Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
Methods Mol Biol. 2022;2450:549-561. doi: 10.1007/978-1-0716-2172-1_29.
Dynamic gene expression seen during whole-body regeneration is likely controlled by genomic regulatory elements that dictate the spatiotemporal activity of the regeneration transcriptome. Identifying and characterizing these non-coding regulatory sequences are key to understanding how genes are connected into networks to deploy the process of whole-body regeneration. Here, we describe the application of the Assay for Transposase Accessible Chromatin (ATAC-seq) in the acoel Hofstenia miamia to identify regions of open chromatin that represent putative regulatory elements. Notably, when paired with gene knockdown techniques such as RNAi, ATAC-seq can be implemented in a functional genomics approach to validate putative regulatory elements. ATAC-seq requires no species-specific reagents, is amenable to small input cell numbers, and can be completed in a single day, making it an ideal assay to identify dynamic chromatin at high resolution during whole-body regeneration in virtually any species with a quality genome assembly.
在整体再生过程中观察到的动态基因表达可能受基因组调控元件控制，这些元件决定了再生转录组的时空活性。鉴定和描述这些非编码调控序列是理解基因如何连接成网络以实现整体再生过程的关键。在这里，我们描述了转座酶可及染色质分析（ATAC-seq）在无腔动物 Hofstenia miamia 中的应用，以鉴定代表潜在调控元件的开放染色质区域。值得注意的是，当与 RNAi 等基因敲低技术结合使用时，ATAC-seq 可以在功能基因组学方法中实施，以验证潜在的调控元件。ATAC-seq 不需要物种特异性试剂，适用于少量输入细胞数量，并且可以在一天内完成，使其成为在具有高质量基因组组装的几乎任何物种中鉴定整体再生过程中高分辨率动态染色质的理想检测方法。
