Transposon insertion site profiling chip (TIP-chip)

Sarah J. Wheelan, Lisa Z. Scheifele, Francisco Martinez-Murillo, Rafael A. Irizarry, Jef D. Boeke

    Research output: Contribution to journalArticle

    Abstract

    Mobile elements are important components of our genomes, with diverse and significant effects on phenotype. Not only can transposons inactivate genes by direct disruption and shuffle the genome through recombination, they can also alter gene expression subtly or powerfully. Currently active transposons are highly polymorphic in host populations, including, among hundreds of others, L1 and Alu elements in humans and Ty1 elements in yeast. For this reason, we wished to develop a simple genome-wide method for identifying all transposons in any given sample. We have designed a transposon insertion site profiling chip (TIP-chip), a microarray intended for use as a high-throughput technique for mapping transposon insertions. By selectively amplifying transposon flanking regions and hybridizing them to the array, we can locate all transposons present in a sample. We have tested the TIP-chip extensively to map Ty1 retrotransposon insertions in yeast and have achieved excellent results in two laboratory strains as well as in evolved Ty1 high-copy strains. We are able to identify all of the theoretically detectable transposons in the FY2 lab strain, with essentially no false positives. In addition, we mapped many new transposon copies in the high-copy Ty1 strain and determined its Ty1 insertion pattern.

    Original languageEnglish (US)
    Pages (from-to)17632-17637
    Number of pages6
    JournalProceedings of the National Academy of Sciences of the United States of America
    Volume103
    Issue number47
    DOIs
    StatePublished - Nov 21 2006

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    Keywords

    • Evolution
    • Integration
    • Microarray
    • Ty1
    • Yeast

    ASJC Scopus subject areas

    • General

    Cite this

    Wheelan, S. J., Scheifele, L. Z., Martinez-Murillo, F., Irizarry, R. A., & Boeke, J. D. (2006). Transposon insertion site profiling chip (TIP-chip). Proceedings of the National Academy of Sciences of the United States of America, 103(47), 17632-17637. https://doi.org/10.1073/pnas.0605450103