Given the technical limitations associated with studying fossil DNA, paleogenomics has mainly focused on annotating genomes from ancient species. Sandoval-Velasco et al. introduced PaleoHi-C, a modified method from Hi-C to assess chromosome organization from dehydrated material. PaleoHi-C was performed on a 52,000-year-old permafrost-preserved woolly mammoth skin sample. After constructing a reference-assisted assembly of the woolly mammoth genome based on their most closely related living species, the authors observed the typical chromosome architecture visible in Hi-C data from modern samples. These features include the presence of chromosome territories, Barr bodies, chromatin compartments, domains and loops. Compartmentalization showed cell-type-specific patterns when compared to a catalog of tissue types in Asian elephants, but also displayed species-specific differences, such as an A–B compartment switch of several genes involved in skin function. These observations stem from the preserved glass-like state of ancient chromatin, characterized by the minimal diffusion of molecules within dehydrated specimens. In conclusion, it is not surprising that woolly mammoths displayed chromosomal organization similar to existing mammals, but what is remarkable is that these features have endured for tens of thousands of years in permafrost. It will be exciting to profile well-preserved samples of other extinct species using PaleoHi-C.

Original reference: Cell 187, 3541–3562.e51 (2024)

鉴于研究化石 DNA 相关的技术限制，古基因组学主要集中于注释古代物种的基因组。桑多瓦尔-贝拉斯科等人。推出了 PaleoHi-C，这是 Hi-C 的改进方法，用于评估脱水材料的染色体组织。 PaleoHi-C 对具有 52,000 年历史的永久冻土保存的猛犸象皮肤样本进行了研究。在基于最密切相关的现存物种构建了猛犸象基因组的参考辅助组装后，作者观察到了现代样本 Hi-C 数据中可见的典型染色体结构。这些特征包括染色体区域、巴尔体、染色质区室、结构域和环的存在。与亚洲象的组织类型目录相比，区室化显示出细胞类型特异性模式，但也显示出物种特异性差异，例如涉及皮肤功能的几个基因的 A-B 区室转换。这些观察结果源于古代染色质保存的玻璃状状态，其特征是脱水样本中分子的扩散最小。总之，猛犸象表现出与现有哺乳动物相似的染色体组织并不奇怪，但值得注意的是这些特征在永久冻土中持续了数万年。使用 PaleoHi-C 来分析保存完好的其他灭绝物种的样本将是令人兴奋的。

原始参考文献： Cell 187，3541–3562.e51 (2024)