Bright Ann Rose, Veenstra Gert Jan C
Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen 6500 HB, The Netherlands.
Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen 6500 HB, The Netherlands
Cold Spring Harb Protoc. 2019 Jan 2;2019(1):pdb.prot098327. doi: 10.1101/pdb.prot098327.
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 Tn-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 embryos.
真核生物基因组的DNA通过核小体包装成染色质。这不仅使DNA紧凑化，还在发育过程中的基因调控和细胞身份确立中发挥核心作用。由于这种包装，核质因子相对难以接近DNA；然而，启动子、增强子和绝缘子等调控元件在很大程度上保持无核小体状态。转座酶可及染色质分析（ATAC-seq）可用于识别“开放”染色质的基因组位置、DNA结合蛋白的足迹以及定位的核小体。因此，它是揭示染色质动态调控格局的有力工具。该方法利用了高活性原核Tn转座酶的作用，该酶优先切割可及染色质中的DNA并用测序接头标记这些位点。在此，我们描述一种用于胚胎的ATAC-seq方案。
