Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.
Lillehei Heart Institute, University of Minnesota, 2231 6Th St SE, Minneapolis, MN, 55455, USA.
Genome Biol. 2023 May 22;24(1):125. doi: 10.1186/s13059-023-02954-5.
Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) reveals chromatin accessibility across the genome. Currently, no method specifically detects differential chromatin accessibility. Here, SeATAC uses a conditional variational autoencoder model to learn the latent representation of ATAC-seq V-plots and outperforms MACS2 and NucleoATAC on six separate tasks. Applying SeATAC to several pioneer factor-induced differentiation or reprogramming ATAC-seq datasets suggests that induction of these factors not only relaxes the closed chromatin but also decreases chromatin accessibility of 20% to 30% of their target sites. SeATAC is a novel tool to accurately reveal genomic regions with differential chromatin accessibility from ATAC-seq data.
转座酶可及染色质测序（ATAC-seq）分析揭示了整个基因组的染色质可及性。目前，尚无专门检测差异染色质可及性的方法。在这里，SeATAC 使用条件变分自动编码器模型来学习 ATAC-seq V 图的潜在表示，并且在六个独立任务上优于 MACS2 和 NucleoATAC。将 SeATAC 应用于几个先驱因子诱导的分化或重编程的 ATAC-seq 数据集表明，这些因子的诱导不仅使封闭的染色质松弛，而且还使 20%至 30%的靶位点的染色质可及性降低。SeATAC 是一种从 ATAC-seq 数据中准确揭示具有差异染色质可及性的基因组区域的新工具。
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