Barr Stephen D, Leipzig Jeremy, Shinn Paul, Ecker Joe R, Bushman Frederic D
University of Pennsylvania School of Medicine, Department of Microbiology, 3610 Hamilton Walk, Philadelphia, PA 19104-6076, USA.
J Virol. 2005 Sep;79(18):12035-44. doi: 10.1128/JVI.79.18.12035-12044.2005.
We have analyzed the placement of sites of integration of avian sarcoma-leukosis virus (ASLV) and human immunodeficiency virus (HIV) DNA in the draft chicken genome sequence, with the goals of assessing species-specific effects on integration and allowing comparison to the distribution of chicken endogenous retroviruses (ERVs). We infected chicken embryo fibroblasts (CEF) with ASLV or HIV and sequenced 863 junctions between host and viral DNA. The relationship with cellular gene activity was analyzed by transcriptional profiling of uninfected or ASLV-infected CEF cells. ASLV weakly favored integration in active transcription units (TUs), and HIV strongly favored active TUs, trends seen previously for integration in human cells. The ERVs, in contrast, accumulated mostly outside TUs, including ERVs related to ASLV. The minority of ERVs present within TUs were mainly in the antisense orientation; consequently, the viral splicing and polyadenylation signals would not disrupt cellular mRNA synthesis. In contrast, de novo ASLV integration sites within TUs showed no orientation bias. Comparing the distribution of de novo ASLV integration sites to ERVs indicated that purifying selection against gene disruption, and not initial integration targeting, probably determined the ERV distribution. Further analysis indicated that ERVs in humans, mice, and rats showed similar distributions, suggesting purifying selection dictated their distributions as well.
我们分析了禽肉瘤-白血病病毒（ASLV）和人类免疫缺陷病毒（HIV）DNA在鸡基因组序列草图中的整合位点，目的是评估物种特异性对整合的影响，并与鸡内源性逆转录病毒（ERV）的分布进行比较。我们用ASLV或HIV感染鸡胚成纤维细胞（CEF），并对宿主与病毒DNA之间的863个连接点进行了测序。通过对未感染或ASLV感染的CEF细胞进行转录谱分析，分析了其与细胞基因活性的关系。ASLV在活跃转录单元（TU）中整合的倾向较弱，而HIV则强烈倾向于活跃的TU，这与之前在人类细胞中观察到的整合趋势一致。相比之下，ERV大多聚集在TU之外，包括与ASLV相关的ERV。少数存在于TU内的ERV主要呈反义方向；因此，病毒剪接和聚腺苷酸化信号不会破坏细胞mRNA的合成。相比之下，TU内的新生ASLV整合位点没有方向偏好。将新生ASLV整合位点的分布与ERV进行比较表明，针对基因破坏的纯化选择而非初始整合靶向，可能决定了ERV的分布。进一步分析表明，人类、小鼠和大鼠中的ERV表现出相似的分布，这表明纯化选择也决定了它们的分布。
