Transposon insertion site profiling chip (TIP-chip)

doi:10.1073/pnas.0605450103

Transposon insertion site profiling chip (TIP-chip)

^†High Throughput Biology Center and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205; and
^‡Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205

Edited by Susan R. Wessler, University of Georgia, Athens, GA, and approved September 19, 2006 (received for review June 29, 2006)

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.

Footnotes

^§To whom correspondence may be addressed. E-mail: rafa{at}jhu.edu or jboeke{at}jhmi.edu
Author contributions: S.J.W. and J.D.B. designed research; S.J.W., L.Z.S., and F.M.-M. performed research; S.J.W., L.Z.S., F.M.-M., and R.A.I. contributed new reagents/analytic tools; S.J.W., L.Z.S., F.M.-M., R.A.I., and J.D.B. analyzed data; and S.J.W. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS direct submission.
Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE5646).
Abbreviations:

TIP,

transposon insertion site profiling;

SGD,

Saccharomyces Genome Database.