LINE-1 Mobile Element Next-Generation Sequencing (NGS) Assay Kit
Cellecta’s LINE-1 Assay Kit provides a convenient, efficient, and targeted Next-Generation Sequencing (NGS) based approach to identify polymorphic insertion sites of LINE-1 in the human genome. The LINE-1 Assay Kit includes all the components needed to detect and identify novel LINE-1-induced genomic variations in genomic DNA isolated from tumors, blood, cells or other samples. Only a few hundred nanograms of DNA are required.
- Amplify and prep of all LINE-1 elements in a sample for profiling with a single-reaction protocol
- Measure the activation of retrotransposon activity in biological samples and tumor extracts simply and easily
- Analyze LINE-1 insertions to discover novel oncogenic drivers and study the evolution of tumor cell populations
Transposable Elements Like LINE-1 Induce Genomic Rearrangement
Almost half of the human genome consists of different classes of repetitive elements such as DNA transposons and retrotransposons, which can be mobilized and inserted in various places in the genome (Fig. 1). The origin and biological role of these elements are currently not well understood. Retrotransposon insertions have been implicated in diseases and overwhelming evidence indicates that there is significant accumulation of de novo retrotransposon insertions in tumors.
Long interspersed nuclear elements (LINEs, such as LINE-1) make up about one-third of all mobile elements in the genome. Members of the L1H subfamily of LINE-1 are active transposons that induce genetic rearrangements throughout the genome. Increased LINE mobilization has been observed in some types of cancers. LINE-1-induced genetic rearrangements could have significant impact in cancer initiation and progression. Additionally, LINE transpositions have been implicated in schizophrenia, Alzheimer’s disease, and other neurodegenerative diseases.
Cellecta’s LINE-1 Assay uses specially designed primers to selectively amplify only the transposable elements of the youngest L1H family of LINE-1 that are still active in the genome, as opposed to the ancient elements fixed in the population. This approach enables detection and identification of all the 3’L1H variations for a sample in a single reaction which enables rapid analysis of multiple samples.
Quantitative NGS Analysis of LINE-1 Rearrangements
The LINE-1 Sequencing Assay method (Fig. 2) uses primers specifically designed to amplify the 3′-ends of youngest, most active LINE-1H subfamily of LINE-1 elements in randomly sheared DNA to detect insertion sites in the genome. An adapter sequence is ligated to DNA generated from a primer extension reaction that starts at the 3′ end of the LINE-1H sequence and extends across the insertion site and into the genomic DNA adjacent to the mobile element. The DNA target produced in the primer extension is then amplified using primers targeting the LINE-1 sequence and adaptor. The amplified DNA product represents a heterogenous mix corresponding to most of the LINE-1H 3′-insertion-chromosome junctions across the genomic DNA. The sample is then deep-sequenced and deconvoluted to reveal the number, locations, and frequency of the specific insertions in the sample.
Cellecta’s LINE-1 Mobile Element NGS Assay Kit is available for purchase now.