Assay for transposase-accessible chromatin with high-throughput sequencing 
(ATAC-seq) is a useful method to map genome-wide chromatin accessibility and 
nucleosome positioning. Genome-wide sequencing is performed utilizing adapter 
sequences inserted by a prokaryotic transposase, Tn5, into the accessible 
regions of chromatin. Here we describe the use of ATAC-seq in the zebrafish 
embryo and thereby the applicability of this approach in whole vertebrate 
embryos.