Spatial gradients of chromatin accessibility endow embryonic cells with positional information [CUT&RUN]

Embryonic patterning relies on the ability of cells to record and process spatial cues they receive from the environment. In vertebrates, this process is orchestrated by the activation of signal transduction patterns by secreted ligands, which provide cells with positional information. How embryonic progenitors encode these spatial values within their regulatory states has remained a central question in developmental biology. Here, we report that spatial gradients of chromatin activation impart cells with positional values during axial specification. By utilizing spatially-resolved genomic analysis, we identified a set of positional cis-regulatory elements (pCREs) that can predict the location of cells in the developing avian embryo. pCREs are located in the loci of spatially-restricted genes and display graded activation patterns along the embryonic axes. pCRE gradients are established in the early gastrula, and their patterns of accessibility are controlled by the signaling systems involved in axial specification. Our results support the existence of a Cartesian system of chromatin activation that ensures the spatial coordination of cell differentiation in vertebrate embryos. Overall design: Spatially-resolved transcriptomic and epigenomic analysis of early gastrula embryos