PDF(Pubmed)
Abstract：
Based on experimentally determined average inter-origin distances of ~100 kb, DNA replication initiates from ~50,000 origins on human chromosomes in each cell cycle. The origins are believed to be specified by binding of factors like the origin recognition complex (ORC) or CTCF or other features like G-quadruplexes. We have performed an integrative analysis of 113 genome-wide human origin profiles (from five different techniques) and five ORC-binding profiles to critically evaluate whether the most reproducible origins are specified by these features. Out of ~7.5 million union origins identified by all datasets, only 0.27% (20,250 shared origins) were reproducibly obtained in at least 20 independent SNS-seq datasets and contained in initiation zones identified by each of three other techniques, suggesting extensive variability in origin usage and identification. Also, 21% of the shared origins overlap with transcriptional promoters, posing a conundrum. Although the shared origins overlap more than union origins with constitutive CTCF-binding sites, G-quadruplex sites, and activating histone marks, these overlaps are comparable or less than that of known transcription start sites, so that these features could be enriched in origins because of the overlap of origins with epigenetically open, promoter-like sequences. Only 6.4% of the 20,250 shared origins were within 1 kb from any of the ~13,000 reproducible ORC-binding sites in human cancer cells, and only 4.5% were within 1 kb of the ~11,000 union MCM2-7-binding sites in contrast to the nearly 100% overlap in the two comparisons in the yeast, Saccharomyces cerevisiae. Thus, in human cancer cell lines, replication origins appear to be specified by highly variable stochastic events dependent on the high epigenetic accessibility around promoters, without extensive overlap between the most reproducible origins and currently known ORC- or MCM-binding sites.
摘要：
根据实验确定的平均原点间距离〜100kb，在每个细胞周期中，DNA复制从人类染色体上的约50,000个起点开始。认为起源是通过结合因子如起源识别复合物(ORC)或CTCF或其他特征如G-四链体来指定的。我们已经对113个基因组范围的人类起源谱（来自五种不同的技术）和五个ORC结合谱进行了综合分析，以严格评估这些特征是否指定了最可重复的起源。在所有数据集确定的约750万个工会起源中，在至少20个独立的SNS-seq数据集中，只有0.27%（20,250个共享来源）可重复获得，并包含在其他三种技术中的每一种识别的起始区域中，表明原产地使用和识别的广泛差异。此外，21%的共同起源与转录启动子重叠，摆出一个难题。尽管共享起源与组成型CTCF结合位点的联合起源重叠更多，G-四链体位点,激活组蛋白标记，这些重叠与已知的转录起始位点相当或更小，所以这些特征可以丰富起源，因为起源与表观遗传开放的重叠，启动子样序列。在20,250个共享起源中，只有6.4％来自人类癌细胞中〜13,000个可复制的ORC结合位点中的任何一个，在1kb内。只有4.5%在1kb的〜11,000个结合MCM2-7结合位点内，与酵母中两个比较中接近100%的重叠相反，酿酒酵母。因此，在人类癌细胞系中，复制起点似乎是由高度可变的随机事件指定的，依赖于启动子周围的高表观遗传可达性，在最可重复的起源和目前已知的ORC或MCM结合位点之间没有广泛的重叠。
