Section on Eukaryotic Transposable Elements, Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA.
Genome Res. 2010 Feb;20(2):239-48. doi: 10.1101/gr.099648.109. Epub 2009 Dec 29.
The biological impact of transposons on the physiology of the host depends greatly on the frequency and position of integration. Previous studies of Tf1, a long terminal repeat retrotransposon in Schizosaccharomyces pombe, showed that integration occurs at the promoters of RNA polymerase II (Pol II) transcribed genes. To determine whether specific promoters are preferred targets of integration, we sequenced large numbers of insertions using high-throughput pyrosequencing. In four independent experiments we identified a total of 73,125 independent integration events. These data provided strong support for the conclusion that Pol II promoters are the targets of Tf1 integration. The size and number of the integration experiments resulted in reproducible measures of integration for each intergenic region and ORF in the S. pombe genome. The reproducibility of the integration activity from experiment to experiment demonstrates that we have saturated the full set of insertion sites that are actively targeted by Tf1. We found Tf1 integration was highly biased in favor of a specific set of Pol II promoters. The overwhelming majority (76%) of the insertions were distributed in intergenic sequences that contained 31% of the promoters of S. pombe. Interestingly, there was no correlation between the amount of integration at these promoters and their level of transcription. Instead, we found Tf1 had a strong preference for promoters that are induced by conditions of stress. This targeting of stress response genes coupled with the ability of Tf1 to regulate the expression of adjacent genes suggests Tf1 may improve the survival of S. pombe when cells are exposed to environmental stress.
转座子对宿主生理的生物学影响在很大程度上取决于整合的频率和位置。先前对 Schizosaccharomyces pombe 中的长末端重复逆转录转座子 Tf1 的研究表明，整合发生在 RNA 聚合酶 II（Pol II）转录的基因的启动子处。为了确定特定的启动子是否是整合的首选靶标，我们使用高通量焦磷酸测序对大量插入进行了测序。在四个独立的实验中，我们总共鉴定了 73,125 个独立的整合事件。这些数据有力地支持了 Pol II 启动子是 Tf1 整合的靶标的结论。整合实验的规模和数量为 S. pombe 基因组中的每个基因间区和 ORF 提供了可重复的整合测量值。实验之间整合活性的可重复性表明，我们已经饱和了 Tf1 主动靶向的所有插入位点。我们发现 Tf1 整合具有强烈的偏向性，有利于一组特定的 Pol II 启动子。绝大多数（76%）的插入分布在含有 S. pombe 启动子 31%的基因间序列中。有趣的是，这些启动子的整合量与其转录水平之间没有相关性。相反，我们发现 Tf1 对受应激条件诱导的启动子有强烈的偏好。这种对应激反应基因的靶向作用，加上 Tf1 调节相邻基因表达的能力，表明当细胞暴露于环境应激时，Tf1 可能会提高 S. pombe 的生存能力。
