Abstract

How a gene is transcribed in space and time is indicative of gene function and regulation. While transcriptome studies have provided a deep temporal analysis of gene expression during embryonic development most work has used pools of embryos. Therefore such analyses reflect transcription from the sum of all embryonic parts, subsequently masking the spatial regulation of gene expression. I will discuss a single cell transcript counting method that we have developed and how we are using this to address cellular heterogeneity during embryonic development with the aim of improving our understanding of gene function. Using decreasing amounts in input RNA from whole embryos to small pools of cells and ultimately single cells, we have identified >100 genes that have previously not been described to be spatially regulated during early stages of zebrafish gastrulation. Building on this topological map of spatially regulated genes, we have identified distinct populations of cells that exist in the zebrafish organiser. The experimental approach that I will describe will be applicable to many different biological scenarios.