Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA.
Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
STAR Protoc. 2022 Mar 15;3(2):101240. doi: 10.1016/j.xpro.2022.101240. eCollection 2022 Jun 17.
Identifying germline differentially methylated regions (DMRs) in outbred mammals remains a challenge because of difficulty in obtaining single-nucleotide polymorphisms (SNPs). To overcome this difficulty, we developed two computational approaches, TARSII and CARSII, which allow accurate prediction of germline DMRs from DNA methylomes independent of SNPs. Furthermore, we introduce an easy and quick way to validate the predicted germline DMRs with allelic DNA methylation using CGmapTools. Collectively, our strategy can greatly facilitate identification of germline DMRs in outbred mammals. For complete details on the use and execution of this protocol, please refer to Chu et al. (2021).
鉴定杂种哺乳动物的种系差异甲基化区域（DMRs）仍然是一个挑战，因为很难获得单核苷酸多态性（SNPs）。为了克服这一困难，我们开发了两种计算方法，TARSII 和 CARSII，它们允许在不依赖 SNPs 的情况下，从 DNA 甲基组中准确预测种系 DMRs。此外，我们引入了一种简单快捷的方法，使用 CGmapTools 用等位基因 DNA 甲基化来验证预测的种系 DMRs。总的来说，我们的策略可以极大地促进杂种哺乳动物中种系 DMRs 的鉴定。有关此方案的使用和执行的完整详细信息，请参阅 Chu 等人（2021 年）。
