New molecular technique that enables the enrichment of uracil-containing DNA molecules during library preparation.. Uracil selection

Contamination with present-day human and microbial DNA is one of the major hindrances for large-scale genomic studies using ancient biological material. We describe a new molecular method, U selection, which exploits one of the most distinctive feature of ancient DNA, the presence of deoxyuracils, for selective enrichment of endogenous DNA against a complex background of contamination at the stage of DNA library preparation. By applying the method to Neanderthal DNA extracts that are heavily contaminated with present-day human DNA, we show that the amount of useful sequence information is increased approximately 10-fold and that the resulting sequences are more efficiently depleted of contaminants than by using purely computational approaches. Furthermore, we show that U selection can lead to a substantial increase in the proportion of endogenous DNA sequences relative to those of microbial contaminants.

使用古代生物材料开展大规模基因组研究时，现代人类与微生物DNA污染是主要阻碍因素之一。本文介绍一种新型分子方法——U选择法（U selection），该方法借助古代DNA最具标志性的特征之一——脱氧尿嘧啶（deoxyuracils）的存在，在DNA文库制备阶段针对复杂污染背景实现内源DNA的选择性富集。通过将该方法应用于被现代人类DNA严重污染的尼安德特人DNA提取物中，研究结果显示：有效序列信息总量提升约10倍，且相较于纯计算方法，所得序列的污染物去除效率更高。此外，本研究表明，U选择法可显著提升内源DNA序列相较于微生物污染序列的占比。