Chatterjee Atreyi Ghatak, Esnault Caroline, Guo Yabin, Hung Stevephen, McQueen Philip G, Levin Henry L
Section on Eukaryotic Transposable Elements, Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
Mathematical & Statistical Computing Laboratory, Division of Computational, Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA.
Nucleic Acids Res. 2014 Jul;42(13):8449-60. doi: 10.1093/nar/gku534. Epub 2014 Jun 19.
Transposable elements (TE) have both negative and positive impact on the biology of their host. As a result, a balance is struck between the host and the TE that relies on directing integration to specific genome territories. The extraordinary capacity of DNA sequencing can create ultra dense maps of integration that are being used to study the mechanisms that position integration. Unfortunately, the great increase in the numbers of insertion sites detected comes with the cost of not knowing which positions are rare targets and which sustain high numbers of insertions. To address this problem we developed the serial number system, a TE tagging method that measures the frequency of integration at single nucleotide positions. We sequenced 1 million insertions of retrotransposon Tf1 in the genome of Schizosaccharomyces pombe and obtained the first profile of integration with frequencies for each individual position. Integration levels at individual nucleotides varied over two orders of magnitude and revealed that sequence recognition plays a key role in positioning integration. The serial number system is a general method that can be applied to determine precise integration maps for retroviruses and gene therapy vectors.
转座元件（TE）对其宿主的生物学特性既有负面影响，也有正面影响。因此，宿主与TE之间达成了一种平衡，这种平衡依赖于将整合引导至特定的基因组区域。DNA测序的非凡能力能够创建超密集的整合图谱，这些图谱正被用于研究定位整合的机制。不幸的是，检测到的插入位点数量大幅增加，但代价是不知道哪些位置是罕见靶点，哪些位置有大量插入。为了解决这个问题，我们开发了序列号系统，这是一种TE标记方法，可测量单核苷酸位置的整合频率。我们对粟酒裂殖酵母基因组中的100万个反转录转座子Tf1插入进行了测序，并获得了每个单独位置频率的首个整合图谱。各个核苷酸处的整合水平在两个数量级上有所不同，这表明序列识别在定位整合中起关键作用。序列号系统是一种通用方法，可用于确定逆转录病毒和基因治疗载体的精确整合图谱。
