DNA sequencing is the current key technology for historic or ancient biological samples and has led to many exciting discoveries in the field of paleogenomics. However, functional insights into tissue identity, cellular composition or gene regulation cannot be gained from DNA. Recent analyses have shown that, under favorable conditions, RNA can also be sequenced from ancient samples, enabling studies at the transcriptomic and regulatory level. Analyzing ancient RNA data from a Pleistocene canid, we find hundreds of intact microRNAs that are taxonomically informative, show tissue-specificity and have functionally predictive characteristics. With an extraordinary age of 14,300 years, these microRNA sequences are by far the oldest ever reported. The authenticity of the sequences is further supported by a) the presence of canid / Caniformia-specific sequences that never evolved outside of this clade, b) tissue-specific expression patterns (cartilage, liver and muscle) that resemble those of modern dogs and c) RNA damage patterns that are clearly distinct from those of fresh samples. By performing computational microRNA-target enrichment analyses on the ancient sequences, we predict microRNA functions consistent with their tissue pattern of expression. For instance, we find a liver-specific microRNA that regulates carbohydrate metabolism and starvation responses in canids. In summary, we show that straightforward paleotranscriptomic microRNA analyses can give functional glimpses into tissue identity, cellular composition and gene regulatory activity of ancient samples and biological processes that took place in the Pleistocene, thus holding great promise for deeper insights into gene regulation in extinct animals based on ancient RNA sequencing. .

中文翻译：

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14,300 年前犬科动物样本的古代 microRNA 图谱证实了分类学起源，并让我们了解更新世的组织特异性基因调控


DNA测序是当前历史或古代生物样本的关键技术，并在古基因组学领域带来了许多令人兴奋的发现。然而，无法从 DNA 中获得对组织身份、细胞组成或基因调控的功能见解。最近的分析表明，在有利的条件下，也可以从古代样本中对 RNA 进行测序，从而实现转录组和调控水平的研究。通过分析更新世犬科动物的古代 RNA 数据，我们发现了数百个完整的 microRNA，它们具有分类学信息、显示组织特异性并具有功能预测特征。这些 microRNA 序列拥有 14,300 年的非凡历史，是迄今为止报道过的最古老的序列。序列的真实性得到进一步支持：a) 犬科动物/犬科动物特异性序列的存在，这些序列从未在该分支之外进化出来；b) 类似于现代狗的组织特异性表达模式（软骨、肝脏和肌肉）；c) ) RNA 损伤模式与新鲜样本明显不同。通过对古代序列进行计算 microRNA 靶标富集分析，我们预测 microRNA 功能与其组织表达模式一致。例如，我们发现了一种肝脏特异性的 microRNA，可以调节犬科动物的碳水化合物代谢和饥饿反应。总之，我们表明，简单的古转录组 microRNA 分析可以对古代样本的组织身份、细胞组成和基因调控活性以及更新世发生的生物过程提供功能性了解，从而为更深入地了解灭绝动物的基因调控带来巨大希望。基于古代RNA测序。 。