Wang Gary P, Ciuffi Angela, Leipzig Jeremy, Berry Charles C, Bushman Frederic D
University of Pennsylvania, School of Medicine, Department of Microbiology, Philadelphia, PA 19104-6076, USA.
Genome Res. 2007 Aug;17(8):1186-94. doi: 10.1101/gr.6286907. Epub 2007 Jun 1.
Integration of retroviral DNA into host cell DNA is a defining feature of retroviral replication. HIV integration is known to be favored in active transcription units, which promotes efficient transcription of the viral genes, but the molecular mechanisms responsible for targeting are not fully clarified. Here we used pyrosequencing to map 40,569 unique sites of HIV integration. Computational prediction of nucleosome positions in target DNA indicated that integration sites are periodically distributed on the nucleosome surface, consistent with favored integration into outward-facing DNA major grooves in chromatin. Analysis of integration site positions in the densely annotated ENCODE regions revealed a wealth of new associations between integration frequency and genomic features. Integration was particularly favored near transcription-associated histone modifications, including H3 acetylation, H4 acetylation, and H3 K4 methylation, but was disfavored in regions rich in transcription-inhibiting modifications, which include H3 K27 trimethylation and DNA CpG methylation. Statistical modeling indicated that effects of histone modification on HIV integration were partially independent of other genomic features influencing integration. The pyrosequencing and bioinformatic methods described here should be useful for investigating many aspects of retroviral DNA integration.
逆转录病毒DNA整合到宿主细胞DNA中是逆转录病毒复制的一个决定性特征。已知HIV整合在活跃转录单元中较为常见，这促进了病毒基因的高效转录，但负责靶向的分子机制尚未完全阐明。在这里，我们使用焦磷酸测序法绘制了40,569个HIV整合的独特位点。对靶DNA中核小体位置的计算预测表明，整合位点在核小体表面呈周期性分布，这与整合到染色质中向外的DNA大沟中较为常见的情况一致。对注释密集的ENCODE区域中整合位点位置的分析揭示了整合频率与基因组特征之间大量新的关联。整合在与转录相关的组蛋白修饰（包括H3乙酰化, H4乙酰化和H3 K4甲基化）附近尤为常见，但在富含转录抑制修饰（包括H3 K27三甲基化和DNA CpG甲基化）的区域中则不常见。统计模型表明，组蛋白修饰对HIV整合的影响部分独立于影响整合的其他基因组特征。本文所述的焦磷酸测序和生物信息学方法应有助于研究逆转录病毒DNA整合的许多方面。
