Detection of Retrotransposition Activity of Hot LINE-1s by Long-Distance Inverse PCR

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http://hdl.handle.net/10138/306352

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Pradhan , B & Kauppi , L 2019 , ' Detection of Retrotransposition Activity of Hot LINE-1s by Long-Distance Inverse PCR ' , Journal of Visualized Experiments , no. 149 , 59880 . https://doi.org/10.3791/59880

Title: Detection of Retrotransposition Activity of Hot LINE-1s by Long-Distance Inverse PCR
Author: Pradhan, Barun; Kauppi, Liisa
Contributor: University of Helsinki, Research Program in Systems Oncology
University of Helsinki, Medicum
Date: 2019-07
Language: eng
Number of pages: 8
Belongs to series: Journal of Visualized Experiments
ISSN: 1940-087X
URI: http://hdl.handle.net/10138/306352
Abstract: Long interspersed nuclear elements 1 (LINE-1s) are the only family of mobile genetic elements in the human genome that can move autonomously. They do so by a process called retrotransposition wherein they transcribe to form an mRNA intermediate which is then consequently inserted into the genome by reverse transcription. Despite being silent in normal cells, LINE-1s are highly active in different epithelial tumors. De novo LINE-1 insertions can potentially drive tumorigenesis, and hence it is important to systematically study LINE-1 retrotransposition in cancer. Out of similar to 150 retrotransposition-competent LINE-1s present in the human genome, only a handful of LINE-1 loci, also referred to as "hot" LINE-1s, account for the majority of de novo LINE-1 insertion in different cancer types. We have developed a simple polymerase chain reaction (PCR)-based method to monitor retrotransposition activity of these hot LINE-1s. This method, based on long-distance inverse (LDI)-PCR, takes advantage of 3 ' transduction, a mechanism by which a LINE-1 mobilizes its flanking non-repetitive region, which can subsequently be used to identify de novo LINE-1 3 ' transduction events stemming from a particular hot LINE-1.
Subject: Cancer Research
Issue 149
PCR
inverse PCR
retrotransposons
LINE-1
retrotransposition
structural variation
cancer
DNA
mobile DNA
genomics
ATLAS
3111 Biomedicine
1184 Genetics, developmental biology, physiology
1182 Biochemistry, cell and molecular biology
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