Assay for Transposase-Accessible Chromatin-Sequencing Using Xenopus Embryos

The DNA of eukaryotic genomes is packaged into chromatin by nucleosomes. This not only compacts the DNA but also plays a central role in gene regulation and establishment of cellular identity during development. Because of this packaging, the DNA is relatively inaccessible to nucleoplasmic factors; however, regulatory elements such as promoters, enhancers, and insulators are largely kept nucleosome-free. The assay for transposase-accessible chromatin (ATAC-seq) can be used to identify genomic locations of “open” chromatin, footprints of DNA-binding proteins, and positioned nucleosomes. It therefore is a powerful tool for unraveling the dynamic regulatory landscape of chromatin. The method exploits the action of hyperactive prokaryotic Tn5-transposase, which preferentially cuts DNA in accessible chromatin and tags the sites with sequencing adaptors. Here we describe an ATAC-seq protocol for use with Xenopus tropicalis embryos.