Identification of direct transcriptional targets of BMP signaling during zebrafish dorsal-ventral axial patterning

To determine the mechanism of BMP morphogen interpretation in the zebrafish gastrula, we identified genes that are dependent on BMP signaling for their expression, as well as the genes directly regulated by BMP signaling using RNA-sequencing. Overall design: BMP-dependent genes were identified by comparing transcript levels in wild-type and bmp7-/- mutant embryos at 6 and 8 hours post fertillization (hpf) using RNA-sequencing. Two biological replicates of 40 embryos each were analyzed per condition. Direct targets of BMP signaling were identified by comparing transcript levels by RNA-sequencing of bmp7-/- embryos treated with cycloheximide at 4 hpf and bmp7-/- embryos treated with cycloheximide and injected with 10 pg BMP2/7 protein at 4 hpf. Three biological replicates of 50 embryos each were analyzed per condition.