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ATLAS: a system to selectively identify human-specific L1 insertions.

Richard M Badge1, Reid S Alisch, John V Moran

  • 1Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA. rmb19@leicester.ac.uk

American Journal of Human Genetics
|March 13, 2003
PubMed
Summary

A new method called ATLAS can identify active long interspersed elements (L1s) and their genetic variations. This tool reveals previously unknown L1 insertions and provides a unique genetic fingerprint for individuals.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Human Genetics

Background:

  • Long interspersed elements (L1s) are mobile genetic elements that shape the human genome.
  • Recent L1 insertions are often dimorphic and underrepresented in current genomic databases.

Purpose of the Study:

  • To develop a novel system, ATLAS (amplification typing of L1 active subfamilies), for detecting and characterizing active human-specific L1 retrotransposons.
  • To assess the utility of ATLAS in identifying novel L1 insertions, assessing retrotransposition activity, and detecting genetic variations.

Main Methods:

  • ATLAS selectively amplifies and displays DNA fragments containing the termini of human-specific L1s and their flanking sequences.
  • The system's robustness and reproducibility were validated using Centre d'Etude du Polymorphisme Humain (CEPH) pedigrees.

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  • Retrotransposition activity was assessed in cultured human cells.

    • Main Results:

    • ATLAS generates reproducible, individual-specific genetic fingerprints.
    • The system identified L1 elements absent from current genome databases.
    • Some newly identified L1s demonstrated high retrotransposition frequencies in cultured cells.
    • ATLAS successfully identified single-nucleotide polymorphisms in older, primate-specific L1s.

    Conclusions:

    • ATLAS is a robust, high-throughput method for assessing genetic variation associated with L1 retrotransposons.
    • The system enhances the characterization of the dynamic human genome by revealing previously undetected L1 insertions.
    • ATLAS offers a valuable tool for population genetics and understanding L1-mediated genomic evolution.