University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA.
J Virol. 2011 Jul;85(14):7393-401. doi: 10.1128/JVI.00635-11. Epub 2011 May 11.
Some of the earliest studies of retroviral integration targeting reported that sites of gammaretroviral DNA integration were positively correlated with DNase I-hypersensitive sites in chromatin. This led to the suggestion that open chromatin was favorable for integration. More recent deep sequencing experiments confirmed that gammaretroviral integration sites and DNase I cleavage sites are associated in genome-wide surveys. Paradoxically, in vitro studies of integration show that nucleosomal DNA is actually favored over naked DNA, raising the question of whether integration target DNA in chromosomes is wrapped in nucleosomes or nucleosome free. In this study we examined gammaretroviral integration by infecting primary human CD4(+) T lymphocytes with a murine leukemia virus (MLV)-based retroviral vector or xenotropic murine leukemia virus-related virus (XMRV), and isolated 32,585 unique integration sites using ligation-mediated PCR and 454 pyrosequencing. CD4(+) T lymphocytes were chosen for study because of the particularly dense genome-wide mapping of chromatin features available for comparison. Analysis relative to predicted nucleosome positions showed that gammaretroviruses direct integration into outward-facing major grooves on nucleosome-wrapped DNA, similar to the integration pattern of HIV. Also, a suite of histone modifications correlated with gene activity are positively associated with integration by both MLV and XMRV. Thus, we conclude that favored integration near DNase I-hypersensitive sites does not imply that integration takes place exclusively in nucleosome-free regions.
一些最早的关于逆转录病毒整合靶向的研究报告指出，γ逆转录病毒 DNA 整合的位点与染色质中 DNA 酶 I 超敏位点呈正相关。这导致了这样的假设：开放染色质有利于整合。最近的深度测序实验证实，γ逆转录病毒整合位点和 DNA 酶 I 切割位点在全基因组调查中是相关的。矛盾的是，整合的体外研究表明，核小体 DNA 实际上比裸露 DNA 更受青睐，这就提出了一个问题，即在染色体上的整合靶 DNA 是否被包装在核小体中或无核小体。在这项研究中，我们通过用基于鼠白血病病毒 (MLV)的逆转录病毒载体或嗜性鼠白血病病毒相关病毒 (XMRV)感染原代人 CD4(+)T 淋巴细胞来检查 γ逆转录病毒的整合，并使用连接介导的 PCR 和 454 焦磷酸测序分离了 32585 个独特的整合位点。选择 CD4(+)T 淋巴细胞进行研究是因为有特别密集的染色质特征的全基因组图谱可供比较。相对于预测的核小体位置的分析表明，γ逆转录病毒将整合导向核小体包裹的 DNA 上向外的主沟，类似于 HIV 的整合模式。此外，一套与基因活性相关的组蛋白修饰与 MLV 和 XMRV 的整合呈正相关。因此，我们得出结论，在 DNA 酶 I 超敏位点附近的有利整合并不意味着整合仅发生在无核小体区域。
