Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading
Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading
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DOI：
10.1101/gr.097873.109
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发表时间：
2010-02-01
期刊：
影响因子：
7
通讯作者：
MacAlpine, David M.
中科院分区：
文献类型：
--
作者：
MacAlpine, Heather K.;Gordan, Raluca;MacAlpine, David M.
起源识别复合物（origin recognition complex，ORC）是真核生物中一种重要的DNA复制起始因子。在酿酒酵母中，ORC与特定的DNA元件结合;然而，在高等真核生物中，ORC在体外或体内几乎没有序列特异性。我们研究了果蝇中ORC的全基因组分布，发现在没有任何可识别的简单基序的情况下，ORC定位于特定的染色体位置。虽然没有出现明确的序列基序，但我们能够使用机器学习方法仅基于一级序列准确区分ORC相关序列和ORC无关序列。定义ORC结合位点的复杂序列特征与核小体定位信号高度相关，并且可能代表ORC关联的优选核小体景观。开放染色质似乎是ORC结合的决定性基础特征。ORC相关序列富含组蛋白变体H3.3，通常在转录起始位点，并耗尽大量核小体。沿着染色体的ORC结合密度反映在序列复制的时间中，早期复制序列具有高密度的ORC结合。最后，我们发现ORC结合位点和粘附素加载位点之间的高度一致性，这表明，除了DNA复制之外，ORC可能是果蝇DNA上粘附素加载所必需的。
The origin recognition complex (ORC) is an essential DNA replication initiation factor conserved in all eukaryotes. In Saccharomyces cerevisiae, ORC binds to specific DNA elements; however, in higher eukaryotes, ORC exhibits little sequence specificity in vitro or in vivo. We investigated the genome-wide distribution of ORC in Drosophila and found that ORC localizes to specific chromosomal locations in the absence of any discernible simple motif. Although no clear sequence motif emerged, we were able to use machine learning approaches to accurately discriminate between ORC-associated sequences and ORC-free sequences based solely on primary sequence. The complex sequence features that define ORC binding sites are highly correlated with nucleosome positioning signals and likely represent a preferred nucleosomal landscape for ORC association. Open chromatin appears to be the underlying feature that is deterministic for ORC binding. ORC-associated sequences are enriched for the histone variant, H3.3, often at transcription start sites, and depleted for bulk nucleosomes. The density of ORC binding along the chromosome is reflected in the time at which a sequence replicates, with early replicating sequences having a high density of ORC binding. Finally, we found a high concordance between sites of ORC binding and cohesin loading, suggesting that, in addition to DNA replication, ORC may be required for the loading of cohesin on DNA in Drosophila.