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Nucleic Acids Research, 1992, Vol. 20, No. 12 2955-2958
© 1992

MOLECULAR BIOLOGY

Artiodactyl retroposons: association with microsatellites and use in SINEmorph detection by PCR

Jaana Kaukinen and Sirkka-Liisa Varvio*

Institute of Biotechnology, University of Helsinki Valimotie 7, SF-00380 Helsinki, Finland

* To whom correspondence should be addressed

Received April 15, 1992. Revised May 22, 1992. Accepted May 22, 1992.

During a search of polymorphic microsatellites for bovine genome mapping, we found that microsatellites often occur as tails of artiodactyl C-A retroposon elements. In this element, C (85bp) is a tRNA derivative, while A (117bp) is of unknown origin. The A element also occurs as dimer element with a connecting 27bp linker sequence comprising hexanucleotide CACTTT repeats. In 10 clones (45% of those selected deliberately for dinucleotide repeats), the microsatellite motif is associated with the C-A retroposon. In 50% of 44 database artiodactyl C-A sequences, the element also has a microsatellite tail. The microsatellite is usually a simple (CA)n repeat, but in some cases it is an apparent derivative of the linker sequence CACTTT. All but one of 33 database dimer elements have trinucleotide repeat tails (AGC)n, n = 1–9. Microsatellites, retroposons, and their truncated versions (C and/or A) often occur as clusters. We derived the consensus sequence (202bp) of the C-A element, and designed four primers for inter-SINE amplification with the aim of finding SINEmorph polymorphisms. The method is potentially powerful for rapidly producing polymorphic markers for artiodactyl genome mapping.


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