Centro Andaluz de Biología del Desarrollo, CSIC/Universidad Pablo de Olavide, Sevilla, Spain.
Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy.
Methods Mol Biol. 2021;2219:253-265. doi: 10.1007/978-1-0716-0974-3_16.
Cis-regulatory elements (CREs) and transcription factors (TFs) associated with them determine temporal and spatial domains of gene expression. Therefore, identification of these CREs and TFs is crucial to elucidating transcriptional programs across taxa. With chromatin accessibility facilitating transcription factor access to DNA, the identification of regions of open chromatin sheds light both on the function of the regulatory elements and their evolution, thus allowing the recognition of potential CREs. Buenrostro and colleagues have developed a novel method for exploring chromatin accessibility: assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), which can be used for the purpose of identifying putative CREs. This method was shown to have considerable advantages when compared to traditional methods such as sequence conservation analyses or functional assays. Here we present the adaptation of the ATAC-seq method to echinoderm species and discuss how it can be used for CRE discovery.
顺式调控元件 (CREs) 和与之相关的转录因子 (TFs) 决定了基因表达的时空域。因此，鉴定这些 CREs 和 TFs 对于阐明跨类群的转录程序至关重要。由于染色质可及性促进转录因子与 DNA 的相互作用，因此开放染色质区域的鉴定不仅揭示了调控元件的功能及其进化，还允许识别潜在的 CREs。Buenrostro 及其同事开发了一种探索染色质可及性的新方法：高吞吐量测序的转座酶可及染色质分析 (ATAC-seq)，可用于识别潜在的 CREs。与传统方法（如序列保守性分析或功能测定）相比，该方法具有相当大的优势。本文介绍了将 ATAC-seq 方法应用于棘皮动物物种的方法，并讨论了其在 CRE 发现中的应用。
