We used DNase-seq and ATAC-seq to identify a set of putative CRMs regulating skeletogenic gene expression during sea urchin embryogenesis. These CRMs, identified by differential chromatin accessibility, are likely to be regulated by two upstream TFs, Alx1 and Ets1, that are part of the skeletogenic GRN. 9/31 od these identified CRMs were validated by reporter gene assay. Our work demonstrates the value of using differential chromatin accessibility for the high-throughput identification of CRMs in embryonic tissues. Overall design: DNase-seq performed on U0126-treated PMC(-) S. purpuratus embryos at 28 hpf and control whole embryos at 28 hpf. There are 2 samples and 3 replicates for each sample. ATAC-seq was performed on isolated PMCs at 24 hpf and other non-PMC cells of the embryo at 24 hpf. There were 2 samples and 2 replicates per sample.