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Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome.
Mobile DNA ( IF 4.7 ) Pub Date : 2019-03-08 , DOI: 10.1186/s13100-019-0148-5
Jared P Steranka 1, 2 , Zuojian Tang 3, 4 , Mark Grivainis 3, 4 , Cheng Ran Lisa Huang 2 , Lindsay M Payer 1 , Fernanda O R Rego 5 , Thiago Luiz Araujo Miller 5, 6 , Pedro A F Galante 5 , Sitharam Ramaswami 7 , Adriana Heguy 7 , David Fenyö 3, 4 , Jef D Boeke 4 , Kathleen H Burns 1, 2
Affiliation  

BACKGROUND Transposable elements make up a significant portion of the human genome. Accurately locating these mobile DNAs is vital to understand their role as a source of structural variation and somatic mutation. To this end, laboratories have developed strategies to selectively amplify or otherwise enrich transposable element insertion sites in genomic DNA. RESULTS Here we describe a technique, Transposon Insertion Profiling by sequencing (TIPseq), to map Long INterspersed Element 1 (LINE-1, L1) retrotransposon insertions in the human genome. This method uses vectorette PCR to amplify species-specific L1 (L1PA1) insertion sites followed by paired-end Illumina sequencing. In addition to providing a step-by-step molecular biology protocol, we offer users a guide to our pipeline for data analysis, TIPseqHunter. Our recent studies in pancreatic and ovarian cancer demonstrate the ability of TIPseq to identify invariant (fixed), polymorphic (inherited variants), as well as somatically-acquired L1 insertions that distinguish cancer genomes from a patient's constitutional make-up. CONCLUSIONS TIPseq provides an approach for amplifying evolutionarily young, active transposable element insertion sites from genomic DNA. Our rationale and variations on this protocol may be useful to those mapping L1 and other mobile elements in complex genomes.

中文翻译:

通过测序进行转座子插入分析 (TIPseq),用于绘制人类基因组中的 LINE-1 插入。

背景技术转座因子构成了人类基因组的重要部分。准确定位这些移动 DNA 对于了解它们作为结构变异和体细胞突变来源的作用至关重要。为此,实验室已经制定了选择性扩增或以其他方式富集基因组 DNA 中的转座子插入位点的策略。结果 在这里,我们描述了一种技术,通过测序 (TIPseq) 进行转座子插入分析,以绘制人类基因组中的长插入元素 1 (LINE-1, L1) 逆转录转座子插入。该方法使用 vectorette PCR 扩增物种特异性 L1 (L1PA1) 插入位点,然后进行双端 Illumina 测序。除了提供循序渐进的分子生物学协议外,我们还为用户提供了我们的数据分析管道 TIPseqHunter 的指南。我们最近对胰腺癌和卵巢癌的研究表明,TIPseq 能够识别不变(固定)、多态(遗传变异)以及体细胞获得的 L1 插入,从而将癌症基因组与患者的体质组成区分开来。结论 TIPseq 提供了一种从基因组 DNA 中扩增进化上年轻、活跃的转座因子插入位点的方法。我们对该协议的基本原理和变化可能对那些在复杂基因组中绘制 L1 和其他移动元素的人有用。来自基因组 DNA 的活性转座因子插入位点。我们对该协议的基本原理和变化可能对那些在复杂基因组中绘制 L1 和其他移动元素的人有用。来自基因组 DNA 的活性转座因子插入位点。我们对该协议的基本原理和变化可能对那些在复杂基因组中绘制 L1 和其他移动元素的人有用。
更新日期:2019-11-01
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