Spatially restricted bmp16 in an extra-embryonic syncytium promotes dorsoventral patterning

How nuclei within a shared cytoplasm organize gene expression programs to direct developmental signaling remains incompletely understood. Here, we combine single-nucleus RNA sequencing, spatial transcriptomic mapping, and functional perturbations to characterize the zebrafish yolk syncytial layer (YSL), an extra-embryonic syncytium that supports embryonic development and patterning. We identify extensive transcriptional covariation among YSL nuclei, revealing coordinated multigene programs organized along dorsoventral and animal-vegetal axes. Within the YSL, we identify an animal-ventral subdomain expressing several BMP ligand transcripts including bmp16, a member of the BMP2/4 subfamily. We found bmp16 expression to be exclusively extra-embryonic during gastrulation, and functional perturbations reveal that bmp16 is sufficient to ventralize embryos upon overexpression and acts synergistically with bmp2b to promote ventral fates. Ventral YSL expression of Bmp transcripts depends on a transcriptional program downstream of mxtx2 and is maintained independently of BMP pathway autoregulation, while negative regulation by hhex restricts bmp16 expression to the ventral YSL. Together, these findings establish the YSL as a spatially organized syncytium in which coordinated nuclear gene expression programs support localized sources of embryonic patterning signals.