Spatial patterning of the epigenome during vertebrate gastrulation

Abstract

SummaryEmbryonic patterning relies on the ability of cells to interpret the spatial information they receive from the environment. In vertebrates, this process begins with the localized activation of signaling systems that mediate axial specification. How embryonic cells record these spatial coordinates within their regulatory states has remained unclear. Here, we report that positional information is encoded within the chromatin landscape of embryonic cells. By utilizing spatially resolved genomic analysis in the avian gastrula, we found that the epigenome is organized in gradients of accessibility along the embryonic axes. Positional gradients of chromatin activation are established at thelociof developmental genes at the onset of gastrulation and can be used to predict the location of cells in amniote embryos. Our results show that axial specification involves the spatial patterning of the epigenome and support the existence of a Cartesian system of chromatin activation in the developing embryo.