Stewart-Morgan Kathleen R, Groth Anja
Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Methods Mol Biol. 2023;2611:71-84. doi: 10.1007/978-1-0716-2899-7_6.
Open or accessible chromatin typifies euchromatic regions and helps define cell type-specific transcription programs. DNA replication massively disorders chromatin composition and structure, and how accessible regions are affected by and recover from this disruption has been unclear. Here, we present repli-ATAC-seq, a protocol to profile accessible chromatin genome-wide on replicated DNA starting from 100,000 cells. In this method, replicated DNA is labeled with a short 5-ethynyl-2'-deoxyuridine (EdU) pulse in cultured cells and isolated from a population of tagmented fragments for amplification and next-generation sequencing. Repli-ATAC-seq provides high-resolution information on chromatin dynamics after DNA replication and reveals new insights into the interplay between DNA replication, transcription, and the chromatin landscape.
开放或可及的染色质是常染色质区域的典型特征，并有助于定义细胞类型特异性转录程序。DNA复制会严重扰乱染色质的组成和结构，而可及区域如何受到这种破坏的影响以及如何从这种破坏中恢复尚不清楚。在这里，我们展示了复制-ATAC-seq，这是一种从100,000个细胞开始在全基因组范围内对复制DNA上的可及染色质进行分析的方法。在这种方法中，复制的DNA在培养细胞中用短的5-乙炔基-2'-脱氧尿苷（EdU）脉冲进行标记，并从一群片段化的片段中分离出来用于扩增和下一代测序。复制-ATAC-seq提供了DNA复制后染色质动态变化的高分辨率信息，并揭示了DNA复制、转录和染色质景观之间相互作用的新见解。
