Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells

Wilson McKerrow, Zuojian Tang, Jared P. Steranka, Lindsay M. Payer, Jef D. Boeke, David Keefe, David Fenyö, Kathleen H. Burns, Chunhong Liu

    Research output: Contribution to journalArticlepeer-review

    Abstract

    Long interspersed element-1 (LINE-1, L1) sequences, which comprise about 17% of human genome, are the product of one of the most active types of mobile DNAs in modern humans. LINE-1 insertion alleles can cause inherited and de novo genetic diseases, and LINE-1-encoded proteins are highly expressed in some cancers. Genome-wide LINE-1 mapping in single cells could be useful for defining somatic and germline retrotransposition rates, and for enabling studies to characterize tumour heterogeneity, relate insertions to transcriptional and epigenetic effects at the cellular level, or describe cellular phylogenies in development. Our laboratories have reported a genome-wide LINE-1 insertion site mapping method for bulk DNA, named transposon insertion profiling by sequencing (TIPseq). There have been significant barriers applying LINE-1 mapping to single cells, owing to the chimeric artefacts and features of repetitive sequences. Here, we optimize a modified TIPseq protocol and show its utility for LINE-1 mapping in single lymphoblastoid cells. Results from single-cell TIPseq experiments compare well to known LINE-1 insertions found by whole-genome sequencing and TIPseq on bulk DNA. Among the several approaches we tested, whole-genome amplification by multiple displacement amplification followed by restriction enzyme digestion, vectorette ligation and LINE-1-targeted PCR had the best assay performance. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.

    Original languageEnglish (US)
    Article number20190335
    JournalPhilosophical Transactions of the Royal Society B: Biological Sciences
    Volume375
    Issue number1795
    DOIs
    StatePublished - Mar 30 2020

    Keywords

    • Mobile genetic element
    • Retrotransposon
    • Somatic mosaicism
    • TIPseq
    • Tumour heterogeneity
    • Whole-genome amplification

    ASJC Scopus subject areas

    • Biochemistry, Genetics and Molecular Biology(all)
    • Agricultural and Biological Sciences(all)

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