Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival
Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival
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来自晚更新世永久冻土层和历史犬科动物的古老 RNA 显示组织特异性转录组存活
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发表时间：
2019
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通讯作者：
M. Gilbert
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作者：
Oliver Smith;G. Dunshea;Mikkel;Sergey Fedorov;M. Germonpré;H. Bocherens;M. Gilbert
虽然从考古材料中测序古代DNA现在很常见，但很少有人尝试对古代转录组进行测序，即使是从典型的稳定沉积环境（如永久冻土）中。这大概是由于假设RNA完全降解相对较快，特别是当处理自溶，核酸酶丰富的哺乳动物组织。然而，考虑到最近对包括植物和动物在内的各种来源的古代RNA（aRNA）进行测序的成功，我们怀疑这些假设可能是不正确或夸大的。为了挑战潜在的教条，我们从通常可能被排除在此类研究之外的来源中生成了鸟枪RNA数据。在这里，我们提出了从两个历史狼皮，和永冻保存的肝脏组织的14,300年前的更新世犬科动物产生的aRNA数据。后者不仅是有史以来被测序的最古老的RNA，而且还显示出生物学相关的组织特异性和与来自现代对照组织的等同数据的密切相似性的证据。RNA-seq数据的其他标志，如外显子-外显子连接的存在和高内源性核糖体RNA含量，证实了我们数据的真实性。通过使用两个高通量测序平台进行独立的技术重复，我们不仅表明aRNA可以在哺乳动物组织中存活很长时间，而且还表明它具有组织鉴定的潜力，并且可能进一步使用，例如使用这种技术进行测序时的体内基因组活性和适应性。
While sequencing ancient DNA from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but also shows evidence of biologically relevant tissue-specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA-seq data such as exon-exon junction presence and high endogenous ribosomal RNA content confirms our data’s authenticity. By performing independent technical replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues, but also that it has potential for tissue identification, and possibly further uses such as in vivo genome activity and adaptation, when sequenced using this technology.