Abstract：
Enzymatic methyl-seq (EM-seq), an enzyme-based method, identifies genome-wide DNA methylation, which enables us to obtain reliable methylome data from purified genomic DNA by avoiding bisulfite-induced DNA damage. However, the loss of DNA during purification hinders the methylome analysis of limited samples. The crude DNA extraction method is the quickest and minimal sample loss approach for obtaining useable DNA without requiring additional dissolution and purification. However, it remains unclear whether crude DNA can be used directly for EM-seq library construction. In this study, we aimed to assess the quality of EM-seq libraries prepared directly using crude DNA. The crude DNA-derived libraries provided appropriate fragment sizes and concentrations for sequencing similar to those of the purified DNA-derived libraries. However, the sequencing results of crude samples exhibited lower reference sequence mapping efficiencies than those of the purified samples. Additionally, the lower-input crude DNA-derived sample exhibited a marginally lower cytosine-to-thymine conversion efficiency and hypermethylated pattern around gene regulatory elements than the higher-input crude DNA- or purified DNA-derived samples. In contrast, the methylation profiles of the crude and purified samples exhibited a significant correlation. Our findings indicate that crude DNA can be used as a raw material for EM-seq library construction.
摘要：
酶促甲基-seq（EM-seq），基于酶的方法，鉴定全基因组DNA甲基化，这使我们能够通过避免亚硫酸氢盐诱导的DNA损伤从纯化的基因组DNA获得可靠的甲基化组数据。然而,纯化过程中DNA的丢失阻碍了有限样品的甲基化分析。粗DNA提取方法是获得可用DNA而无需额外溶解和纯化的最快和最小样品损失的方法。然而,目前尚不清楚粗DNA是否可直接用于EM-seq文库构建。在这项研究中,我们旨在评估使用粗DNA直接制备的EM-seq文库的质量。粗DNA衍生文库提供了与纯化的DNA衍生文库相似的用于测序的适当片段大小和浓度。然而,粗样品的测序结果显示出比纯化样品更低的参考序列图像效率。此外,与较高输入的粗DNA或纯化的DNA来源样品相比，较低输入的粗DNA来源样品显示出稍微较低的胞嘧啶至胸腺嘧啶的转化效率和基因调控元件周围的高甲基化模式。相比之下,粗样品和纯化样品的甲基化谱表现出显著的相关性.我们的发现表明，粗DNA可以用作EM-seq文库构建的原料。
