Abstract
BackgroundMobile elements are ubiquitous components of mammalian genomes and constitute more than half of the human genome. Polymorphic mobile element insertions (pMEIs) are a major source of human genomic variation and are gaining research interest because of their involvement in gene expression regulation, genome integrity, and disease.ResultsBuilding on our previous Mobile Element Scanning (ME-Scan) protocols, we developed an integrated ME-Scan protocol to identify three major active families of human mobile elements, AluYb, L1HS, and SVA. This approach selectively amplifies insertion sites of currently active retrotransposons for Illumina sequencing. By pooling the libraries together, we can identify pMEIs from all three mobile element families in one sequencing run. To demonstrate the utility of the new ME-Scan protocol, we sequenced 12 human parent-offspring trios. Our results showed high sensitivity (> 90%) and accuracy (> 95%) of the protocol for identifying pMEIs in the human genome. In addition, we also tested the feasibility of identifying somatic insertions using the protocol.ConclusionsThe integrated ME-Scan protocol is a cost-effective way to identify novel pMEIs in the human genome. In addition, by developing the protocol to detect three mobile element families, we demonstrate the flexibility of the ME-Scan protocol. We present instructions for the library design, a sequencing protocol, and a computational pipeline for downstream analyses as a complete framework that will allow researchers to easily adapt the ME-Scan protocol to their own projects in other genomes.
Highlights
Mobile elements are ubiquitous components of mammalian genomes and constitute more than half of the human genome
Three families of non-Long Terminal Repeat retrotransposons account for the vast majority of human-specific mobile element insertions (MEIs): the Alu element, the long interspersed element 1
Protocol overview We previously described the Mobile element (ME)-Scan protocol with two rounds of nested PCRs for AluYb8/9 elements [28, 29] and full-length SVA elements [40]
Summary
Mobile elements are ubiquitous components of mammalian genomes and constitute more than half of the human genome. Polymorphic mobile element insertions (pMEIs) are a major source of human genomic variation and are gaining research interest because of their involvement in gene expression regulation, genome integrity, and disease. L1), and the composite SINE-R/VNTR/Alu (SVA) element [3,4,5] Some of these insertions happened recently in humans and are still present as polymorphic sites among human populations [4, 6, 7]. Retrotransposon expression has been associated with different types of cancer [16,17,18], and neurological disorders [19, 20] For these reasons, it is important to understand the distribution and prevalence of pMEIs in human populations
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