Mobile interspersed repeats are major structural variants in the human genome

Cheng Ran Lisa Huang, Anna M. Schneider, Yunqi Lu, Tejasvi Niranjan, Peilin Shen, Matoya A. Robinson, Jared P. Steranka, David Valle, Curt I. Civin, Tao Wang, Sarah J. Wheelan, Hongkai Ji, Jef D. Boeke, Kathleen H. Burns

    Research output: Contribution to journalArticle

    Abstract

    Characterizing structural variants in the human genome is of great importance, but a genome wide analysis to detect interspersed repeats has not been done. Thus, the degree to which mobile DNAs contribute to genetic diversity, heritable disease, and oncogenesis remains speculative. We perform transposon insertion profiling by microarray (TIP-chip) to map human L1(Ta) retrotransposons (LINE-1 s) genome-wide. This identified numerous novel human L1(Ta) insertional polymorphisms with highly variant allelic frequencies. We also explored TIP-chip's usefulness to identify candidate alleles associated with different phenotypes in clinical cohorts. Our data suggest that the occurrence of new insertions is twice as high as previously estimated, and that these repeats are under-recognized as sources of human genomic and phenotypic diversity. We have just begun to probe the universe of human L1(Ta) polymorphisms, and as TIP-chip is applied to other insertions such as Alu SINEs, it will expand the catalog of genomic variants even further.

    Original languageEnglish (US)
    Pages (from-to)1171-1182
    Number of pages12
    JournalCell
    Volume141
    Issue number7
    DOIs
    StatePublished - Jun 2010

    Keywords

    • DNA
    • EVO_ECOL

    ASJC Scopus subject areas

    • Biochemistry, Genetics and Molecular Biology(all)

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  • Cite this

    Huang, C. R. L., Schneider, A. M., Lu, Y., Niranjan, T., Shen, P., Robinson, M. A., Steranka, J. P., Valle, D., Civin, C. I., Wang, T., Wheelan, S. J., Ji, H., Boeke, J. D., & Burns, K. H. (2010). Mobile interspersed repeats are major structural variants in the human genome. Cell, 141(7), 1171-1182. https://doi.org/10.1016/j.cell.2010.05.026