Understanding Early Patterning of the Vertebrate Body

Vertebrates begin as a single-cell embryo. As the embryo develops, the cell divides, differentiating into an organized three-dimensional arrangement of progenitor cells that eventually become skin, muscle, and other organs and tissues—all based on the blueprint provided by the organism’s genome.

Understanding the mechanisms that regulate embryonic development requires analysis of gene expression in space and time. While emerging technologies like RNA-seq produce a snapshot of gene expression in a single cell at a given moment, current methods cannot reveal the processes that yield a spatially controlled architecture of cellular differentiation.

Marcos Simoes-Costa, Molecular Biology and Genetics, is pioneering a new approach—using spatial transcriptomics and epigenomic profiling—to map gene expression in early embryonic development. Using an array of single-cell technologies, Simoes-Costa is assembling tridimensional models of early vertebrate embryos. In these virtual embryos, each cell is represented by a pixel that contains regulatory information from all genes expressed at a given developmental stage. From this data, researchers will be able to reconstruct spatial domains of gene expression on a genome-wide scale and identify new factors that control the early patterning of the vertebrate body plan.

The research will provide insights into the genetic basis of congenital disabilities and could also inform new techniques for using stem cells to repair and regenerate damaged tissues.

NIH Award Number: 1DP2HD102043-01

Cornell Researchers

Funding Received

$2.4 Million spanning 5 years