Long Interspersed Element-1 (LINE-1, L1) is a retrotransposon that has the ability to amplify its copy in the genome autonomously. L1Hs is a human-specific active subtype of L1 reported to amplify its copy in neural progenitor cells causing genomic mosaicism. This chapter describes a new method named NECO-seq (Novel Elements Concentrated-sequence) to identify the genomic locus of L1Hs insertions at the single-cell level. This protocol contains the steps of (1) preparation of neuronal cell nuclei from a postmortem human brain, (2) whole genome amplification from single neural nuclei (snWGA), (3) single nucleotide polymorphisms (SNPs) genotyping for quality control of snWGA products, (4) library preparation for next-generation sequencing to enrich the genomic locus of L1Hs insertions, and (5) bioinformatic analysis to detect novel somatic L1Hs insertions. This method can detect approximately 97% of L1Hs originally existing in reference human genome and approximately 10–20 newly inserted L1Hs copies in a neuronal cell of a postmortem human brain.
CITATION STYLE
Bundo, M., & Iwamoto, K. (2023). A Method for Detection of Somatic LINE-1 Insertions at the Single-Cell Level from Postmortem Human Brain. In Methods in Molecular Biology (Vol. 2577, pp. 147–159). Humana Press Inc. https://doi.org/10.1007/978-1-0716-2724-2_10
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