A method to detect
conserved transposable element insertions in orthologous regions between species
Daniel Svenback1, Louie
N. van de Lagemaat2, Dixie L. Mager2 and Patrik Medstrand1
Department of Cell and Molecular Biology, Section for Developmental Biology,
Lund University, Biomedical Center, BMC B13, 221 84 Lund, Sweden.
Terry Fox Laboratory, British Columbia Cancer
Agency, Vancouver, B. C., V5Z1L3, Canada and Department of Medical Genetics,
University of British Columbia.
number of studies have shown that transposable elements (TEs, i.e. retroelements
and other mobile elements) can affect nearby gene expression by donating
functional transcriptional regulatory signals. We recently found that 427 human
mRNA transcripts begin within TEs which increases the likelihood that the TE
serves a regulatory role in initiation of the transcript. Here, we present a
strategy to identify the extant of conserved TE insertions between the human and
mouse genome. We found that a combination of the programs BLASTZ and
Repeatmasker were most sensitive to detect such TE insertions. Among the 427
TEs found in putative human promoters, 157 were identified at orthologous sites
in the mouse genome. Our results indicate that many ancient TE insertions are
conserved in gene regions between human and mouse.