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.