TIGER: inferring DNA replication timing from whole-genome sequence data
TIGER: inferring DNA replication timing from whole-genome sequence data
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DOI：
10.1093/bioinformatics/btab166
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发表时间：
2021-10-26
期刊：
影响因子：
5.8
通讯作者：
Robinson, Peter
中科院分区：
文献类型：
--
作者：
Koren, Amnon;Massey, Dashiell J.;Robinson, Peter
动机：基因组DNA复制根据一个可重复的时空程序，与一些位点复制早在S期，而其他复制晚。尽管是一个中央的细胞过程中，DNA复制时间的研究已被限制在规模上，由于technical challenges.Results：我们提出TIGER（定时推断基因组复制），计算方法提取DNA复制时间信息从全基因组序列数据从增殖细胞样品。生物样本中复制细胞的存在导致基因组DNA的不均匀表示，这取决于不同基因组基因座的复制时机。因此，通过分析沿着染色体的DNA拷贝数，同时考虑序列覆盖变化的其他来源，可以在基因组序列数据中观察到复制动态。TIGER适用于任何具有连续基因组组装的物种，并可与DNA复制时间的实验测量质量相媲美。它提供了一个简单的方法来衡量复制的时间，可以很容易地应用于规模。
Motivation: Genomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges.Results: We present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale.