Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features
Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features
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DOI：
10.1101/gr.121830.111
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发表时间：
2011-09-01
期刊：
影响因子：
7
通讯作者：
Mechali, Marcel
中科院分区：
文献类型：
--
作者：
Cayrou, Christelle;Coulombe, Philippe;Mechali, Marcel
在后生动物中，成千上万的DNA复制起点（Oris）在每个细胞周期被激活。它们的基因组结构和遗传性质仍然难以捉摸。在这里，我们通过新生链（NS）纯化和果蝇和小鼠细胞的全基因组分析来表征Oris。我们发现，在这两个物种中，大多数CpG岛（CGI）含有Oris，虽然甲基化几乎是不存在的果蝇，表明这种表观遗传标记是不是至关重要的定义激活的起源。DNA合成的起始起始于CGI的边界，导致NS的显著双峰分布，提示双重起始事件。Oris在NS峰周围含有独特的核苷酸偏斜，其特征在于分别在Oris位点的5'和3'处的G/T和C/A过表达。重复的GC丰富的元素被检测到，这是很好的预测Oris，这表明共同的序列特征是后生动物Oris的一部分。在果蝇4号异染色质染色体上，Oris与HP 1结合位点相关。在染色体水平上，富含Oris的区域是早期复制，而缺乏Oris的区域是晚期复制。全基因组分析与DNA梳理分析相结合，揭开了Oris的组织结构。结果显示，Oris腕表的使用量是过剩的，但它们的激活并非随机发生。它们被组织成位点特异性但灵活的起源的组，这些起源定义了复制子，其中在每个复制子中激活单个起源。这种组织在每个复制子中提供了位点特异性和Ori发射灵活性，允许对环境线索和细胞命运的可能适应。
In metazoans, thousands of DNA replication origins (Oris) are activated at each cell cycle. Their genomic organization and their genetic nature remain elusive. Here, we characterized Oris by nascent strand (NS) purification and a genome-wide analysis in Drosophila and mouse cells. We show that in both species most CpG islands (CGI) contain Oris, although methylation is nearly absent in Drosophila, indicating that this epigenetic mark is not crucial for defining the activated origin. Initiation of DNA synthesis starts at the borders of CGI, resulting in a striking bimodal distribution of NS, suggestive of a dual initiation event. Oris contain a unique nucleotide skew around NS peaks, characterized by G/T and C/A over-representation at the 5' and 3' of Ori sites, respectively. Repeated GC-rich elements were detected, which are good predictors of Oris, suggesting that common sequence features are part of metazoan Oris. In the heterochromatic chromosome 4 of Drosophila, Oris correlated with HP1 binding sites. At the chromosome level, regions rich in Oris are early replicating, whereas Ori-poor regions are late replicating. The genome-wide analysis was coupled with a DNA combing analysis to unravel the organization of Oris. The results indicate that Oris are in a large excess, but their activation does not occur at random. They are organized in groups of site-specific but flexible origins that define replicons, where a single origin is activated in each replicon. This organization provides both site specificity and Ori firing flexibility in each replicon, allowing possible adaptation to environmental cues and cell fates.