Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.
Genome Res. 2011 Feb;21(2):164-74. doi: 10.1101/gr.116038.110. Epub 2010 Dec 22.
DNA replication initiates from thousands of start sites throughout the Drosophila genome and must be coordinated with other ongoing nuclear processes such as transcription to ensure genetic and epigenetic inheritance. Considerable progress has been made toward understanding how chromatin modifications regulate the transcription program; in contrast, we know relatively little about the role of the chromatin landscape in defining how start sites of DNA replication are selected and regulated. Here, we describe the Drosophila replication program in the context of the chromatin and transcription landscape for multiple cell lines using data generated by the modENCODE consortium. We find that while the cell lines exhibit similar replication programs, there are numerous cell line-specific differences that correlate with changes in the chromatin architecture. We identify chromatin features that are associated with replication timing, early origin usage, and ORC binding. Primary sequence, activating chromatin marks, and DNA-binding proteins (including chromatin remodelers) contribute in an additive manner to specify ORC-binding sites. We also generate accurate and predictive models from the chromatin data to describe origin usage and strength between cell lines. Multiple activating chromatin modifications contribute to the function and relative strength of replication origins, suggesting that the chromatin environment does not regulate origins of replication as a simple binary switch, but rather acts as a tunable rheostat to regulate replication initiation events.
DNA 复制从果蝇基因组中的数千个起始位点开始，必须与其他正在进行的核过程（如转录）相协调，以确保遗传和表观遗传的遗传。在理解染色质修饰如何调节转录程序方面已经取得了相当大的进展；相比之下，我们对染色质景观在确定 DNA 复制起始位点如何被选择和调节方面的作用知之甚少。在这里，我们使用 modENCODE 联盟生成的数据，描述了多个细胞系中染色质和转录景观背景下的果蝇复制程序。我们发现，虽然细胞系表现出相似的复制程序，但存在许多细胞系特异性差异，这些差异与染色质结构的变化相关。我们确定了与复制时间、早期起始使用和 ORC 结合相关的染色质特征。主要序列、激活的染色质标记和 DNA 结合蛋白（包括染色质重塑因子）以累加的方式特异性指定 ORC 结合位点。我们还从染色质数据生成准确和可预测的模型来描述细胞系之间的起始使用和强度。多种激活的染色质修饰有助于复制起始点的功能和相对强度，这表明染色质环境不会像简单的二进制开关那样调节复制起始点，而是作为一个可调的变阻器来调节复制起始事件。
