNA sequences from fixed cells and tissue sections directly (in situ sequencing). We are particularly interested in using hybridization- and sequencing-based readouts for in situ readout of nucleic acid barcodes in tissue sections.

Further reading: Highly multiplexed subcellular RNA sequencing in situ.

Funders & Partners