Transposon insertion site profiling chip (TIP-chip)

Sarah 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

Fingerprint

Genome Components
Long Interspersed Nucleotide Elements
Yeasts
Alu Elements
Genome
Retroelements
Genetic Recombination
Phenotype
Gene Expression
Population
Genes

Keywords

  • Evolution
  • Integration
  • Microarray
  • Ty1
  • Yeast

ASJC Scopus subject areas

  • Genetics
  • General

Cite this

Transposon insertion site profiling chip (TIP-chip). / Wheelan, Sarah; Scheifele, Lisa Z.; Martinez-Murillo, Francisco; Irizarry, Rafael A.; Boeke, Jef D.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 47, 21.11.2006, p. 17632-17637.

Research output: Contribution to journalArticle

Wheelan, Sarah ; Scheifele, Lisa Z. ; Martinez-Murillo, Francisco ; Irizarry, Rafael A. ; Boeke, Jef D. / Transposon insertion site profiling chip (TIP-chip). In: Proceedings of the National Academy of Sciences of the United States of America. 2006 ; Vol. 103, No. 47. pp. 17632-17637.
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