Molecular archeology of an SP100 splice variant revisited: dating the retrotranscription and Alu insertion events

BACKGROUND: SP100 is a nuclear protein that displays a number of alternative splice variants. In Old World monkeys, apes and humans one of these variants is extended by a retroprocessed pseudogene, HMG1L3, whose antecedent gene is a member of the family of high-mobility-group proteins, HMG1. This is one of only a few documented cases of a retropseudogene being incorporated into another gene as a functional exon. In addition to the HMG1L3 insertion, Old World monkey genomes also contain an Alu sequence within the last SP100-HMG intron. PCR amplification of the 3' end of the SP100 gene using genomic DNAs from human and New World and Old World monkey species, followed by direct sequencing of the amplicons has made dating the HMG1L3 and Alu insertion events possible. RESULTS: PCR amplifications confirm that the HMG1L3 retrotransposition into the SP100 locus occurred after divergence of New World and Old World monkey lineages, some 35-40 million years ago. PCR amplification also shows that an upstream Alu sequence was inserted in the last SP100-HMG intron after divergence of the Old World monkey and ape lineages. Direct sequencing of the Alu in five Old World monkey species places the latter event at around 19 million years ago. Finally, ten single base mutations and one deletion in the Alu differentiate African from Asian Old World monkey species. CONCLUSIONS: PCR and DNA sequence analysis of 'genetic fossils' such as retropseudogenes and Alu elements in primates give details as to the timing of such events and can reveal sequence features useful for other molecular phylogenetic applications.